Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 10 of 373
Found at i:2873884 original size:26 final size:27
Alignment explanation
Indices: 2873848--2873934 Score: 86
Period size: 26 Copynumber: 3.2 Consensus size: 27
2873838 ACATGTAACA
2873848 AAAAATTATAAAAAATA-AAAATTAAT
1 AAAAATTATAAAAAATATAAAATTAAT
* * * *
2873874 AAAAGTTATAAAAATTATAAATTTTAT
1 AAAAATTATAAAAAATATAAAATTAAT
* **
2873901 AAAAATCATAAAAAAATTATAAAATGCAT
1 AAAAATTAT-AAAAAA-TATAAAATTAAT
2873930 AAAAA
1 AAAAA
2873935 AGCCCTTTAA
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
26 15 0.31
27 14 0.29
28 5 0.10
29 14 0.29
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (27 bp):
AAAAATTATAAAAAATATAAAATTAAT
Found at i:2873911 original size:9 final size:9
Alignment explanation
Indices: 2873848--2873924 Score: 77
Period size: 9 Copynumber: 8.4 Consensus size: 9
2873838 ACATGTAACA
2873848 AAAAATTAT
1 AAAAATTAT
2873857 AAAAA--AT
1 AAAAATTAT
2873864 AAAAATTAAT
1 AAAAATT-AT
*
2873874 AAAAGTTAT
1 AAAAATTAT
2873883 AAAAATTAT
1 AAAAATTAT
**
2873892 AAATTTTAT
1 AAAAATTAT
*
2873901 AAAAATCATAA
1 AAAAAT--TAT
2873912 AAAAATTAT
1 AAAAATTAT
2873921 AAAA
1 AAAA
2873925 TGCATAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
7 7 0.13
9 32 0.58
10 8 0.15
11 8 0.15
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:2873922 original size:20 final size:20
Alignment explanation
Indices: 2873897--2873935 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2873887 ATTATAAATT
2873897 TTATAAAAAT-CATAAAAAAA
1 TTAT-AAAATGCATAAAAAAA
2873917 TTATAAAATGCATAAAAAA
1 TTATAAAATGCATAAAAAA
2873936 GCCCTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
TTATAAAATGCATAAAAAAA
Found at i:2874033 original size:20 final size:20
Alignment explanation
Indices: 2874010--2874066 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
2874000 TAATTTTTTC
2874010 TATATTTTTATAAAAAAATT
1 TATATTTTTATAAAAAAATT
* *
2874030 TATAATTTT-TAATAAAATT
1 TATATTTTTATAAAAAAATT
2874049 TAAATATTTTTATTAAAA
1 T--ATATTTTTA-TAAAA
2874067 GTTAATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 10 0.34
20 8 0.28
21 7 0.24
23 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATATTTTTATAAAAAAATT
Found at i:2874059 original size:21 final size:20
Alignment explanation
Indices: 2874011--2874080 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
2874001 AATTTTTTCT
*
2874011 ATATTTTTATAAAAAAATTT-
1 ATATTTTT-TAATAAAATTTA
*
2874031 ATAATTTTTAATAAAATTTA
1 ATATTTTTTAATAAAATTTA
* *
2874051 A-ATATTTTTATTAAAAGTTA
1 ATAT-TTTTTAATAAAATTTA
2874071 ATATTTTTTA
1 ATATTTTTTA
2874081 TTTTTATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
19 11 0.26
20 29 0.69
21 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (20 bp):
ATATTTTTTAATAAAATTTA
Found at i:2887830 original size:8 final size:8
Alignment explanation
Indices: 2887808--2887841 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2887798 TTAGTTTTTG
2887808 TTAAAATA
1 TTAAAATA
*
2887816 -AAAAATA
1 TTAAAATA
2887823 TTAAAATA
1 TTAAAATA
2887831 TTAAAATA
1 TTAAAATA
2887839 TTA
1 TTA
2887842 TCAACTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TTAAAATA
Found at i:2893314 original size:12 final size:12
Alignment explanation
Indices: 2893297--2893321 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2893287 GGTGTGCATT
2893297 CGGTTAACCGAC
1 CGGTTAACCGAC
2893309 CGGTTAACCGAC
1 CGGTTAACCGAC
2893321 C
1 C
2893322 CGAATTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:2893495 original size:9 final size:9
Alignment explanation
Indices: 2893481--2893555 Score: 107
Period size: 9 Copynumber: 8.4 Consensus size: 9
2893471 TGGTTAAAAA
2893481 TTAACCGAT
1 TTAACCGAT
*
2893490 TTAACCTAT
1 TTAACCGAT
2893499 TTAACCGA-
1 TTAACCGAT
*
2893507 TTAACCGAC
1 TTAACCGAT
2893516 TTAACCGAT
1 TTAACCGAT
2893525 TTAACCGAT
1 TTAACCGAT
* *
2893534 TTAACCAAC
1 TTAACCGAT
2893543 TTAACCGAT
1 TTAACCGAT
2893552 TTAA
1 TTAA
2893556 ATCACTAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
8 8 0.14
9 50 0.86
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (9 bp):
TTAACCGAT
Found at i:2893514 original size:26 final size:26
Alignment explanation
Indices: 2893480--2893555 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
2893470 TTGGTTAAAA
* *
2893480 ATTAACCGATTTAACCTATTTAACCG
1 ATTAACCGACTTAACCGATTTAACCG
2893506 ATTAACCGACTTAACCGATTTAACCG
1 ATTAACCGACTTAACCGATTTAACCG
*
2893532 ATTTAACCAACTTAACCGATTTAA
1 A-TTAACCGACTTAACCGATTTAA
2893556 ATCACTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 25 0.54
27 21 0.46
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (26 bp):
ATTAACCGACTTAACCGATTTAACCG
Found at i:2893677 original size:37 final size:37
Alignment explanation
Indices: 2893555--2893663 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
2893545 AACCGATTTA
2893555 AATCACTAAATAATTAAAAA-ATTACATAAGTCTTTG
1 AATCACTAAATAATTAAAAACATTACATAAGTCTTTG
* * *
2893591 AATCACTACATAACTAAAAACATTACATAAAAT-TTTG
1 AATCACTAAATAATTAAAAACATTACAT-AAGTCTTTG
2893628 AATCACTAAATAATTAAAAACATTACATAAGTCTTT
1 AATCACTAAATAATTAAAAACATTACATAAGTCTTT
2893664 AACACATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
36 21 0.33
37 40 0.62
38 3 0.05
ACGTcount: A:0.50, C:0.14, G:0.04, T:0.32
Consensus pattern (37 bp):
AATCACTAAATAATTAAAAACATTACATAAGTCTTTG
Found at i:2893925 original size:7 final size:7
Alignment explanation
Indices: 2893895--2893955 Score: 68
Period size: 7 Copynumber: 8.4 Consensus size: 7
2893885 ATGTACAGAA
2893895 GAAAGCAT
1 GAAA-CAT
2893903 GAAACAT
1 GAAACAT
* **
2893910 GCAGTAT
1 GAAACAT
2893917 GAAACAT
1 GAAACAT
*
2893924 GAAATCGT
1 GAAA-CAT
2893932 GAAACAT
1 GAAACAT
2893939 GAAACAT
1 GAAACAT
2893946 GAAACAT
1 GAAACAT
2893953 GAA
1 GAA
2893956 TTGTTCTTGG
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
7 34 0.77
8 10 0.23
ACGTcount: A:0.51, C:0.13, G:0.20, T:0.16
Consensus pattern (7 bp):
GAAACAT
Found at i:2893976 original size:13 final size:13
Alignment explanation
Indices: 2893958--2893984 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2893948 AACATGAATT
2893958 GTTCTTGGGCTTA
1 GTTCTTGGGCTTA
2893971 GTTCTTGGGCTTA
1 GTTCTTGGGCTTA
2893984 G
1 G
2893985 AGCCTGGAGG
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:0.07, C:0.15, G:0.33, T:0.44
Consensus pattern (13 bp):
GTTCTTGGGCTTA
Found at i:2894208 original size:18 final size:19
Alignment explanation
Indices: 2894187--2894223 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2894177 CAGAATTCGG
2894187 TCGG-TTAACCGAATTTTT
1 TCGGTTTAACCGAATTTTT
2894205 TCGGTTTTAACCGAATTTT
1 TCGG-TTTAACCGAATTTT
2894224 GCACACCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (19 bp):
TCGGTTTAACCGAATTTTT
Found at i:2896585 original size:31 final size:31
Alignment explanation
Indices: 2896550--2896612 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
2896540 TTTACTCGAG
* **
2896550 TATTGATTCATTTACTGATTATCATAGTATA
1 TATTGATCCATTTACCCATTATCATAGTATA
2896581 TATTGATCCATTTACCCATTATCATAGTATA
1 TATTGATCCATTTACCCATTATCATAGTATA
2896612 T
1 T
2896613 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (31 bp):
TATTGATCCATTTACCCATTATCATAGTATA
Found at i:2897414 original size:16 final size:16
Alignment explanation
Indices: 2897380--2897430 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
2897370 TTTAAGTGCT
* *
2897380 AATCGTTTCAAGTTCA
1 AATCGTTTCAAATTTA
*
2897396 AATCGTTTTAAATTTA
1 AATCGTTTCAAATTTA
* *
2897412 AATTGTTTCGAATTTA
1 AATCGTTTCAAATTTA
2897428 AAT
1 AAT
2897431 TCAATAGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (16 bp):
AATCGTTTCAAATTTA
Found at i:2897628 original size:49 final size:49
Alignment explanation
Indices: 2897556--2897653 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
2897546 CAACTAAGTT
2897556 AATATCATTCATCAAAACGGATTTAAATTCTATTGAGGACCGACTCGTA
1 AATATCATTCATCAAAACGGATTTAAATTCTATTGAGGACCGACTCGTA
2897605 AATATCATTCATCAAAACGGATTTAAATTCTATTGAGGACCGACTCGTA
1 AATATCATTCATCAAAACGGATTTAAATTCTATTGAGGACCGACTCGTA
2897654 TAAACAACGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (49 bp):
AATATCATTCATCAAAACGGATTTAAATTCTATTGAGGACCGACTCGTA
Found at i:2903151 original size:18 final size:18
Alignment explanation
Indices: 2903128--2903177 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2903118 TTATTTTAAG
*
2903128 ATTTTTTGCATTTTAATT
1 ATTTTTTGCATTTTAACT
*
2903146 ATTTTTT-CTATTTTACCT
1 ATTTTTTGC-ATTTTAACT
*
2903164 ATTTTTTGTATTTT
1 ATTTTTTGCATTTT
2903178 TAAATTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.70
Consensus pattern (18 bp):
ATTTTTTGCATTTTAACT
Found at i:2911610 original size:14 final size:15
Alignment explanation
Indices: 2911582--2911610 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2911572 AACCCATTAT
2911582 CATTTAAATATTTTA
1 CATTTAAATATTTTA
2911597 CATTTAAA-ATTTTA
1 CATTTAAATATTTTA
2911611 AAAATTACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (15 bp):
CATTTAAATATTTTA
Found at i:2911685 original size:14 final size:14
Alignment explanation
Indices: 2911651--2911692 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2911641 ATCTCACAAA
* *
2911651 AAATTAAATATACC
1 AAATTAAATTTAAC
2911665 AAA-TAAATTTAAC
1 AAATTAAATTTAAC
*
2911678 AAATTAAATTCAAC
1 AAATTAAATTTAAC
2911692 A
1 A
2911693 CTCCTTAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATTAAATTTAAC
Found at i:2914057 original size:6 final size:6
Alignment explanation
Indices: 2914046--2914080 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2914036 TCTGAAATTG
2914046 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
2914081 TATGTATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:2915709 original size:31 final size:30
Alignment explanation
Indices: 2915673--2915735 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
2915663 TAATTATAAT
*
2915673 AAAATTATATTTTAATCTTTTAAAAATGATA
1 AAAATTATAATTTAAT-TTTTAAAAATGATA
* *
2915704 AAAATTCTAATTTAATTTTTAAAAATTATA
1 AAAATTATAATTTAATTTTTAAAAATGATA
2915734 AA
1 AA
2915736 TATTTTTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 15 0.52
31 14 0.48
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
AAAATTATAATTTAATTTTTAAAAATGATA
Found at i:2918304 original size:31 final size:29
Alignment explanation
Indices: 2918269--2918333 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 29
2918259 TTCAAAAATC
2918269 ATTTTTATTTAATTACAATATATATTT-TAAA
1 ATTTTTATTTAATTA-AA-AT-TATTTATAAA
* *
2918300 ATTTTTCTTTTATTAAAATTATTTATAAA
1 ATTTTTATTTAATTAAAATTATTTATAAA
2918329 ATTTT
1 ATTTT
2918334 ACAAATAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 5 0.16
29 11 0.35
30 2 0.06
31 13 0.42
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTTATTTAATTAAAATTATTTATAAA
Found at i:2921748 original size:9 final size:9
Alignment explanation
Indices: 2921734--2921783 Score: 73
Period size: 9 Copynumber: 5.6 Consensus size: 9
2921724 TTTATACAAA
2921734 TAATTCGGT
1 TAATTCGGT
*
2921743 TAATTCGGG
1 TAATTCGGT
*
2921752 TAATTCAGT
1 TAATTCGGT
*
2921761 TAATTCGAT
1 TAATTCGGT
2921770 TAATTCGGT
1 TAATTCGGT
2921779 TAATT
1 TAATT
2921784 TTATACTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.44
Consensus pattern (9 bp):
TAATTCGGT
Found at i:2939641 original size:4 final size:4
Alignment explanation
Indices: 2939632--2939658 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2939622 CATTTTAACC
2939632 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
2939659 GAAATTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:2942260 original size:29 final size:28
Alignment explanation
Indices: 2942225--2942289 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
2942215 TTTCAGAAAA
*
2942225 ATTTTAAAATTTT-AATTTTATTTAT-AT
1 ATTTTAAAATTTTAAAATTT-TTTATAAT
*
2942252 ATTTTTTAAATTTTAAAATTTTTTATAAT
1 A-TTTTAAAATTTTAAAATTTTTTATAAT
2942281 ATTTTAAAA
1 ATTTTAAAA
2942290 AATATAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 23 0.72
29 8 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTAAAATTTTAAAATTTTTTATAAT
Found at i:2942262 original size:28 final size:29
Alignment explanation
Indices: 2942226--2942301 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
2942216 TTCAGAAAAA
*
2942226 TTTTAAAATTTT-AATTTTATTTAT-ATAT
1 TTTTAAAATTTTAAAATTT-TTTATAATAT
*
2942254 TTTTTAAATTTTAAAATTTTTTATAATAT
1 TTTTAAAATTTTAAAATTTTTTATAATAT
* * *
2942283 TTTAAAAAATATAAAATTT
1 TTTTAAAATTTTAAAATTT
2942302 AGAATTTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
28 16 0.40
29 24 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTTAAAATTTTAAAATTTTTTATAATAT
Found at i:2942286 original size:20 final size:18
Alignment explanation
Indices: 2942253--2942289 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
2942243 TATTTATATA
2942253 TTTTTTAAATTTTAAAAT
1 TTTTTTAAATTTTAAAAT
2942271 TTTTTATAATATTTTAAAA
1 TTTTT-TAA-ATTTTAAAA
2942290 AATATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTTAAATTTTAAAAT
Found at i:2942325 original size:18 final size:17
Alignment explanation
Indices: 2942252--2942327 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 17
2942242 TTATTTATAT
2942252 ATTTTT-TAAATTTTAAA
1 ATTTTTATAAATTTT-AA
2942269 ATTTTTTATAATATTTTAA
1 A-TTTTTATAA-ATTTTAA
*** *
2942288 A-AAATATAAAATTTAGA
1 ATTTTTATAAATTTTA-A
2942305 ATTTTTATAATATTTTAA
1 ATTTTTATAA-ATTTTAA
2942323 ATTTT
1 ATTTT
2942328 AAAAATTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
16 5 0.11
17 8 0.18
18 16 0.36
19 11 0.24
20 5 0.11
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (17 bp):
ATTTTTATAAATTTTAA
Found at i:2943273 original size:30 final size:30
Alignment explanation
Indices: 2943239--2943363 Score: 196
Period size: 30 Copynumber: 4.2 Consensus size: 30
2943229 ATAAAAAAAA
*
2943239 CACCAACTCCACTAGCCACATTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
* *
2943269 CACCAACTCTACTAGCCACACTCGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
*
2943299 CACCTACTCCACTAGCCACACTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
* *
2943329 CACCTACTCCATTAGCCACACTTGCTCCAC
1 CACCAACTCCACTAGCCACACTTGCTCCAC
2943359 CACCA
1 CACCA
2943364 CTTGTACCTA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.26, C:0.49, G:0.06, T:0.19
Consensus pattern (30 bp):
CACCAACTCCACTAGCCACACTTGCTCCAC
Found at i:2943944 original size:27 final size:25
Alignment explanation
Indices: 2943851--2943974 Score: 103
Period size: 25 Copynumber: 5.1 Consensus size: 25
2943841 ATTATATTTC
*
2943851 TTAATATTATATTATGTATATAT-T
1 TTAATACTATATTATGTATATATAT
** * * *
2943875 TTTTTAATATATTAGGTATAT-T-C
1 TTAATACTATATTATGTATATATAT
* * *
2943898 TAAATTCTATATTACGTATATATAT
1 TTAATACTATATTATGTATATATAT
* *
2943923 ATT-ATACTATTTTATGTATATATCT
1 -TTAATACTATATTATGTATATATAT
*
2943948 TTAATACTATATTATTTATATATAT
1 TTAATACTATATTATGTATATATAT
2943973 TT
1 TT
2943975 TTTTCTACAT
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
23 16 0.21
24 20 0.26
25 39 0.51
26 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.56
Consensus pattern (25 bp):
TTAATACTATATTATGTATATATAT
Found at i:2944016 original size:27 final size:27
Alignment explanation
Indices: 2943933--2944016 Score: 80
Period size: 28 Copynumber: 3.0 Consensus size: 27
2943923 ATTATACTAT
2943933 TTTATGTATATATCTTTAATACTATATTA
1 TTTATGTATATAT-TTTAATA-TATATTA
* * ** * *
2943962 TTTATATATATTTTTTTCTACATGTTA
1 TTTATGTATATATTTTAATATATATTA
2943989 TCTTATGTATATATTTTAAT-TATATTA
1 T-TTATGTATATATTTTAATATATATTA
2944016 T
1 T
2944017 GTATTTTTAT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
27 12 0.29
28 19 0.45
29 11 0.26
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTATGTATATATTTTAATATATATTA
Found at i:2983384 original size:27 final size:27
Alignment explanation
Indices: 2983351--2983409 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
2983341 ATATTAAAAT
2983351 TATACATAGAATTTAATTTTGTTTAAA
1 TATACATAGAATTTAATTTTGTTTAAA
2983378 TATACATAGAATTTAATTTTGTTTAAA
1 TATACATAGAATTTAATTTTGTTTAAA
2983405 TATAC
1 TATAC
2983410 TGTAGAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (27 bp):
TATACATAGAATTTAATTTTGTTTAAA
Found at i:2983803 original size:31 final size:31
Alignment explanation
Indices: 2983747--2983807 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
2983737 TACACATATT
* *
2983747 AAACTTTGATTTTGGTTTAAATGTATACATA
1 AAACTTTGATTTTGATTCAAATGTATACATA
**
2983778 AAACTTTGATTTTGATTCAGTTGTATACAT
1 AAACTTTGATTTTGATTCAAATGTATACAT
2983808 TTATACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (31 bp):
AAACTTTGATTTTGATTCAAATGTATACATA
Found at i:2984452 original size:10 final size:11
Alignment explanation
Indices: 2984440--2984481 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
2984430 GATTTTCTTT
2984440 ATTTTTTAAT-
1 ATTTTTTAATA
*
2984450 ATTTTTT-ATG
1 ATTTTTTAATA
2984460 ATTTTTTAATA
1 ATTTTTTAATA
2984471 ATTTATTTAAT
1 ATTT-TTTAAT
2984482 TAAACTGGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 2 0.07
10 14 0.50
11 6 0.21
12 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTTTTAATA
Found at i:2985913 original size:9 final size:9
Alignment explanation
Indices: 2985901--2985950 Score: 75
Period size: 9 Copynumber: 5.6 Consensus size: 9
2985891 AATAAATTTT
2985901 ATAATTCAA
1 ATAATTCAA
2985910 ATAATTCAA
1 ATAATTCAA
2985919 ATAACTT-AA
1 ATAA-TTCAA
*
2985928 ATACTTCAA
1 ATAATTCAA
2985937 ATAATTCAA
1 ATAATTCAA
2985946 ATAAT
1 ATAAT
2985951 AGATTGATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 2 0.05
9 33 0.89
10 2 0.05
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (9 bp):
ATAATTCAA
Found at i:2985920 original size:27 final size:27
Alignment explanation
Indices: 2985890--2985949 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
2985880 CAATTTTTTA
**
2985890 AAATAAATTTTATAATTCAAATAATTC
1 AAATAAATTAAATAATTCAAATAATTC
* *
2985917 AAATAACTTAAATACTTCAAATAATTC
1 AAATAAATTAAATAATTCAAATAATTC
2985944 AAATAA
1 AAATAA
2985950 TAGATTGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (27 bp):
AAATAAATTAAATAATTCAAATAATTC
Found at i:2991414 original size:26 final size:26
Alignment explanation
Indices: 2991377--2991429 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2991367 TGGCCAATGT
* *
2991377 ACATGGATTGCATAGATAACTTATGC
1 ACATGGACTGCATACATAACTTATGC
2991403 ACATGGACTGCATACATAACTTATGC
1 ACATGGACTGCATACATAACTTATGC
2991429 A
1 A
2991430 TAGTGTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (26 bp):
ACATGGACTGCATACATAACTTATGC
Found at i:2995303 original size:22 final size:22
Alignment explanation
Indices: 2995276--2995318 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2995266 CCCTCGATTG
2995276 AATTAATT-AACTAAATTCAGTC
1 AATTAATTGAA-TAAATTCAGTC
*
2995298 AATTAATTGAATTAATTCAGT
1 AATTAATTGAATAAATTCAGT
2995319 TTTACCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (22 bp):
AATTAATTGAATAAATTCAGTC
Found at i:2995658 original size:13 final size:13
Alignment explanation
Indices: 2995631--2995668 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2995621 AGAATTTGAG
2995631 TAAAAATATAAATT
1 TAAAAA-ATAAATT
*
2995645 TAAAAAATATATT
1 TAAAAAATAAATT
2995658 TAAAAAATAAA
1 TAAAAAATAAA
2995669 ATTCTTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAAAAATAAATT
Found at i:2995752 original size:11 final size:11
Alignment explanation
Indices: 2995738--2995846 Score: 51
Period size: 11 Copynumber: 9.6 Consensus size: 11
2995728 GTTTTGTCGC
*
2995738 TATTTTTTTAT
1 TATTTTATTAT
*
2995749 TATTTTACTAT
1 TATTTTATTAT
*
2995760 TATTTTGTTAT
1 TATTTTATTAT
* *
2995771 ATATCGTTACTAT
1 -TAT-TTTATTAT
*
2995784 T-TTATTGTTAT
1 TATT-TTATTAT
*
2995795 TATTTAGATT-T
1 TATTT-TATTAT
* * * *
2995806 TGTATAATTTT
1 TATTTTATTAT
2995817 TATTTTATTAT
1 TATTTTATTAT
*
2995828 TAATTTTACTAT
1 T-ATTTTATTAT
2995840 TATTTTA
1 TATTTTA
2995847 AAGGTATTTG
Statistics
Matches: 71, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
10 3 0.04
11 45 0.63
12 18 0.25
13 5 0.07
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:3006255 original size:25 final size:28
Alignment explanation
Indices: 3006185--3006258 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 28
3006175 TCTTTTTAAT
* *
3006185 TAATAACTCTTTTATTTATATAAATAAAA
1 TAATAAATATTTTA-TTATATAAATAAAA
* *
3006214 TAATAAATATGTAATTATAT-AAT-AAA
1 TAATAAATATTTTATTATATAAATAAAA
*
3006240 -AATATATATTTTATTATAT
1 TAATAAATATTTTATTATAT
3006259 CATTATGTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 16 0.42
26 3 0.08
27 3 0.08
28 6 0.16
29 10 0.26
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATAAATATTTTATTATATAAATAAAA
Found at i:3006364 original size:21 final size:18
Alignment explanation
Indices: 3006340--3006378 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
3006330 TATATGTTTT
3006340 TATATTTATCATTATTTTAAA
1 TATATTT-T-ATT-TTTTAAA
3006361 TATATTTTATTTTTTAAA
1 TATATTTTATTTTTTAAA
3006379 ACATCAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 1 0.06
21 7 0.39
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATATTTTATTTTTTAAA
Found at i:3006780 original size:19 final size:19
Alignment explanation
Indices: 3006743--3006788 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3006733 CATAATGATA
* *
3006743 TATATAA-TATATTTTTAT
1 TATATAATTACATATTTAT
3006761 TATATAATTACATATTTAT
1 TATATAATTACATATTTAT
*
3006780 TATTTAATT
1 TATATAATT
3006789 TTTATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATAATTACATATTTAT
Found at i:3006906 original size:14 final size:14
Alignment explanation
Indices: 3006889--3006915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3006879 TAAAAAATAT
3006889 AAAAAGCATTATTC
1 AAAAAGCATTATTC
3006903 AAAAAGCATTATT
1 AAAAAGCATTATT
3006916 AATTAGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (14 bp):
AAAAAGCATTATTC
Found at i:3019182 original size:76 final size:74
Alignment explanation
Indices: 3018996--3019187 Score: 215
Period size: 76 Copynumber: 2.5 Consensus size: 74
3018986 CATATCAAAG
* * * * *
3018996 CATTAGAGTTATGATTTCACTTTAATTTTATTTTATTTTGGACCCTTTTATTTAAATCTTTTGGT
1 CATTAGAATTATGATTTCACTTGAATTTTATTTTTTTTTGGACCCTTTTATTTAAATCCTTTAGT
3019061 GTTCAATAT
66 GTTCAATAT
* ** * *
3019070 CATTAGAATTGTGGCTTCATTTCGACTTTATATTTTTTTTTGGACCCTTTTATTTAAATCCTTTA
1 CATTAGAATTATGATTTCACTT-GAATTT-TATTTTTTTTTGGACCCTTTTATTTAAATCCTTTA
*
3019135 GTGTT-AGTAGT
64 GTGTTCAATA-T
*
3019146 CATTTCAGAATTATGATTTCACTTGAATTTTGTTTTTGTTTT
1 CA-TT-AGAATTATGATTTCACTTGAATTTTATTTTT-TTTT
3019188 TTTCTTTTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
74 17 0.18
75 7 0.07
76 46 0.48
77 11 0.12
78 14 0.15
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.54
Consensus pattern (74 bp):
CATTAGAATTATGATTTCACTTGAATTTTATTTTTTTTTGGACCCTTTTATTTAAATCCTTTAGT
GTTCAATAT
Found at i:3019865 original size:14 final size:14
Alignment explanation
Indices: 3019846--3019877 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3019836 AACTTTCAAT
3019846 GTATATATCAACAA
1 GTATATATCAACAA
3019860 GTATATATCAACAA
1 GTATATATCAACAA
3019874 GTAT
1 GTAT
3019878 TGAGGTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (14 bp):
GTATATATCAACAA
Found at i:3024873 original size:15 final size:16
Alignment explanation
Indices: 3024848--3024878 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3024838 GCAAACCCTT
3024848 TAAATACAAAAAAATC
1 TAAATACAAAAAAATC
3024864 TAAATA-AAAAAAATC
1 TAAATACAAAAAAATC
3024879 AACATACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAATACAAAAAAATC
Found at i:3043492 original size:17 final size:17
Alignment explanation
Indices: 3043470--3043503 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3043460 ATCTTGGAAA
* *
3043470 CTAAAATTACCTTAAAC
1 CTAAAACTAACTTAAAC
3043487 CTAAAACTAACTTAAAC
1 CTAAAACTAACTTAAAC
3043504 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (17 bp):
CTAAAACTAACTTAAAC
Found at i:3052464 original size:26 final size:24
Alignment explanation
Indices: 3052421--3052478 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
3052411 TTATTTCATT
* *
3052421 AAATAAA-AAATTTTAAAATATAA
1 AAATAAATACATTTAAAAATATAA
3052444 TAAATCAAATACATTTAAAAATATAA
1 -AAAT-AAATACATTTAAAAATATAA
3052470 AAATAAATA
1 AAATAAATA
3052479 TTAAAACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 9 0.30
25 7 0.23
26 14 0.47
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.29
Consensus pattern (24 bp):
AAATAAATACATTTAAAAATATAA
Found at i:3055916 original size:16 final size:16
Alignment explanation
Indices: 3055836--3055917 Score: 53
Period size: 16 Copynumber: 5.1 Consensus size: 16
3055826 TTTAATGTTT
3055836 ATATATATAAATTT-AA
1 ATAT-TATAAATTTAAA
* *
3055852 ATTTTATGAATTATAAA
1 ATATTATAAATT-TAAA
* *
3055869 TTA-TATAATATATAAA
1 ATATTATAA-ATTTAAA
* *
3055885 A-ATAATATAATATAAA
1 ATATTATA-AATTTAAA
3055901 ATATTATAAATTTAAA
1 ATATTATAAATTTAAA
3055917 A
1 A
3055918 AAAATGAAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
15 8 0.16
16 31 0.62
17 11 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (16 bp):
ATATTATAAATTTAAA
Found at i:3057004 original size:60 final size:60
Alignment explanation
Indices: 3056903--3057055 Score: 200
Period size: 60 Copynumber: 2.6 Consensus size: 60
3056893 TACACTACTC
* * * * *
3056903 GTCACCCAACTATTAGTAAATTTCTCTTTTAGTCATATAACTGTGAAAAGTTACAAAATA
1 GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACATAACTATGAAAAGTTACAAAATA
* * * * *
3056963 GTCACCTAATTATTTGTAAATTTGTTTTTTGGTCACCTAACTATGAAAAGTTATAAAATA
1 GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACATAACTATGAAAAGTTACAAAATA
*
3057023 ATCACCTAACTATTAGTAAA-TTCTTTTTTGGTC
1 GTCACCTAACTATTAGTAAATTTCTTTTTTGGTC
3057056 GCCCAACTAT
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 12 0.15
60 67 0.85
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (60 bp):
GTCACCTAACTATTAGTAAATTTCTTTTTTGGTCACATAACTATGAAAAGTTACAAAATA
Found at i:3059582 original size:29 final size:29
Alignment explanation
Indices: 3059526--3059583 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3059516 AAAAATGTAA
* **
3059526 AAAAAAATTACGTGAGTAGATCGTTTTTT
1 AAAAAAATTACGAGAGTAGATCAATTTTT
* *
3059555 AAAAAAATTATGAGATTAGATCAATTTTT
1 AAAAAAATTACGAGAGTAGATCAATTTTT
3059584 GAATGGAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (29 bp):
AAAAAAATTACGAGAGTAGATCAATTTTT
Found at i:3059916 original size:43 final size:43
Alignment explanation
Indices: 3059855--3059939 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
3059845 GTCCAGTAAG
3059855 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
1 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
3059898 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAAT
1 TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAAT
3059940 CATACTGCTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.19, C:0.09, G:0.14, T:0.58
Consensus pattern (43 bp):
TTGTGAGTTTAGTCTTTGTTCTCCAATTTGATTATTTTTAATT
Found at i:3062520 original size:21 final size:21
Alignment explanation
Indices: 3062479--3062522 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3062469 CTTAAAATAA
*
3062479 TTTATATAATTTTTTTATATT
1 TTTATATAATATTTTTATATT
3062500 TTTATATATATATTTTT-TATT
1 TTTATATA-ATATTTTTATATT
3062521 TT
1 TT
3062523 ATTAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTATATAATATTTTTATATT
Found at i:3064176 original size:24 final size:24
Alignment explanation
Indices: 3064135--3064182 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3064125 AAAATTAGAA
*
3064135 ATATTTTTAATACTAAATACATAAT
1 ATATTTTTAATAC-AAATAAATAAT
3064160 ATATTTTTAATGA-AAATAAATAA
1 ATATTTTTAAT-ACAAATAAATAA
3064183 ATTTAACCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 11 0.52
26 1 0.05
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
ATATTTTTAATACAAATAAATAAT
Found at i:3065603 original size:23 final size:22
Alignment explanation
Indices: 3065557--3065603 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3065547 GATAAAAATT
*
3065557 AAACCCTAAAACTTGAAAATAA
1 AAACCCTAAAACTTGAAAACAA
3065579 AAACCCTCAAAACTT-AAATACAA
1 AAACCCT-AAAACTTGAAA-ACAA
3065602 AA
1 AA
3065604 TTCTCTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.60, C:0.21, G:0.02, T:0.17
Consensus pattern (22 bp):
AAACCCTAAAACTTGAAAACAA
Found at i:3068338 original size:13 final size:13
Alignment explanation
Indices: 3068320--3068347 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3068310 AATATGAATC
3068320 TTATATCAAACCA
1 TTATATCAAACCA
3068333 TTATATCAAACCA
1 TTATATCAAACCA
3068346 TT
1 TT
3068348 GAACCAGATG
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:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (13 bp):
TTATATCAAACCA
Found at i:3069513 original size:9 final size:9
Alignment explanation
Indices: 3069499--3069523 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3069489 TAAGTTTAAC
3069499 TGTTAATAT
1 TGTTAATAT
3069508 TGTTAATAT
1 TGTTAATAT
3069517 TGTTAAT
1 TGTTAAT
3069524 GTGAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
TGTTAATAT
Found at i:3071068 original size:42 final size:42
Alignment explanation
Indices: 3071008--3071096 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
3070998 GCCCTTAGCT
* * *
3071008 CGTGTGCAACACTGACTTTAAAACACGGCCATGACGCACGCC
1 CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
* * * *
3071050 CGTGTACAATACTAACTTTAATACACGGCCATGGCACACGTC
1 CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
3071092 CGTGT
1 CGTGT
3071097 GGCCTGCCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.21
Consensus pattern (42 bp):
CGTGTACAACACTAACTTTAAAACACGGCCATGACACACGCC
Found at i:3073309 original size:26 final size:26
Alignment explanation
Indices: 3073280--3073332 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3073270 ATTATGCTAG
3073280 TACACTAAAATATAAATAAAATAATT
1 TACACTAAAATATAAATAAAATAATT
3073306 TACACTAAAATATAAATAAAATAATT
1 TACACTAAAATATAAATAAAATAATT
3073332 T
1 T
3073333 TCTTAGCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (26 bp):
TACACTAAAATATAAATAAAATAATT
Found at i:3074265 original size:24 final size:24
Alignment explanation
Indices: 3074236--3074283 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3074226 AAAAACATAG
3074236 TGTTTGAAATCTCCTATAGTCACA
1 TGTTTGAAATCTCCTATAGTCACA
3074260 TGTTTGAAATCTCCTATAGTCACA
1 TGTTTGAAATCTCCTATAGTCACA
3074284 GGTCCTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (24 bp):
TGTTTGAAATCTCCTATAGTCACA
Found at i:3075635 original size:85 final size:86
Alignment explanation
Indices: 3075487--3075653 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 86
3075477 GAGGATTCAC
* *
3075487 TTTGACCATAGGTAAGACAATGTCAAAGTTAATGTCAGAATCCAATTTCTGATAATCCTGTGACA
1 TTTGACCATAGGTAAGACAATGTCAAAGATAATGTCAGAATCCAATATCTGATAATCCTGTGACA
*
3075552 TACCTACAATAACACAAATAT
66 TACCTACAACAACACAAATAT
* * * * *
3075573 TTTG-CCATAGGTAAGGCAATGTCAGAGAT-ATGGTTAGAATCTAATAT-TGGATGATCCTGTGA
1 TTTGACCATAGGTAAGACAATGTCAAAGATAAT-GTCAGAATCCAATATCT-GATAATCCTGTGA
*
3075635 CATACCTGCAACAACACAA
64 CATACCTACAACAACACAA
3075654 GTATGTGGAA
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 3 0.04
85 63 0.90
86 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (86 bp):
TTTGACCATAGGTAAGACAATGTCAAAGATAATGTCAGAATCCAATATCTGATAATCCTGTGACA
TACCTACAACAACACAAATAT
Found at i:3077441 original size:32 final size:31
Alignment explanation
Indices: 3077337--3077442 Score: 95
Period size: 32 Copynumber: 3.3 Consensus size: 31
3077327 CATAAATCTG
* * * *
3077337 GTTTTCAGAAAACTTTATACTAGGATTATCGA
1 GTTTTCAGAAAACTTTATTC-AAGATTTTTGA
* * *
3077369 GTTTTCAGAATACTTTATCTCAAAATTTTTGG
1 GTTTTCAGAAAACTTTAT-TCAAGATTTTTGA
* *
3077401 GTTCTCAGAAAACTTTATTGCGAGATTTTTGA
1 GTTTTCAGAAAACTTTATT-CAAGATTTTTGA
*
3077433 CTTTTCAGAA
1 GTTTTCAGAA
3077443 TTCAAGCTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
31 1 0.02
32 56 0.97
33 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (31 bp):
GTTTTCAGAAAACTTTATTCAAGATTTTTGA
Found at i:3078937 original size:16 final size:16
Alignment explanation
Indices: 3078916--3078949 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3078906 GTATGCTTCC
*
3078916 CATAGCTCAGCTTCAA
1 CATAGCTAAGCTTCAA
3078932 CATAGCTAAGCTTCAA
1 CATAGCTAAGCTTCAA
3078948 CA
1 CA
3078950 GTTGAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (16 bp):
CATAGCTAAGCTTCAA
Found at i:3079165 original size:11 final size:12
Alignment explanation
Indices: 3079149--3079177 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
3079139 AATAAACAAG
3079149 TTAAATTTTTT-
1 TTAAATTTTTTA
3079160 TTAAATTTTTTA
1 TTAAATTTTTTA
3079172 TTAAAT
1 TTAAAT
3079178 AAACCGACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TTAAATTTTTTA
Found at i:3091151 original size:43 final size:44
Alignment explanation
Indices: 3091058--3091145 Score: 149
Period size: 44 Copynumber: 2.0 Consensus size: 44
3091048 AATATTCCTG
*
3091058 AAATTTTTAAAAAGCATTGAAAGTAAATATTTTATATGACTCCA
1 AAATTTTAAAAAAGCATTGAAAGTAAATATTTTATATGACTCCA
* *
3091102 AAATTTTAAAAAAGCATTGTAAGTAAATCTTTTATATGACTCCA
1 AAATTTTAAAAAAGCATTGAAAGTAAATATTTTATATGACTCCA
3091146 TATTTTCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (44 bp):
AAATTTTAAAAAAGCATTGAAAGTAAATATTTTATATGACTCCA
Found at i:3091397 original size:22 final size:23
Alignment explanation
Indices: 3091372--3091417 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3091362 CAACCAAACC
3091372 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3091394 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3091417 A
1 A
3091418 CGTCATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3091423 original size:23 final size:22
Alignment explanation
Indices: 3091379--3091428 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
3091369 ACCAATTCAA
*
3091379 CATATTTTCAAGATAAATTCAT
1 CATATTTTCAAGATAAAGTCAT
*
3091401 GCATATTTAT-AAGATAACGTCAT
1 -CATATTT-TCAAGATAAAGTCAT
3091424 CATAT
1 CATAT
3091429 ACTCAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.21
23 18 0.75
24 1 0.04
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (22 bp):
CATATTTTCAAGATAAAGTCAT
Found at i:3096339 original size:20 final size:20
Alignment explanation
Indices: 3096277--3096345 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
3096267 ATATAGATAT
* *
3096277 TTATTATT-TATTATTATTA
1 TTATTATTAAATTATAATTA
*
3096296 TT-CTATTAAATTATAATT-
1 TTATTATTAAATTATAATTA
*
3096314 TATATTATTAAATTATGATTA
1 T-TATTATTAAATTATAATTA
3096335 TTATTATTAAA
1 TTATTATTAAA
3096346 AATAAATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
18 5 0.12
19 11 0.27
20 24 0.59
21 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (20 bp):
TTATTATTAAATTATAATTA
Found at i:3097730 original size:12 final size:12
Alignment explanation
Indices: 3097713--3097737 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3097703 GCCGACTACT
3097713 GTTACTGTTACC
1 GTTACTGTTACC
3097725 GTTACTGTTACC
1 GTTACTGTTACC
3097737 G
1 G
3097738 ATTCGACACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:3097765 original size:45 final size:45
Alignment explanation
Indices: 3097715--3097825 Score: 170
Period size: 45 Copynumber: 2.5 Consensus size: 45
3097705 CGACTACTGT
*
3097715 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
*
3097760 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
* *
3097805 TACTGCTACTGTTACTGTTAC
1 TACTGTTACCGTTACTGTTAC
3097826 TGCTACCGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 60 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.40
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:3097774 original size:51 final size:50
Alignment explanation
Indices: 3097709--3097833 Score: 145
Period size: 45 Copynumber: 2.6 Consensus size: 50
3097699 ATATGCCGAC
3097709 TACTGTTACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCG-A
1 TACTG-TACTGTTACCGTTACTGTTACCGATTCAG-CACTTTGTGTGTCGAA
* *
3097759 -A---TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTACTGTTACCGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
* *
3097805 TACTGCTACTGTTACTGTTACTGCTACCG
1 TACTG-TACTGTTACCGTTACTGTTACCG
3097834 TTACTGATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
45 39 0.62
46 2 0.03
47 1 0.02
49 1 0.02
51 20 0.32
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (50 bp):
TACTGTACTGTTACCGTTACTGTTACCGATTCAGCACTTTGTGTGTCGAA
Found at i:3097828 original size:18 final size:19
Alignment explanation
Indices: 3097805--3097846 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
3097795 GTGTGTTGAA
*
3097805 TACTGCTACTGTTACTG-T
1 TACTGCTACCGTTACTGAT
3097823 TACTGCTACCGTTACTGAT
1 TACTGCTACCGTTACTGAT
3097842 TACTG
1 TACTG
3097847 ATTAGGTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (19 bp):
TACTGCTACCGTTACTGAT
Found at i:3097903 original size:23 final size:18
Alignment explanation
Indices: 3097854--3097891 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3097844 CTGATTAGGT
3097854 ACTGTGTACCGTTAAGGC
1 ACTGTGTACCGTTAAGGC
3097872 ACTGTGTACCGTTAAGGC
1 ACTGTGTACCGTTAAGGC
3097890 AC
1 AC
3097892 ATTGTGCCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (18 bp):
ACTGTGTACCGTTAAGGC
Found at i:3101955 original size:22 final size:23
Alignment explanation
Indices: 3101930--3101975 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3101920 CAACCAAACC
3101930 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3101952 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3101975 A
1 A
3101976 TGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3110094 original size:12 final size:11
Alignment explanation
Indices: 3110077--3110114 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
3110067 AAAATATTAT
3110077 TTTATATTAATA
1 TTTATATTAA-A
3110089 TTTATA-TAAA
1 TTTATATTAAA
3110099 TTTATAATTAAA
1 TTTAT-ATTAAA
3110111 TTTA
1 TTTA
3110115 AATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.25
11 4 0.17
12 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTATATTAAA
Found at i:3110095 original size:22 final size:22
Alignment explanation
Indices: 3110077--3110120 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3110067 AAAATATTAT
3110077 TTTAT-ATTAATATTTATATAAA
1 TTTATAATTAA-ATTTATATAAA
*
3110099 TTTATAATTAAATTTAAATAAA
1 TTTATAATTAAATTTATATAAA
3110121 AATATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATAATTAAATTTATATAAA
Found at i:3112823 original size:172 final size:172
Alignment explanation
Indices: 3112537--3112885 Score: 698
Period size: 172 Copynumber: 2.0 Consensus size: 172
3112527 GTTTTCAAAA
3112537 CCAAGCAATGTATAGATTGGCCAATATCAGACCTTCCCAGAATCGCACATGACTTAGTAGCGCTA
1 CCAAGCAATGTATAGATTGGCCAATATCAGACCTTCCCAGAATCGCACATGACTTAGTAGCGCTA
3112602 GGGTAGATATGATCGTCGGGCCTAATGTTATTAACAAGCATTGTCCGGAAAAACTGGATTGCAAG
66 GGGTAGATATGATCGTCGGGCCTAATGTTATTAACAAGCATTGTCCGGAAAAACTGGATTGCAAG
3112667 GGAAGGGAATTCATTTTGAGCGAAAGAGGAGATAACAGAGCT
131 GGAAGGGAATTCATTTTGAGCGAAAGAGGAGATAACAGAGCT
3112709 CCAAGCAATGTATAGATTGGCCAATATCAGACCTTCCCAGAATCGCACATGACTTAGTAGCGCTA
1 CCAAGCAATGTATAGATTGGCCAATATCAGACCTTCCCAGAATCGCACATGACTTAGTAGCGCTA
3112774 GGGTAGATATGATCGTCGGGCCTAATGTTATTAACAAGCATTGTCCGGAAAAACTGGATTGCAAG
66 GGGTAGATATGATCGTCGGGCCTAATGTTATTAACAAGCATTGTCCGGAAAAACTGGATTGCAAG
3112839 GGAAGGGAATTCATTTTGAGCGAAAGAGGAGATAACAGAGCT
131 GGAAGGGAATTCATTTTGAGCGAAAGAGGAGATAACAGAGCT
3112881 CCAAG
1 CCAAG
3112886 TAGTGGAGCT
Statistics
Matches: 177, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
172 177 1.00
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (172 bp):
CCAAGCAATGTATAGATTGGCCAATATCAGACCTTCCCAGAATCGCACATGACTTAGTAGCGCTA
GGGTAGATATGATCGTCGGGCCTAATGTTATTAACAAGCATTGTCCGGAAAAACTGGATTGCAAG
GGAAGGGAATTCATTTTGAGCGAAAGAGGAGATAACAGAGCT
Found at i:3113487 original size:18 final size:18
Alignment explanation
Indices: 3113466--3113505 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3113456 ATTTTAAAAT
*
3113466 TTTTATAAA-TATTTTATA
1 TTTTAAAAAGTATTTTA-A
3113484 TTTTAAAAAGTATTTTAA
1 TTTTAAAAAGTATTTTAA
3113502 TTTT
1 TTTT
3113506 TTGTTGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTAAAAAGTATTTTAA
Found at i:3113506 original size:19 final size:18
Alignment explanation
Indices: 3113463--3113506 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3113453 TAAATTTTAA
*
3113463 AATTTTTATAAATATTTT
1 AATTTTTAAAAATATTTT
3113481 -ATATTTTAAAAAGTATTTT
1 AAT-TTTTAAAAA-TATTTT
3113500 AATTTTT
1 AATTTTT
3113507 TGTTGAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 10 0.45
20 2 0.09
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
AATTTTTAAAAATATTTT
Found at i:3115158 original size:16 final size:16
Alignment explanation
Indices: 3115139--3115187 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
3115129 TTAATTTTTT
3115139 ATATAAAAAATTAAAA
1 ATATAAAAAATTAAAA
* * *
3115155 ATATAATACATCAAAA
1 ATATAAAAAATTAAAA
3115171 ATACTAAAAACATTAAA
1 ATA-TAAAAA-ATTAAA
3115188 TTTAATACTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 16 0.64
17 4 0.16
18 5 0.20
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (16 bp):
ATATAAAAAATTAAAA
Found at i:3118961 original size:11 final size:11
Alignment explanation
Indices: 3118922--3118962 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
3118912 CTGCTCTCTC
3118922 TTTTTCTTTTAT
1 TTTTTCTTTT-T
3118934 TTTTTCTTTTT
1 TTTTTCTTTTT
**
3118945 AATTTCTTTTT
1 TTTTTCTTTTT
3118956 TTTTTCT
1 TTTTTCT
3118963 CGGGATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:3121504 original size:27 final size:27
Alignment explanation
Indices: 3121474--3121526 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
3121464 AAAATGTCAA
* *
3121474 AAATGACTAAATTGAAGGGAATTATCT
1 AAATGAATAAATTGAAGGAAATTATCT
* *
3121501 AAATTAATAAATTGAATGAAATTATC
1 AAATGAATAAATTGAAGGAAATTATC
3121527 AATTTAAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (27 bp):
AAATGAATAAATTGAAGGAAATTATCT
Found at i:3122659 original size:31 final size:31
Alignment explanation
Indices: 3122572--3122651 Score: 151
Period size: 31 Copynumber: 2.6 Consensus size: 31
3122562 AACCTACTAA
3122572 AAAAACTTTTGAATAGTTTAGTAATTTAAAT
1 AAAAACTTTTGAATAGTTTAGTAATTTAAAT
3122603 AAAAACTTTTGAATAGTTTAGTAATTTAAAT
1 AAAAACTTTTGAATAGTTTAGTAATTTAAAT
*
3122634 AAAAACTTTCGAATAGTT
1 AAAAACTTTTGAATAGTT
3122652 CTTTAATTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (31 bp):
AAAAACTTTTGAATAGTTTAGTAATTTAAAT
Found at i:3123480 original size:17 final size:17
Alignment explanation
Indices: 3123460--3123498 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3123450 ATTAAAATAT
3123460 TTAAAATATATATTATA
1 TTAAAATATATATTATA
* *
3123477 TTAATATTTATATTATA
1 TTAAAATATATATTATA
3123494 TTAAA
1 TTAAA
3123499 TAAAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAAATATATATTATA
Found at i:3124327 original size:16 final size:16
Alignment explanation
Indices: 3124295--3124326 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3124285 TTCATGCTAG
3124295 ATGTTTAAAGTTGAAA
1 ATGTTTAAAGTTGAAA
3124311 ATGTTTAAAG-TGAAA
1 ATGTTTAAAGTTGAAA
3124326 A
1 A
3124327 AGATTGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
ATGTTTAAAGTTGAAA
Found at i:3125759 original size:13 final size:13
Alignment explanation
Indices: 3125741--3125768 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3125731 AATTTTTCAT
3125741 GATTTTGTTAATA
1 GATTTTGTTAATA
3125754 GATTTTGTTAATA
1 GATTTTGTTAATA
3125767 GA
1 GA
3125769 ATATATTTAG
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:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (13 bp):
GATTTTGTTAATA
Found at i:3127259 original size:42 final size:42
Alignment explanation
Indices: 3127212--3127297 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
3127202 TTAAATATTT
3127212 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
1 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
3127254 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
1 ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
3127296 AT
1 AT
3127298 TTGAACATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (42 bp):
ATCCTTTCTCAAATACTACAATTTTAGGGTATTACAACTTAG
Found at i:3127426 original size:24 final size:26
Alignment explanation
Indices: 3127385--3127434 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
3127375 ATATACCTAT
3127385 ATATAAATTTTTAATAAA-TGAAAAAA
1 ATATAAA-TTTTAATAAATTGAAAAAA
*
3127411 ATATAAA-TTTATTAAATTGAAAAA
1 ATATAAATTTTAATAAATTGAAAAA
3127435 TGAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 7 0.32
26 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (26 bp):
ATATAAATTTTAATAAATTGAAAAAA
Found at i:3130817 original size:38 final size:38
Alignment explanation
Indices: 3130756--3130990 Score: 326
Period size: 38 Copynumber: 6.1 Consensus size: 38
3130746 ATTTGATGTG
*
3130756 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAATA
3130796 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * * * *
3130834 TATCCGGTTTTAAAGGCCCGCAAGCTTTGTGCTGGTATTA
1 TATCCGG-GTTAAA-TCCCGCAGGCTTCGTGCTGGTAATA
3130874 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
*
3130912 TATCCCGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * * * *
3130950 TATCCCGGTTAAATCCCGCAGGCCTAGTACTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
3130988 TAT
1 TAT
3130991 TCAGGCCTTT
Statistics
Matches: 177, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
38 126 0.71
39 15 0.08
40 36 0.20
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
Found at i:3130885 original size:78 final size:76
Alignment explanation
Indices: 3130756--3130990 Score: 328
Period size: 78 Copynumber: 3.0 Consensus size: 76
3130746 ATTTGATGTG
3130756 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
1 TATCC-GG-TTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
3130821 CGTGCTGGTAATA
64 CGTGCTGGTAATA
* * * *
3130834 TATCCGGTTTTAAAGGCCCGCAAGCTTTGTGCTGGTATTATATCCGGGTTAAATCCCGCAGGCTT
1 TATCCGG--TTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTT
3130899 CGTGCTGGTAATA
64 CGTGCTGGTAATA
* * * *
3130912 TATCCCGGTTAAA-TCCCGCAGGCTTCGTGCTGGTAATATATCCCGGTTAAATCCCGCAGGCCTA
1 TAT-CCGGTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTC
* *
3130976 GTACTGGTATTA
65 GTGCTGGTAATA
3130988 TAT
1 TAT
3130991 TCAGGCCTTT
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
76 57 0.40
77 7 0.05
78 73 0.52
79 4 0.03
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.30
Consensus pattern (76 bp):
TATCCGGTTAAAGACCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
TGCTGGTAATA
Found at i:3131052 original size:45 final size:45
Alignment explanation
Indices: 3130987--3131118 Score: 139
Period size: 45 Copynumber: 3.0 Consensus size: 45
3130977 TACTGGTATT
* * * *
3130987 ATATTCAGGCCTTTGAGCCTAGCAAGCTATTATGTCGGTGAGAT-
1 ATATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
* *
3131031 ACTATTCGGGCCTTTGAGCCTAGTAGGCTATAATGCCGGTGACATG
1 A-TATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
* * *
3131077 ATA-TCGAGCC-TTGAGCCTAGCAGGCGA-AATGCCGGTGA-ATG
1 ATATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
3131118 A
1 A
3131119 ATAAAAGTCT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
41 4 0.05
42 11 0.14
43 15 0.19
44 7 0.09
45 39 0.51
46 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (45 bp):
ATATTCGGGCCTTTGAGCCTAGCAAGCTATAATGCCGGTGACATG
Found at i:3141007 original size:19 final size:20
Alignment explanation
Indices: 3140983--3141021 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
3140973 ATAATATACT
3140983 TATTTTTTTTCT-AATTTAA
1 TATTTTTTTTCTCAATTTAA
3141002 TATTTTTTTTCTCAATTTAA
1 TATTTTTTTTCTCAATTTAA
3141022 CATGAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTTTTTCTCAATTTAA
Found at i:3162257 original size:19 final size:19
Alignment explanation
Indices: 3162231--3162277 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
3162221 ACCGGTCAAG
*
3162231 TTAAAAAATTATTAA-AAA
1 TTAAAAAATTAATAATAAA
*
3162249 TTCAAAAAAATAATAATAAA
1 TT-AAAAAATTAATAATAAA
3162269 TTAAAAAAT
1 TTAAAAAAT
3162278 CCAGTTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 17 0.71
20 5 0.21
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
TTAAAAAATTAATAATAAA
Found at i:3166945 original size:37 final size:36
Alignment explanation
Indices: 3166846--3166948 Score: 151
Period size: 32 Copynumber: 2.9 Consensus size: 36
3166836 AGAAAGAAAG
3166846 AATAACAATCCATTAGATTAAATTCATT-AAAAAAT
1 AATAACAATCCATTAGATTAAATTCATTAAAAAAAT
3166881 AAT---AATCCATTAGATTAAATTCATTAAAAAAAT
1 AATAACAATCCATTAGATTAAATTCATTAAAAAAAT
* *
3166914 AATAACAATCCATAAAGATTAAATTCGTTAAAAAA
1 AATAACAATCCAT-TAGATTAAATTCATTAAAAAA
3166949 TCGCAAAGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
32 22 0.36
33 10 0.16
35 3 0.05
36 7 0.11
37 19 0.31
ACGTcount: A:0.55, C:0.11, G:0.04, T:0.30
Consensus pattern (36 bp):
AATAACAATCCATTAGATTAAATTCATTAAAAAAAT
Found at i:3193577 original size:30 final size:30
Alignment explanation
Indices: 3193538--3193628 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
3193528 ATAAGTTTGT
*
3193538 TTCTAATAATATTGCTTGTGATGAAAGAAA
1 TTCTGATAATATTGCTTGTGATGAAAGAAA
* * * *
3193568 TTTTGATAATATTGCTTTTGGTGAACGAAA
1 TTCTGATAATATTGCTTGTGATGAAAGAAA
* *
3193598 TTCTGATAATATTACTTGTGATGAAGGAAA
1 TTCTGATAATATTGCTTGTGATGAAAGAAA
3193628 T
1 T
3193629 GAGAAACAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (30 bp):
TTCTGATAATATTGCTTGTGATGAAAGAAA
Found at i:3197269 original size:19 final size:17
Alignment explanation
Indices: 3197245--3197281 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
3197235 TAGTTAAATG
3197245 ATAAAATAATACAAAGAAA
1 ATAAAAT-ATA-AAAGAAA
3197264 ATAAAATATAAAAGAAA
1 ATAAAATATAAAAGAAA
3197281 A
1 A
3197282 ACAAAGAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 3 0.17
19 7 0.39
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (17 bp):
ATAAAATATAAAAGAAA
Found at i:3197354 original size:9 final size:9
Alignment explanation
Indices: 3197331--3197364 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3197321 CAGGGGAAGA
3197331 AAAAGAAAG
1 AAAAGAAAG
3197340 -AAAGAAAG
1 AAAAGAAAG
3197348 AAAAGAAAG
1 AAAAGAAAG
3197357 AAAAGAAA
1 AAAAGAAA
3197365 AAGGTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:3197354 original size:13 final size:13
Alignment explanation
Indices: 3197331--3197364 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3197321 CAGGGGAAGA
3197331 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
3197344 -AAAGAAAAGAAAG
1 AAAAG-AAAGAAAG
3197357 AAAAGAAA
1 AAAAGAAA
3197365 AAGGTAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.21
13 11 0.58
14 4 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:3197940 original size:12 final size:12
Alignment explanation
Indices: 3197923--3197947 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3197913 GCCGACTACT
3197923 GTTACTGTTACC
1 GTTACTGTTACC
3197935 GTTACTGTTACC
1 GTTACTGTTACC
3197947 G
1 G
3197948 ATTCGACAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:3197975 original size:45 final size:45
Alignment explanation
Indices: 3197925--3198035 Score: 134
Period size: 45 Copynumber: 2.5 Consensus size: 45
3197915 CGACTACTGT
* * *
3197925 TACTGTTACCGTTACTGTTACCGATTC-GACAGTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCAAA
* * *
3197970 TACTGTTACCGTTACTATTATAGATTCAGCACTTTGTGTGTTAAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAA
**
3198015 TACTGTTATTGTTACTGTTAC
1 TACTGTTACCGTTACTGTTAC
3198036 TGTTACCGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAA
Found at i:3198033 original size:6 final size:6
Alignment explanation
Indices: 3198015--3198058 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3198005 GTGTGTTAAA
* * *
3198015 TACTGT TATTGT TACTGT TACTGT TACCGT TTCTGAT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT T
3198059 TAGGTACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TACTGT
Found at i:3199672 original size:93 final size:93
Alignment explanation
Indices: 3199559--3199823 Score: 485
Period size: 93 Copynumber: 2.8 Consensus size: 93
3199549 CGCCCATAAG
* * *
3199559 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3199624 ACGAGTTCGGATGCCTAGTTACATCCCA
66 ACGAGTTCGGATGCCTAGTTACATCCCA
*
3199652 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
3199717 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCCCA
3199745 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
3199810 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
3199824 TCAACCATCC
Statistics
Matches: 166, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 166 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCCCA
Found at i:3199820 original size:46 final size:46
Alignment explanation
Indices: 3199552--3199820 Score: 293
Period size: 46 Copynumber: 5.8 Consensus size: 46
3199542 TGTAACCCGC
* * *
3199552 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
3199598 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3199648 CC--CA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
3199691 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
3199741 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
3199784 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
3199821 TGCTCAACCA
Statistics
Matches: 187, Mismatches: 18, Indels: 36
0.78 0.07 0.15
Matches are distributed among these distances:
42 4 0.02
43 10 0.05
44 3 0.02
45 3 0.02
46 91 0.49
47 57 0.30
48 3 0.02
49 3 0.02
50 9 0.05
51 4 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:3201351 original size:20 final size:20
Alignment explanation
Indices: 3201326--3201379 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
3201316 CTTCAGTAAA
3201326 CTTTTGGTGATGTGTATTTT
1 CTTTTGGTGATGTGTATTTT
*
3201346 CTTTTGGTGATGTATATTTT
1 CTTTTGGTGATGTGTATTTT
* *
3201366 CGTTTGGTAATGTG
1 CTTTTGGTGATGTG
3201380 GCATGTACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.06, G:0.26, T:0.56
Consensus pattern (20 bp):
CTTTTGGTGATGTGTATTTT
Found at i:3204106 original size:13 final size:13
Alignment explanation
Indices: 3204088--3204120 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3204078 ATGTTTTAAT
3204088 TATAATGAT-ATAA
1 TATAAT-ATGATAA
3204101 TATAATATGATAA
1 TATAATATGATAA
3204114 TATAATA
1 TATAATA
3204121 ATAATTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (13 bp):
TATAATATGATAA
Found at i:3207063 original size:117 final size:116
Alignment explanation
Indices: 3206853--3207081 Score: 323
Period size: 117 Copynumber: 2.0 Consensus size: 116
3206843 GTTTTGTGGC
* * * *
3206853 TAAAGATGATTTGGTGGATAAGACCATAACTGGGTTATGACACTATGAACGTAAAACCATAGTTG
1 TAAAGATGAATTGATGAATAAGACCATAACTCGGTTATGACACTATGAACGTAAAACCATAGTTG
* * *
3206918 GACCATGGCAGTATTTATATGTAAGACCATAGATGGGCTATGGCATTAATG
66 AACCATGACAGTATTTATATGTAAGACCATAGATAGGCTATGGCATTAATG
* * *
3206969 TAAATGATGAATTGATGAATAAGACCGTAACTCGGTTATGACACTATGAACGTAAGACCATGGTT
1 TAAA-GATGAATTGATGAATAAGACCATAACTCGGTTATGACACTATGAACGTAAAACCATAGTT
* * * *
3207034 GAACTATGATAGTGTTTATATGTAAGACCATAGCTAGGCTATGGCATT
65 GAACCATGACAGTATTTATATGTAAGACCATAGATAGGCTATGGCATT
3207082 CTGGTGATAA
Statistics
Matches: 98, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
116 4 0.04
117 94 0.96
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (116 bp):
TAAAGATGAATTGATGAATAAGACCATAACTCGGTTATGACACTATGAACGTAAAACCATAGTTG
AACCATGACAGTATTTATATGTAAGACCATAGATAGGCTATGGCATTAATG
Found at i:3210633 original size:90 final size:89
Alignment explanation
Indices: 3209945--3211490 Score: 732
Period size: 90 Copynumber: 17.3 Consensus size: 89
3209935 TTGTAATATT
* * ** ** * *
3209945 TTTTTCAGAATAATTAAAATAATTTTTATTTAATTT-ATTTCATTTTTGGGATATTTGGGTTTGA
1 TTTTTC-GAATAATTATAATAATTGTTATTT-ATTTCATTTCATTCATGGGGCACTTGGGCTTGA
* *
3210009 GTCTGGTGTTGTAATAATA----TT-
64 GTCTGGTGCTGCAATAATATTTTTTA
* ** * *
3210030 TTTTTCGAAATAATTATAATAATTGATATTTATTTCATTTCATT-ATTAAGGCACCTAGGCTTGA
1 TTTTTCG-AATAATTATAATAATTGTTATTTATTTCATTTCATTCA-TGGGGCACTTGGGCTTGA
* * *
3210094 GCCTGGTGGTACAATAATA---TTT-
64 GTCTGGTGCTGCAATAATATTTTTTA
** * *
3210116 TTTTTCGAAATAATTATAATAATTGCAATTGTTTTTCATTTCATTCTCGAGAGTTGGGACACTTG
1 TTTTTCG-AATAATTATAATAATTGTTATT-TATTTCATTTCA-T-TC---A--TGGGGCACTTG
* *
3210181 GGCTTGAATCTAGTGCTGCAATAATATTTTTT-
57 GGCTTGAGTCTGGTGCTGCAATAATATTTTTTA
* * * * **
3210213 TGATTTTCAAAATACTTATACT-ATATATTATTTATTTCATTTCATT-ATCGGGGCACTTAAGCT
1 T--TTTTC-GAATAATTATAATAAT-TGTTATTTATTTCATTTCATTCAT-GGGGCACTTGGGCT
* * *
3210276 TGAGACTTGTGCTACAAT-ATATTTTTTA
61 TGAGTCTGGTGCTGCAATAATATTTTTTA
* * * * * ** * * * * *
3210304 TTTTCCAAAATAACTACAATAATTGCTATTTGCTTCATTTCATTCCTGAGACACTTAGGTTTGAG
1 TTTTTC-GAATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGAG
*
3210369 GCTGGTGCTGCAATAATATATTTTTTTA
65 TCTGGTGCTGCAAT-A-ATA-TTTTTTA
* * * * *
3210397 TTTTCTAGAATAATTATAATAATTTTTATTTATTTCACTTCATTTAT-GGGCACTTGGACTTGAG
1 TTTT-TCGAATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGAG
* *
3210461 -CTTGGAGCTGCAGT-A-A---TTT-
65 TC-TGGTGCTGCAATAATATTTTTTA
* * * ** * * * *
3210480 TTTCT-GAAATAATTAAAATAAATGTTATTTATTTCATTTCATTTTTGAGGCATTTAGGTTTGAG
1 TTTTTCG-AATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGAG
*
3210544 TCTGGTGCTGTAATAATAATTTTTTA
65 TCTGGTGCTGCAATAAT-ATTTTTTA
* * * * * *
3210570 TTTCTCGAATAACTACAATACTTGTTATTTATTTCATTTTATTCATGGGGCACTTGGGCTTGAGA
1 TTTTTCGAATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGAGT
** * *
3210635 AAGGTGTTGCGATAATATTTTTTA
66 CTGGTGCTGCAATAATATTTTTTA
* ** *
3210659 TTTTTTGAAATAATTATAATAATTACTATTTATTTCATTTCATTTCGAT---GCACTTGAGCTTG
1 TTTTTCG-AATAATTATAATAATTGTTATTTATTTCATTTCA-TTC-ATGGGGCACTTGGGCTTG
** * * *
3210721 AGT-TTATGCTACAATAGTTTTTTTTTCTAA
63 AGTCTGGTGCTGCAATA--ATATTTTT-T-A
* * * * * * *
3210751 TTTTTAGAATAATTAGAATAATT-TCTATTTATTTCATTTTATTTCA--AGGCATTTGAGATTGA
1 TTTTTCGAATAATTATAATAATTGT-TATTTATTTCATTTCA-TTCATGGGGCACTTGGGCTTGA
* * * *
3210813 GTTTGGTGTTGCGACAATATATTTTTA
64 GTCTGGTGCTGCAATAATAT-TTTTTA
* * * * *
3210840 TTTTTAAGAATAATTATAATAATTATAATTTATTTCATTTCATTCAAGGAGCACTTGGGCTTGAG
1 TTTTT-CGAATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGAG
3210905 T-TGGTGCTGCAAT-AT-TTTTTTA
65 TCTGGTGCTGCAATAATATTTTTTA
* * * * * * * * * * *
3210927 CTTTCCAAAATAATAATAATAATAATTGCTATATATTTCATTTAATTCCTTGGGTACATGGGATT
1 TTTTTC-GAATAAT--T-ATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTT
* *
3210992 GAGTCTAGTG--G-AACAAT-TTTTTT-
62 GAGTCTGGTGCTGCAATAATATTTTTTA
* * * * * * * *
3211015 TCTTTCCAAAATAATTATAATATTTGCTATATATTTCATTTAATTC-TCGAGCACTTGGGCTTGA
1 T-TTTTC-GAATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGA
** *
3211079 GTCTATTGCTGCAAGAATATTTTGTTA
64 GTCTGGTGCTGCAATAATATTTT-TTA
* * * *
3211106 TTTTTTGGAATAACTATAATAATTGTAATTCA-TTCATTTCATTTCA-GGGGCACTTGGGCTTGA
1 -TTTTTCGAATAATTATAATAATTGTTATTTATTTCATTTCA-TTCATGGGGCACTTGGGCTTGA
* * *
3211169 GTCTTGTGCTACAATAA-AGTTATTTAA
64 GTCTGGTGCTGCAATAATA-TT-TTTTA
* * ** * * *
3211196 TTTTT-GAATTAATTATAATAATTGCTATTAATTT--TTTCATTC-TCGGGAAAGTTGGTCTGGA
1 TTTTTCGAA-TAATTATAATAATTGTTATTTATTTCATTTCATTCAT-GGGGCACTTGGGCTTGA
** * * *
3211257 GTCTATTACTACAATAATATTTCTTA
64 GTCTGGTGCTGCAATAATATTTTTTA
** * * *
3211283 TTTTCTAAAATAATTATAATAATTGTTATTTATTTCATTTCATTTTCA--GGACACTTAGGTTTG
1 TTTT-TCGAATAATTATAATAATTGTTATTTATTTCATTTCA--TTCATGGGGCACTTGGGCTTG
*
3211346 AGTATGGTGCTGCAATAA-ATTTTTTAA
63 AGTCTGGTGCTGCAATAATATTTTTT-A
* * * * * *
3211373 CTTTTAGAATAATTATAATAATTGCTATTTAATTT--TCTTCATT-TTCGAGGTACTTGGGCTTG
1 TTTTTCGAATAATTATAATAATTGTTATTT-ATTTCAT-TTCATTCAT-GGGGCACTTGGGCTTG
* * *
3211435 AGTTTAGTGCACTGCAATTACATTTTTTTTA
63 AGTCTGGTG--CTGCAA-TA-ATATTTTTTA
* * *
3211466 TTTTCCAAAATAGTTATAATAATTG
1 TTTTTC-GAATAATTATAATAATTG
3211491 CTATGTAATG
Statistics
Matches: 1120, Mismatches: 243, Indels: 187
0.72 0.16 0.12
Matches are distributed among these distances:
81 1 0.00
82 35 0.03
83 24 0.02
84 10 0.01
85 79 0.07
86 60 0.05
87 40 0.04
88 78 0.07
89 213 0.19
90 284 0.25
91 113 0.10
92 48 0.04
93 47 0.04
94 50 0.04
96 1 0.00
97 5 0.00
98 13 0.01
99 19 0.02
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.46
Consensus pattern (89 bp):
TTTTTCGAATAATTATAATAATTGTTATTTATTTCATTTCATTCATGGGGCACTTGGGCTTGAGT
CTGGTGCTGCAATAATATTTTTTA
Found at i:3210657 original size:175 final size:177
Alignment explanation
Indices: 3210300--3210704 Score: 408
Period size: 175 Copynumber: 2.3 Consensus size: 177
3210290 CAATATATTT
** * * * * ** *
3210300 TTTATTTTCCAAAATAACTACAATAATTGCTATTTGCTTCATTTCATTCCTGAGACACTTAGGTT
1 TTTATTTTCTGAAATAATTAAAATAAATACTATTTATTTCATTTCATTTCTGAGACACTTAGGTT
* * *
3210365 TGAGGCTGGTGCTGCAATAATATATTTTTTTATTTTCTAGAATAATTATAATAATTTTTATTTAT
66 TGAGGCTGGTGCTGCAATAATATATTTTTTTATTTTCTAGAATAACTACAATAATTGTTATTTAT
* ***
3210430 TTCACTTCATTTATGGGCACTTGGACTTGAGCTTGGAGCTGCAGTAA
131 TTCACTTCATTCATGGGCACTTGGACTTGAGAAAGGAGCTGCAGTAA
** * * *
3210477 -TT-TTTTCTGAAATAATTAAAATAAATGTTATTTATTTCATTTCATTTTTGAGGCATTTAGGTT
1 TTTATTTTCTGAAATAATTAAAATAAATACTATTTATTTCATTTCATTTCTGAGACACTTAGGTT
* * * *
3210540 TGAGTCTGGTGCTGTAATAATA-A-TTTTTTA-TTTCTCGAATAACTACAATACTTGTTATTTAT
66 TGAGGCTGGTGCTGCAATAATATATTTTTTTATTTTCTAGAATAACTACAATAATTGTTATTTAT
* * * * *
3210602 TTCATTTTATTCATGGGGCACTTGGGCTTGAGAAAGGTGTTGC-GATAATA
131 TTCACTTCATTCAT-GGGCACTTGGACTTGAGAAAGGAGCTGCAG-T-A-A
* * *
3210652 TTTTTTATTTTTTGAAATAATTATAATAATTACTATTTATTTCATTTCATTTC
1 ---TTTATTTTCTGAAATAATTAAAATAAATACTATTTATTTCATTTCATTTC
3210705 GATGCACTTG
Statistics
Matches: 185, Mismatches: 34, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
172 39 0.21
173 30 0.16
174 2 0.01
175 70 0.38
176 2 0.01
179 2 0.01
180 40 0.22
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (177 bp):
TTTATTTTCTGAAATAATTAAAATAAATACTATTTATTTCATTTCATTTCTGAGACACTTAGGTT
TGAGGCTGGTGCTGCAATAATATATTTTTTTATTTTCTAGAATAACTACAATAATTGTTATTTAT
TTCACTTCATTCATGGGCACTTGGACTTGAGAAAGGAGCTGCAGTAA
Found at i:3210994 original size:181 final size:177
Alignment explanation
Indices: 3210637--3211080 Score: 395
Period size: 181 Copynumber: 2.5 Consensus size: 177
3210627 GCTTGAGAAA
* *
3210637 GGTGTTGCGATAATATTTTTTATTTTTTGAAATAATTATAATAATTACTATTTATTTCATTTCAT
1 GGTGTTGCGACAATATTTTTTATTTTTAGAAATAATTATAATAATTACTATTTATTTCATTTCAT
* * * *
3210702 TTCGATGCACTTGAGCTTGAGTTTATGCTACAATAGTTTTTTTTTCTAATTTTTAGAATAATTAG
66 TTCGATGCACTTGAGCTTGAGTTGATGCTACAATAGTTTTTTTTTCCAA---TAAGAATAATAAG
* * * * **
3210767 AATAATTTCTATTTATTTCATTTTATTTCAAGGCATTTGAGATTGAGTTT
128 AATAATTGCTATATATTTCATTTAATTCCAAGGCACATGAGATTGAGTTT
3210817 GGTGTTGCGACAATATATTTTTATTTTTA-AGAATAATTATAATAATTA-TAATTTATTTCATTT
1 GGTGTTGCGACAATAT-TTTTTATTTTTAGA-AATAATTATAATAATTACT-ATTTATTTCATTT
* * * * *
3210880 CA-TTCAAGGA-GCACTTGGGCTTGAGTTGGTGCTGCAATATTTTTTTACTTTCCAA-AATAATA
63 CATTTC---GATGCACTTGAGCTTGAGTTGATGCTACAATAGTTTTTT--TTTCCAATAAGAATA
* ** * * *
3210942 ATAATAATAATTGCTATATATTTCATTTAATTCCTTGGGTACATGGGATTGAGTCT
123 ATAAGAATAATTGCTATATATTTCATTTAATTCC-AAGGCACATGAGATTGAGTTT
* * * * ** * * * *
3210998 AGTG--G-AACAATTTTTTTTCTTTCCA-AAATAATTATAATATTTGCTATATATTTCATTTAAT
1 GGTGTTGCGACAATATTTTTTATTTTTAGAAATAATTATAATAATTACTATTTATTTCATTTCAT
*
3211059 TCTCGA-GCACTTGGGCTTGAGT
66 T-TCGATGCACTTGAGCTTGAGT
3211081 CTATTGCTGC
Statistics
Matches: 219, Mismatches: 33, Indels: 29
0.78 0.12 0.10
Matches are distributed among these distances:
175 18 0.08
176 28 0.13
177 12 0.05
178 8 0.04
179 1 0.00
180 53 0.24
181 60 0.27
182 31 0.14
183 2 0.01
184 6 0.03
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (177 bp):
GGTGTTGCGACAATATTTTTTATTTTTAGAAATAATTATAATAATTACTATTTATTTCATTTCAT
TTCGATGCACTTGAGCTTGAGTTGATGCTACAATAGTTTTTTTTTCCAATAAGAATAATAAGAAT
AATTGCTATATATTTCATTTAATTCCAAGGCACATGAGATTGAGTTT
Found at i:3211307 original size:177 final size:180
Alignment explanation
Indices: 3211077--3211415 Score: 447
Period size: 178 Copynumber: 1.9 Consensus size: 180
3211067 ACTTGGGCTT
* * * * **
3211077 GAGTCTATTGCTGCAAGAATATTTTGTTATTTTTTGGAATAACTATAATAATTGTAATTCA-TTC
1 GAGTCTATTACTACAAGAATATTTTCTTATTTTCTAAAATAACTATAATAATTGTAATTCATTTC
* * * * *
3211141 ATTTCA-TTTCAGGGGCACTTGGGCTTGAGTCTTGTGCTACAATAAAGTTATTTAA-TTTTTGAA
66 ATTTCATTTTCA-GGACACTTAGGCTTGAGTATGGTGCTACAATAAA-TTATTTAACTTTTAGAA
3211204 TTAATTATAATAATTGCTA-TTAATTTT-TTCATTCTCGGGAAAGTTGGTCTG
129 -TAATTATAATAATTGCTATTTAATTTTCTTCATTCTCGGGAAAGTTGGTCTG
* * * *
3211255 GAGTCTATTACTACAATAATA-TTTCTTATTTTCTAAAATAATTATAATAATTGTTATTTATTTC
1 GAGTCTATTACTACAAGAATATTTTCTTATTTTCTAAAATAACTATAATAATTGTAATTCATTTC
* * *
3211319 ATTTCATTTTCAGGACACTTAGGTTTGAGTATGGTGCTGCAATAAATTTTTTAACTTTTAGAATA
66 ATTTCATTTTCAGGACACTTAGGCTTGAGTATGGTGCTACAATAAATTATTTAACTTTTAGAATA
3211384 ATTATAATAATTGCTATTTAATTTTCTTCATT
131 ATTATAATAATTGCTATTTAATTTTCTTCATT
3211416 TTCGAGGTAC
Statistics
Matches: 138, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
177 57 0.41
178 70 0.51
179 11 0.08
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.46
Consensus pattern (180 bp):
GAGTCTATTACTACAAGAATATTTTCTTATTTTCTAAAATAACTATAATAATTGTAATTCATTTC
ATTTCATTTTCAGGACACTTAGGCTTGAGTATGGTGCTACAATAAATTATTTAACTTTTAGAATA
ATTATAATAATTGCTATTTAATTTTCTTCATTCTCGGGAAAGTTGGTCTG
Found at i:3212270 original size:88 final size:88
Alignment explanation
Indices: 3212121--3212289 Score: 320
Period size: 88 Copynumber: 1.9 Consensus size: 88
3212111 CCAAATCTGG
*
3212121 AAGATTCAAATACGAAGCTAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTTATTGTT
1 AAGATTCAAATACGAAGCTAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTTATTCTT
3212186 TACAAACAAGTATCAAGATCCGA
66 TACAAACAAGTATCAAGATCCGA
*
3212209 AAGATTCAAATACGAAGCTAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGATTTTTATTCTT
1 AAGATTCAAATACGAAGCTAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTTATTCTT
3212274 TACAAACAAGTATCAA
66 TACAAACAAGTATCAA
3212290 TGTAAGTTCG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (88 bp):
AAGATTCAAATACGAAGCTAGATCGAGGAAAGGAAAAAGTTCGGGATTAGTAGAATTTTATTCTT
TACAAACAAGTATCAAGATCCGA
Found at i:3213967 original size:91 final size:89
Alignment explanation
Indices: 3213826--3214170 Score: 232
Period size: 90 Copynumber: 3.8 Consensus size: 89
3213816 GCTGCAACAA
* * * ** * * * *
3213826 TATTTTTTTTTGAAATAATTATAATAGTTGCGATTTATTT-TATTTTATTTTTAGGTTC-TTGGG
1 TATTTTATTTTGGAATAATTATAATAATTGATATTTATTTCT-TTTCATTTTCAAG-ACATTGGG
***
3213889 CTTGAGTATGATGTTGTAATAATATT
64 CTTGAGTATGATGCACTAATAATATT
3213915 TGATTTTATTTTAGGAATAATTATAATAATTGATATTTATTTCTTTTCATTTTCAAGACAATTGG
1 T-ATTTTATTTT-GGAATAATTATAATAATTGATATTTATTTCTTTTCATTTTCAAGAC-ATTGG
* * *
3213980 GTTTGAGTCTGGTGCACTAATAATATT
63 GCTTGAGTATGATGCACTAATAATATT
* ** * * * * * * *
3214007 TTTTTTATTTTTTAATAATTATAATGACTGATATTTATTTCATTTCATTCTCGAGGCACTTGGCC
1 TATTTTATTTTGGAATAATTATAATAATTGATATTTATTTCTTTTCATTTTCAAGACA-TTGGGC
* *
3214072 TTGAGTCT-AGTGCTAC-AATAATTTT
65 TTGAGTATGA-TGC-ACTAATAATATT
* * * * * * *
3214097 TGTTTTATTTTTTTGGAATAGTTATAATAAGTGCTATTCATTT-TATTTTATTTTCAAGATATTT
1 TATTTTA---TTTTGGAATAATTATAATAATTGATATTTATTTCT-TTTCATTTTCAAGACA-TT
3214161 GGGCTTGAGT
61 GGGCTTGAGT
3214171 TTGGCGTTGC
Statistics
Matches: 200, Mismatches: 44, Indels: 20
0.76 0.17 0.08
Matches are distributed among these distances:
89 2 0.01
90 77 0.38
91 46 0.23
92 27 0.14
93 48 0.24
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.51
Consensus pattern (89 bp):
TATTTTATTTTGGAATAATTATAATAATTGATATTTATTTCTTTTCATTTTCAAGACATTGGGCT
TGAGTATGATGCACTAATAATATT
Found at i:3214044 original size:90 final size:91
Alignment explanation
Indices: 3213905--3214170 Score: 250
Period size: 90 Copynumber: 2.9 Consensus size: 91
3213895 TATGATGTTG
* ** * * *
3213905 TAATAATATTTGATTTTATTTTAGGAATAATTATAATAATTGATATTTATTTCTTTTCATTTTCA
1 TAATAATATTT-TTTTTATTTT-TTAATAATTATAATAACTGATATTTATTTCATTTCATTCTCA
** *
3213970 AGACAATTGGGTTTGAGTCTGGTGC-AC
64 AGACAATTGGCCTTGAGTCTAGTGCTAC
* *
3213997 TAATAATATTTTTTTTATTTTTTAATAATTATAATGACTGATATTTATTTCATTTCATTCTCGAG
1 TAATAATATTTTTTTTATTTTTTAATAATTATAATAACTGATATTTATTTCATTTCATTCTCAAG
* *
3214062 GCACTTGGCCTTGAGTCTAGTGCTAC
66 ACAATTGGCCTTGAGTCTAGTGCTAC
* * * * * * *
3214088 -AATAAT-TTTTGTTTTATTTTTTTGGAATAGTTATAATAAGTGCTATTCATTTTATTTTATTTT
1 TAATAATATTTT-TTTTA-TTTTTT--AATAATTATAATAACTGATATTTATTTCATTTCATTCT
* * *
3214151 CAAGATATTTGGGCTTGAGT
62 CAAGACAATTGGCCTTGAGT
3214171 TTGGCGTTGC
Statistics
Matches: 143, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
89 4 0.03
90 66 0.46
91 17 0.12
92 11 0.08
93 45 0.31
ACGTcount: A:0.28, C:0.09, G:0.14, T:0.50
Consensus pattern (91 bp):
TAATAATATTTTTTTTATTTTTTAATAATTATAATAACTGATATTTATTTCATTTCATTCTCAAG
ACAATTGGCCTTGAGTCTAGTGCTAC
Found at i:3215670 original size:21 final size:21
Alignment explanation
Indices: 3215630--3215694 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
3215620 CGAATACTCC
3215630 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
3215649 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
*
3215670 AACAGAAGCTCGTAGGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
3215691 AACA
1 AACA
3215695 AAAACTCATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.27
20 2 0.05
21 28 0.68
ACGTcount: A:0.40, C:0.18, G:0.28, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:3217533 original size:44 final size:42
Alignment explanation
Indices: 3217390--3217540 Score: 162
Period size: 43 Copynumber: 3.5 Consensus size: 42
3217380 TGCCGACGTT
* * * *
3217390 CCAGACATGGTCTTACATGTAATCAAATATCGATGCCACTGTC
1 CCAGACGTGGTCTTACACGAAATCAAATA-CGATGCCAATGTC
*
3217433 CCAGACAG-GGTCTTACACGAAATCAAATACGATGCCAACGTC
1 CCAGAC-GTGGTCTTACACGAAATCAAATACGATGCCAATGTC
* * *
3217475 CTAGATGTGGTCTTACACGTAAATCATAAGT-TGATGCCAATGTC
1 CCAGACGTGGTCTTACACG-AAATCA-AA-TACGATGCCAATGTC
*
3217519 CCAGACGTGATCTTACACGAAA
1 CCAGACGTGGTCTTACACGAAA
3217541 ACACATATCG
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 34 0.37
44 29 0.32
45 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
CCAGACGTGGTCTTACACGAAATCAAATACGATGCCAATGTC
Found at i:3218393 original size:163 final size:163
Alignment explanation
Indices: 3218123--3218449 Score: 636
Period size: 163 Copynumber: 2.0 Consensus size: 163
3218113 ATTGCTAAGC
3218123 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
1 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
*
3218188 AAGTGTCGAAACCCTAAGAGCTTTTATTCTTTCTTTTGTTCTTCAAATTTCAAAAAAATGAGCAT
66 AAGTGTCGAAACCCTAAGAGCTTTTATTATTTCTTTTGTTCTTCAAATTTCAAAAAAATGAGCAT
3218253 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
131 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
3218286 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
1 AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
*
3218351 AAGTGTCGAAACCCTAAGAGCTTTTATTATTTCTTTTGTTCTTCAAATTTCGAAAAAATGAGCAT
66 AAGTGTCGAAACCCTAAGAGCTTTTATTATTTCTTTTGTTCTTCAAATTTCAAAAAAATGAGCAT
3218416 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
131 ATAATGAACATTTTCATGTTTTGTTTAATTAAT
3218449 A
1 A
3218450 TTAACATAAT
Statistics
Matches: 162, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 162 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (163 bp):
AACGATTACAAAAACATAGAAATTATCAAAAACCGATCAAAACACATACCTTAATCCACAATCAC
AAGTGTCGAAACCCTAAGAGCTTTTATTATTTCTTTTGTTCTTCAAATTTCAAAAAAATGAGCAT
ATAATGAACATTTTCATGTTTTGTTTAATTAAT
Found at i:3222582 original size:15 final size:15
Alignment explanation
Indices: 3222562--3222592 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3222552 CCAACCTTCA
3222562 AATTTTACCTCAATT
1 AATTTTACCTCAATT
3222577 AATTTTACCTCAATT
1 AATTTTACCTCAATT
3222592 A
1 A
3222593 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:3224853 original size:11 final size:11
Alignment explanation
Indices: 3224837--3224863 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3224827 TAGAAATTAG
3224837 TTTGTGAAACT
1 TTTGTGAAACT
3224848 TTTGTGAAACT
1 TTTGTGAAACT
3224859 TTTGT
1 TTTGT
3224864 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:3226395 original size:93 final size:92
Alignment explanation
Indices: 3226263--3226457 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
3226253 TTGATTTTAG
* *
3226263 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
3226327 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
3226355 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
3226420 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
3226448 CAAATTCATA
1 TAAATTCATA
3226458 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Done.