Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 352 of 356
Found at i:112656384 original size:30 final size:30
Alignment explanation
Indices: 112656328--112656422 Score: 129
Period size: 30 Copynumber: 3.2 Consensus size: 30
112656318 AAAAAATTGT
* *
112656328 ATTTTGACCCCTAAACTTT-TCCTAAATTTC
1 ATTTTGACCCTTAAACTTTCT-TTAAATTTC
112656358 ATTTTGACCCTTAAACTTTCTTTAAATTTC
1 ATTTTGACCCTTAAACTTTCTTTAAATTTC
* * *
112656388 ACTTAGACCCTTAAACTTTCATTAAATTTC
1 ATTTTGACCCTTAAACTTTCTTTAAATTTC
112656418 ATTTT
1 ATTTT
112656423 AATCCTAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 56 0.98
31 1 0.02
ACGTcount: A:0.28, C:0.22, G:0.03, T:0.46
Consensus pattern (30 bp):
ATTTTGACCCTTAAACTTTCTTTAAATTTC
Found at i:112656773 original size:3 final size:3
Alignment explanation
Indices: 112656765--112656841 Score: 70
Period size: 3 Copynumber: 25.7 Consensus size: 3
112656755 CCAAGGCGTA
112656765 AAG AAG AAG AAG AAG AAG AAG AAGG AAG AAG AAAG AAG AAGG AAG AA-
1 AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG -AAG AAG AA-G AAG AAG
* * * *
112656812 AA- AAG AAA AAG -AG AAA AAA AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
112656842 AAAAGAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
2 6 0.10
3 48 0.76
4 9 0.14
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:112656802 original size:17 final size:17
Alignment explanation
Indices: 112656764--112656849 Score: 88
Period size: 17 Copynumber: 5.2 Consensus size: 17
112656754 ACCAAGGCGT
112656764 AAAGAAGAA-GAAGAAG
1 AAAGAAGAAGGAAGAAG
112656780 -AAGAAGAAGGAAGAAG
1 AAAGAAGAAGGAAGAAG
*
112656796 AAAGAAGAAGGAAGAAA
1 AAAGAAGAAGGAAGAAG
* *
112656813 AAAGAAAAAGAGAA-AAA
1 AAAGAAGAAG-GAAGAAG
* * *
112656830 AAAGAAAAAGAAAAAAG
1 AAAGAAGAAGGAAGAAG
112656847 AAA
1 AAA
112656850 AATAATAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
15 8 0.13
16 9 0.15
17 42 0.68
18 3 0.05
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAGGAAGAAG
Found at i:112656842 original size:6 final size:6
Alignment explanation
Indices: 112656764--112656851 Score: 63
Period size: 6 Copynumber: 14.5 Consensus size: 6
112656754 ACCAAGGCGT
* * * * * * *
112656764 AAAGAA GAAGAA GAAGAA GAAGAA GGAAGAA GAAAGAA GAAGGA AGA-AA
1 AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA -AAAGAA AAAGAA AAAGAA
*
112656813 AAAGAA AAAGAG AAA-AA AAAGAA AAAGAAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA AAAGAA AAA
112656852 TAATAAAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
5 7 0.10
6 43 0.63
7 18 0.26
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:112656849 original size:7 final size:7
Alignment explanation
Indices: 112656793--112656851 Score: 64
Period size: 7 Copynumber: 8.1 Consensus size: 7
112656783 AAGAAGGAAG
*
112656793 AAGAAAG
1 AAGAAAA
**
112656800 AAGAAGG
1 AAGAAAA
112656807 AAGAAAA
1 AAGAAAA
112656814 AAGAAAA
1 AAGAAAA
112656821 AGAGAAAA
1 A-AGAAAA
*
112656829 AAAAGAAA
1 AAGA-AAA
112656837 AAGAAAA
1 AAGAAAA
112656844 AAGAAAA
1 AAGAAAA
112656851 A
1 A
112656852 TAATAAAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
7 32 0.71
8 13 0.29
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:112657065 original size:26 final size:26
Alignment explanation
Indices: 112657014--112657066 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
112657004 AGGGGGCAGG
** *
112657014 CCAACAGCAGGCCCAATTCCAGCAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
*
112657040 CCAACAGCAGGCCCTAGCCCAACAGC
1 CCAACAGCAGGCCCAAGCCCAACAGC
112657066 C
1 C
112657067 AGCCTGTCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.45, G:0.19, T:0.06
Consensus pattern (26 bp):
CCAACAGCAGGCCCAAGCCCAACAGC
Found at i:112657157 original size:5 final size:5
Alignment explanation
Indices: 112657149--112657211 Score: 56
Period size: 5 Copynumber: 11.8 Consensus size: 5
112657139 GCCCAGCAGA
* *
112657149 AAAAG AAAAG AAAAAAG AAAA- AAAAG AAAAA AAAAG AAAAAAG AAGAG
1 AAAAG AAAAG --AAAAG AAAAG AAAAG AAAAG AAAAG --AAAAG AAAAG
112657197 AAAAAG AAAAG AAAA
1 -AAAAG AAAAG AAAA
112657212 ATTCAATTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
4 4 0.08
5 30 0.62
6 4 0.08
7 10 0.21
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:112657162 original size:11 final size:11
Alignment explanation
Indices: 112657149--112657212 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
112657139 GCCCAGCAGA
112657149 AAAAG-AAAAG
1 AAAAGAAAAAG
*
112657159 AAAA-AAGAAAA
1 AAAAGAA-AAAG
112657170 AAAAGAAAAA-
1 AAAAGAAAAAG
112657180 AAAAGAAAAAAG
1 AAAAG-AAAAAG
*
112657192 AAGAGAAAAAG
1 AAAAGAAAAAG
112657203 AAAAGAAAAA
1 AAAAGAAAAA
112657213 TTCAATTTGT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
10 10 0.22
11 30 0.65
12 6 0.13
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:112657163 original size:12 final size:12
Alignment explanation
Indices: 112657148--112657212 Score: 78
Period size: 12 Copynumber: 5.3 Consensus size: 12
112657138 AGCCCAGCAG
112657148 AAAAAGAAAAGA
1 AAAAAGAAAAGA
*
112657160 AAAAAGAAAAAAA
1 AAAAAG-AAAAGA
*
112657173 AGAAAAAAAAAGA
1 A-AAAAGAAAAGA
*
112657186 AAAAAGAAGAG-
1 AAAAAGAAAAGA
112657197 AAAAAGAAAAGA
1 AAAAAGAAAAGA
112657209 AAAA
1 AAAA
112657213 TTCAATTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.23
12 18 0.41
13 12 0.27
14 4 0.09
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:112657751 original size:18 final size:18
Alignment explanation
Indices: 112657729--112658118 Score: 153
Period size: 17 Copynumber: 22.0 Consensus size: 18
112657719 GGAAAATTTT
112657729 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
112657747 CCGTG-TTGCAAAAATTT
1 TCGTGTTTTCAAAAATTC
*
112657764 TCATGTTTTTCAAAAATTC
1 TCGTG-TTTTCAAAAATTC
112657783 TCGTGTTTTCAAAAAAATTC
1 TCGTGTTTTC--AAAAATTC
** * *
112657803 -C-AATTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTC
112657819 TCGTGTTTTCTAAAAAACTTC
1 TCGTGTTTTC--AAAAA-TTC
*
112657840 T-GTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
112657856 TCGTG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTC
* *
112657873 TCGT-ATTTCAAAAATTT
1 TCGTGTTTTCAAAAATTC
* * *
112657890 TCTTGTTTTC-AAATTTT
1 TCGTGTTTTCAAAAATTC
* * *
112657907 TCGT-ATTTAAAAAATCC
1 TCGTGTTTTCAAAAATTC
112657924 TCGTGTTTTC-AAAATTC
1 TCGTGTTTTCAAAAATTC
* *
112657941 -CAGTG-TTTCAAAATTTT
1 TC-GTGTTTTCAAAAATTC
112657958 TCGTG-TTTCAAAAAAAAATTC
1 TCGTGTTTTC----AAAAATTC
* *
112657979 CCGT-TTTCCAAAAACTT-
1 TCGTGTTTTCAAAAA-TTC
*
112657996 TCGCGTTTT-AAGAAATTGAC
1 TCGTGTTTTCAA-AAATT--C
* *
112658016 -CGTG-TTTCATAAATTT
1 TCGTGTTTTCAAAAATTC
*
112658032 TCGTG-TTTCAAAGAAATC
1 TCGTGTTTTCAAA-AATTC
*
112658050 TCGTG-TTTC-AAAATTT
1 TCGTGTTTTCAAAAATTC
*
112658066 TCGTGTTTTTTTAAAAATT-
1 TCGTG--TTTTCAAAAATTC
*
112658085 T-GTG-TTTCTAAAATTC
1 TCGTGTTTTCAAAAATTC
* * *
112658101 TTGTATTTTAAAAAATTC
1 TCGTGTTTTCAAAAATTC
112658119 GTGTTTAAAA
Statistics
Matches: 280, Mismatches: 54, Indels: 76
0.68 0.13 0.19
Matches are distributed among these distances:
15 9 0.03
16 26 0.09
17 114 0.41
18 68 0.24
19 27 0.10
20 21 0.08
21 15 0.05
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTC
Found at i:112657774 original size:36 final size:35
Alignment explanation
Indices: 112657721--112657789 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
112657711 TAAAAATCGG
* *
112657721 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
112657756 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
112657790 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:112657861 original size:17 final size:17
Alignment explanation
Indices: 112657721--112658073 Score: 196
Period size: 17 Copynumber: 19.9 Consensus size: 17
112657711 TAAAAATCGG
*
112657721 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
** *
112657739 AAAAATTCCCGTGTTGC
1 AAAAATTTTCGTGTTTC
*
112657756 AAAAATTTTCATGTTTTTC
1 AAAAATTTTC--GTGTTTC
*
112657775 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
112657793 AAAAAAATTCCAAT-TTTC
1 -AAAAATTTTC-GTGTTTC
*
112657811 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
**
112657829 TAAAAAACTTCTGTGTTTC
1 -AAAAATTTTC-GTGTTTC
112657848 AAAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
112657865 TAAAATTTTCGTATTTC
1 AAAAATTTTCGTGTTTC
*
112657882 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTG-TTTC
* * *
112657900 -AAATTTTTCGTATTTA
1 AAAAATTTTCGTGTTTC
**
112657916 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTG-TTTC
*
112657934 -AAAA-TTCCAGTGTTTC
1 AAAAATTTTC-GTGTTTC
*
112657950 AAAATTTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
**
112657967 AAAAAAAAATTCCCGT-TTTCC
1 ----AAAAATTTTCGTGTTT-C
* * *
112657988 AAAAACTTTCGCGTTTT
1 AAAAATTTTCGTGTTTC
**
112658005 AAGAAATTGACCGTGTTTC
1 AA-AAATT-TTCGTGTTTC
*
112658024 ATAAATTTTCGTGTTTC
1 AAAAATTTTCGTGTTTC
* *
112658041 AAAGAAATCTCGTGTTTC
1 AAA-AATTTTCGTGTTTC
112658059 -AAAATTTTCGTGTTT
1 AAAAATTTTCGTGTTT
112658074 TTTTAAAAAT
Statistics
Matches: 248, Mismatches: 63, Indels: 50
0.69 0.17 0.14
Matches are distributed among these distances:
16 20 0.08
17 108 0.44
18 64 0.26
19 39 0.16
20 7 0.03
21 10 0.04
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.44
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:112658114 original size:17 final size:16
Alignment explanation
Indices: 112658073--112658124 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
112658063 TTTTCGTGTT
112658073 TTTTTAAAAATTTGTG
1 TTTTTAAAAATTTGTG
* * *
112658089 TTTCTAAAATTCTTGTA
1 TTTTTAAAAAT-TTGTG
* *
112658106 TTTTAAAAAATTCGTG
1 TTTTTAAAAATTTGTG
112658122 TTT
1 TTT
112658125 AAAAAAAGGA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.54
Consensus pattern (16 bp):
TTTTTAAAAATTTGTG
Found at i:112658123 original size:33 final size:33
Alignment explanation
Indices: 112658016--112658129 Score: 99
Period size: 33 Copynumber: 3.4 Consensus size: 33
112658006 AGAAATTGAC
*
112658016 CGTGTTTCATAAATTTTCGTG--TTTCAAAGAAATCT
1 CGTGTTTCA-AAA-TTTCGTGTATTTTAAA-AAAT-T
* *
112658051 CGTGTTTCAAAATTTTCGTGTTTTTTTAAAAATT
1 CGTGTTTCAAAA-TTTCGTGTATTTTAAAAAATT
* *
112658085 TGTGTTTCTAAAA-TTCTTGTATTTTAAAAAATT
1 CGTGTTTC-AAAATTTCGTGTATTTTAAAAAATT
*
112658118 CGTGTTTAAAAA
1 CGTGTTTCAAAA
112658130 AAGGAAAAAG
Statistics
Matches: 68, Mismatches: 8, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 4 0.06
33 23 0.34
34 19 0.28
35 17 0.25
36 5 0.07
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (33 bp):
CGTGTTTCAAAATTTCGTGTATTTTAAAAAATT
Found at i:112662190 original size:43 final size:43
Alignment explanation
Indices: 112662142--112662227 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
112662132 TATGTCTAAT
*
112662142 TTCGAATAATATAAATTGGAAAAAGAAATTCTTCAAGTAACAA
1 TTCGAATAACATAAATTGGAAAAAGAAATTCTTCAAGTAACAA
112662185 TTCGAATAACATAAATTGGAAAAAGAAATTCTTCAAGTAACAA
1 TTCGAATAACATAAATTGGAAAAAGAAATTCTTCAAGTAACAA
112662228 AGAAAAAGCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (43 bp):
TTCGAATAACATAAATTGGAAAAAGAAATTCTTCAAGTAACAA
Found at i:112665114 original size:31 final size:31
Alignment explanation
Indices: 112665076--112665138 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
112665066 TCACTGATTG
* *
112665076 AAGATAGAATCGAGTCCTAGAAAGGAAATGA
1 AAGATAGAATCAAGTCCCAGAAAGGAAATGA
112665107 AAGATAGAATCAAGTCCCAGAAAGGAAATGA
1 AAGATAGAATCAAGTCCCAGAAAGGAAATGA
112665138 A
1 A
112665139 CTTTGTTCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.24, T:0.14
Consensus pattern (31 bp):
AAGATAGAATCAAGTCCCAGAAAGGAAATGA
Found at i:112675240 original size:14 final size:14
Alignment explanation
Indices: 112675221--112675250 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
112675211 GGATTTAGAT
112675221 TTAAATTTATCAAA
1 TTAAATTTATCAAA
*
112675235 TTAAATTTATTAAA
1 TTAAATTTATCAAA
112675249 TT
1 TT
112675251 CGAGTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAAATTTATCAAA
Found at i:112681587 original size:26 final size:27
Alignment explanation
Indices: 112681544--112681601 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
112681534 TTTTCCATAG
112681544 TTTTAGGGTTAGATTTTTTTCTTTTCAT
1 TTTTAGGGTTAGATTTTTTTCTTTT-AT
112681572 TTTTA-GGTTAGA-TTTTTTCTTTTAT
1 TTTTAGGGTTAGATTTTTTTCTTTTAT
112681597 TTTTA
1 TTTTA
112681602 TATTATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 7 0.23
26 11 0.37
27 7 0.23
28 5 0.17
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.67
Consensus pattern (27 bp):
TTTTAGGGTTAGATTTTTTTCTTTTAT
Found at i:112689840 original size:25 final size:26
Alignment explanation
Indices: 112689798--112689847 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 26
112689788 AGATGTCCTT
112689798 TCTTTTCATTTTTAGATTAGATTTTC
1 TCTTTTCATTTTTAGATTAGATTTTC
112689824 TCTTTTC-TTTTTAGATTAGATTTT
1 TCTTTTCATTTTTAGATTAGATTTT
112689848 ATTTTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.64
Consensus pattern (26 bp):
TCTTTTCATTTTTAGATTAGATTTTC
Found at i:112700283 original size:27 final size:27
Alignment explanation
Indices: 112700239--112700302 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
112700229 GTAATTATAG
* *
112700239 TAATT-AAAAATATGTTATTTAAAAAA
1 TAATTAAAAAACATATTATTTAAAAAA
*
112700265 TAATTAAAAAACATATTATTTAAAAAC
1 TAATTAAAAAACATATTATTTAAAAAA
112700292 TAATTAAAAAA
1 TAATTAAAAAA
112700303 TTAAATGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (27 bp):
TAATTAAAAAACATATTATTTAAAAAA
Found at i:112700291 original size:15 final size:15
Alignment explanation
Indices: 112700242--112700291 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
112700232 ATTATAGTAA
* *
112700242 TTAAAAATATGTTAT
1 TTAAAAACATATTAT
112700257 TTAAAAA-ATA--AT
1 TTAAAAACATATTAT
*
112700269 TAAAAAACATATTAT
1 TTAAAAACATATTAT
112700284 TTAAAAAC
1 TTAAAAAC
112700292 TAATTAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 8 0.28
13 3 0.10
14 2 0.07
15 16 0.55
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (15 bp):
TTAAAAACATATTAT
Found at i:112702816 original size:22 final size:22
Alignment explanation
Indices: 112702791--112702837 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
112702781 ATATATTACT
*
112702791 TTAAATTAATT-ATAATATATAA
1 TTAAATTAATTGATAA-AAATAA
*
112702813 TTAAATTATTTGATAAAAATAA
1 TTAAATTAATTGATAAAAATAA
112702835 TTA
1 TTA
112702838 TTAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAATTAATTGATAAAAATAA
Found at i:112707692 original size:2 final size:2
Alignment explanation
Indices: 112707680--112707713 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
112707670 TTAAGCACTA
* *
112707680 AT AT CT AT AT AT AT AT AC 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
112707714 CAATTTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:112708166 original size:20 final size:21
Alignment explanation
Indices: 112708132--112708186 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
112708122 ACAAATAATT
112708132 TAAAAATTATAAAATA-TTCAA
1 TAAAAATTATAAAATAGTTC-A
112708153 TAAAAATTAT-AAATAGTTCA
1 TAAAAATTATAAAATAGTTCA
* *
112708173 TAAAATTTCTAAAA
1 TAAAAATTATAAAA
112708187 AAATTAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAAATTATAAAATAGTTCA
Found at i:112712493 original size:43 final size:43
Alignment explanation
Indices: 112712432--112712586 Score: 152
Period size: 43 Copynumber: 3.6 Consensus size: 43
112712422 ATCTACTCTG
* **
112712432 CTGTAACTTCAGAGAGATAAGATCTTTATTTCAATCCACTCCA
1 CTGTAACTTCAGGGAGATAAGATCTTTATTTCAATCTGCTCCA
* * * * * *
112712475 CTGTAACTTCAGGGAGATAGGATAGTGTCTTT-GATCTGCTCCG
1 CTGTAACTTCAGGGAGATAAGAT-CTTTATTTCAATCTGCTCCA
***
112712518 CTGTAA-TCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACT-TCAGGGAGATAAGATCT-TTATTTCAATCTGCTCCA
*
112712562 CTGTAACCTCAGGGAGATAAGATCT
1 CTGTAACTTCAGGGAGATAAGATCT
112712587 GAAATTCTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
42 2 0.02
43 50 0.56
44 37 0.42
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (43 bp):
CTGTAACTTCAGGGAGATAAGATCTTTATTTCAATCTGCTCCA
Found at i:112712622 original size:46 final size:44
Alignment explanation
Indices: 112712470--112712629 Score: 166
Period size: 44 Copynumber: 3.6 Consensus size: 44
112712460 TTTCAATCCA
*
112712470 CTCCACTGTAA-CTTCAGGGAGATAGGA--TAGTGTCTTTGATCTG
1 CTCCACTGTAATC-TCAGGGAGATAAGATCTA-TGTCTTTGATCTG
* * * **
112712513 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTG
* *
112712557 CTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTTGGTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATCT---ATGTCTTTGATCTG
*
112712603 TTCCACTGTAATCTCAGGGAGATAAGA
1 CTCCACTGTAATCTCAGGGAGATAAGA
112712630 CCTGTATAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
43 23 0.24
44 39 0.41
45 1 0.01
46 32 0.33
47 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (44 bp):
CTCCACTGTAATCTCAGGGAGATAAGATCTATGTCTTTGATCTG
Found at i:112713834 original size:1 final size:1
Alignment explanation
Indices: 112713828--112713877 Score: 100
Period size: 1 Copynumber: 50.0 Consensus size: 1
112713818 CCTCTCCAAG
112713828 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
112713878 AGGAAGCAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:112749968 original size:35 final size:35
Alignment explanation
Indices: 112749865--112749970 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 35
112749855 GAATACTATT
* *
112749865 TAAATTTTAAAATATTTTAATTAATATTATATCAA
1 TAAAATTTAAAATATTTTAATTAATATTGTATCAA
* * * *
112749900 TAAGATTTATTTAA-ATTTT-A--AAT-TGGT-T-TA
1 TAAAATTTA--AAATATTTTAATTAATATTGTATCAA
112749930 TAAAATTTAAAATATTTTAATTAATATTGTATCAA
1 TAAAATTTAAAATATTTTAATTAATATTGTATCAA
112749965 TAAAAT
1 TAAAAT
112749971 GATTTAGTAC
Statistics
Matches: 52, Mismatches: 10, Indels: 18
0.65 0.12 0.22
Matches are distributed among these distances:
28 2 0.04
29 5 0.10
30 10 0.19
31 1 0.02
32 5 0.10
33 6 0.12
34 1 0.02
35 15 0.29
36 5 0.10
37 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (35 bp):
TAAAATTTAAAATATTTTAATTAATATTGTATCAA
Found at i:112754102 original size:21 final size:21
Alignment explanation
Indices: 112754077--112754141 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
112754067 TAGCCTTCGG
112754077 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * * *
112754098 GCTTCAG-ATAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
112754116 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
112754137 GCTTC
1 GCTTC
112754142 AGAGCATGCA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 7 0.21
21 12 0.36
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:112754102 original size:39 final size:39
Alignment explanation
Indices: 112754059--112754144 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
112754049 GCTCTGGTGA
*
112754059 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGATAGCCTTCGGGCTTCCGTTTAGCACTTATGT
112754098 GCTTCAGATAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGATAGCCTTCGGGCTTCCGTTTAGCACTTATGT
112754137 GCTTCAGA
1 GCTTCAGA
112754145 GCATGCAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTCAGATAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:112755883 original size:78 final size:78
Alignment explanation
Indices: 112755764--112755998 Score: 434
Period size: 78 Copynumber: 3.0 Consensus size: 78
112755754 GTTGAGTTAG
*
112755764 TACTTGAACATTCAAAACCTAAGTTTATCCCGACCCATTTTTTTAGTTTGTAATATTTTATATTA
1 TACTTGAACATTCAAAACCTAAGTTTGTCCCGACCCATTTTTTTAGTTTGTAATATTTTATATTA
*
112755829 TGTTGATTTTATA
66 TGTTAATTTTATA
112755842 TACTTGAACATTCAAAACCTAAGTTTGTCCCGACCCATTTTTTTAGTTTGTAATATTTTATATTA
1 TACTTGAACATTCAAAACCTAAGTTTGTCCCGACCCATTTTTTTAGTTTGTAATATTTTATATTA
112755907 TGTTAATTTTATA
66 TGTTAATTTTATA
* *
112755920 TACTTGAACATTCAAAACCTAAGTTTGTCTCGACCCTTTTTTTTAGTTTGTAATATTTTATATTA
1 TACTTGAACATTCAAAACCTAAGTTTGTCCCGACCCATTTTTTTAGTTTGTAATATTTTATATTA
112755985 TGTTAATTTTATA
66 TGTTAATTTTATA
112755998 T
1 T
112755999 GTTACGTAAT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 153 1.00
ACGTcount: A:0.29, C:0.14, G:0.09, T:0.49
Consensus pattern (78 bp):
TACTTGAACATTCAAAACCTAAGTTTGTCCCGACCCATTTTTTTAGTTTGTAATATTTTATATTA
TGTTAATTTTATA
Found at i:112756829 original size:12 final size:12
Alignment explanation
Indices: 112756814--112756847 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
112756804 GTGAATAAAG
112756814 AAGATAAATGGA
1 AAGATAAATGGA
112756826 AAGAT-AATGGA
1 AAGATAAATGGA
112756837 AAGATAGAATG
1 AAGATA-AATG
112756848 TGGCGTGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 5 0.25
13 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (12 bp):
AAGATAAATGGA
Found at i:112768264 original size:57 final size:57
Alignment explanation
Indices: 112768174--112768298 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
112768164 AACTTTAAAT
* *
112768174 TTAATTCCTTTCTTTAAGGATGGTGAAATGTATCTCCACTTACCAATTTATCCTTCA
1 TTAATTCCTTTCTTTAAGGATGGTGAAAAGTATCTCCACTTACCAATTAATCCTTCA
*
112768231 TTAATTCCTTTCTTTAAGGATGGTGAAAAGTATCTCCAGTTACCAATTAATCCTTCA
1 TTAATTCCTTTCTTTAAGGATGGTGAAAAGTATCTCCACTTACCAATTAATCCTTCA
112768288 TTAATTCCTTT
1 TTAATTCCTTT
112768299 ATGGATCCAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.42
Consensus pattern (57 bp):
TTAATTCCTTTCTTTAAGGATGGTGAAAAGTATCTCCACTTACCAATTAATCCTTCA
Found at i:112772808 original size:58 final size:57
Alignment explanation
Indices: 112772701--112772813 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 57
112772691 TATTTTCCTT
*
112772701 ATTGCATAATACGTCCCAACTCAAGAAAAAACACATTTATGTTTTTTTTAAGTGTTTC
1 ATTGCATAATACGTCCCAACTCAAGAAAAAACACATTTATGTTCTTTTT-AGTGTTTC
*
112772759 ATTGCATAATACGTCCCAA-TGCAGGAAAAAAACACATTTATG-TCTTTTTAGTGTT
1 ATTGCATAATACGTCCCAACT-CAAG-AAAAAACACATTTATGTTCTTTTTAGTGTT
112772814 CGAAACACTA
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
57 7 0.14
58 28 0.55
59 16 0.31
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (57 bp):
ATTGCATAATACGTCCCAACTCAAGAAAAAACACATTTATGTTCTTTTTAGTGTTTC
Found at i:112773376 original size:88 final size:88
Alignment explanation
Indices: 112773227--112773404 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 88
112773217 TCAATATACA
112773227 GTATGATAAAATTGATCTCGTATAGACTGAGCAGTGTCCAAATGTAGAAGAAACACTTACTGTTA
1 GTATGATAAAATTGATCTCGTATAGACTGAGCAGTGTCCAAATGTAGAAGAAACACTTACTGTTA
*
112773292 CTAAAAATATAACTCCATATTTT
66 CTAAAAACATAACTCCATATTTT
112773315 GTATGATAAAATTGATCTCGTATAGACTGAGCAGTGTCCAAATGTAGAAGAAACACTTACTGTTA
1 GTATGATAAAATTGATCTCGTATAGACTGAGCAGTGTCCAAATGTAGAAGAAACACTTACTGTTA
112773380 CTAAAAACATAACTCCATATTTT
66 CTAAAAACATAACTCCATATTTT
112773403 GT
1 GT
112773405 GCACAAATGG
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (88 bp):
GTATGATAAAATTGATCTCGTATAGACTGAGCAGTGTCCAAATGTAGAAGAAACACTTACTGTTA
CTAAAAACATAACTCCATATTTT
Found at i:112776668 original size:28 final size:28
Alignment explanation
Indices: 112776629--112776684 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
112776619 AGCGTTAAGT
112776629 GAGAGTACAATTCTCATCAAAATTGAAA
1 GAGAGTACAATTCTCATCAAAATTGAAA
112776657 GAGAGTACAATTCTCATCAAAATTGAAA
1 GAGAGTACAATTCTCATCAAAATTGAAA
112776685 TAATATAATA
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:0.46, C:0.14, G:0.14, T:0.25
Consensus pattern (28 bp):
GAGAGTACAATTCTCATCAAAATTGAAA
Found at i:112777712 original size:17 final size:19
Alignment explanation
Indices: 112777668--112777713 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
112777658 ATATGTAAAA
112777668 TAAATAATTAAGAATATATT
1 TAAATAA-TAAGAATATATT
*
112777688 GAAA-AATAA-AATAT-TT
1 TAAATAATAAGAATATATT
112777704 TAAATAATAA
1 TAAATAATAA
112777714 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 5 0.22
17 10 0.43
18 3 0.13
19 2 0.09
20 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
TAAATAATAAGAATATATT
Found at i:112778669 original size:24 final size:24
Alignment explanation
Indices: 112778638--112778685 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
112778628 TCTAAAAGTG
112778638 AATACTTATTAAACAATGAAAAAC
1 AATACTTATTAAACAATGAAAAAC
112778662 AATACTTATTAAACAATGAAAAAC
1 AATACTTATTAAACAATGAAAAAC
112778686 CAAATAAAAA
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:0.58, C:0.12, G:0.04, T:0.25
Consensus pattern (24 bp):
AATACTTATTAAACAATGAAAAAC
Found at i:112782626 original size:40 final size:39
Alignment explanation
Indices: 112782506--112782663 Score: 244
Period size: 39 Copynumber: 4.0 Consensus size: 39
112782496 TTGATTCCAC
* * *
112782506 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTAC
1 TCCCCCATACTACTTTGTTTTATTATTAATTAAAACCAT
*
112782545 TCCCCCATACTACTTTGTTTTATTATTAATTAAAACTAT
1 TCCCCCATACTACTTTGTTTTATTATTAATTAAAACCAT
*
112782584 TCCCCCATACTATTTTGTTTTCATTATTAATTAAAACCAT
1 TCCCCCATACTACTTTGTTTT-ATTATTAATTAAAACCAT
*
112782624 TCCCCCATACTATTTTGTTTTTATTATTAATTAAAACCAT
1 TCCCCCATACTACTTTG-TTTTATTATTAATTAAAACCAT
112782664 ACTTTATTTT
Statistics
Matches: 113, Mismatches: 4, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
39 57 0.50
40 52 0.46
41 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.03, T:0.46
Consensus pattern (39 bp):
TCCCCCATACTACTTTGTTTTATTATTAATTAAAACCAT
Found at i:112782634 original size:79 final size:79
Alignment explanation
Indices: 112782506--112782660 Score: 249
Period size: 79 Copynumber: 2.0 Consensus size: 79
112782496 TTGATTCCAC
* *
112782506 TCCCCCATGCTACTTTGTTTTATTATTAATTAAAACTACTCCCCCATACTACTTTG-TTTTATTA
1 TCCCCCATACTACTTTGTTTTATTATTAATTAAAACCACTCCCCCATACTACTTTGTTTTTATTA
112782570 TTAATTAAAACTAT
66 TTAATTAAAACTAT
* * *
112782584 TCCCCCATACTATTTTGTTTTCATTATTAATTAAAACCATTCCCCCATACTATTTTGTTTTTATT
1 TCCCCCATACTACTTTGTTTT-ATTATTAATTAAAACCACTCCCCCATACTACTTTGTTTTTATT
112782649 ATTAATTAAAAC
65 ATTAATTAAAAC
112782661 CATACTTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 19 0.27
79 32 0.46
80 19 0.27
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (79 bp):
TCCCCCATACTACTTTGTTTTATTATTAATTAAAACCACTCCCCCATACTACTTTGTTTTTATTA
TTAATTAAAACTAT
Found at i:112784086 original size:16 final size:18
Alignment explanation
Indices: 112784047--112784080 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
112784037 AAAGTTTATA
112784047 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
112784064 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
112784081 AATTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:112785235 original size:30 final size:31
Alignment explanation
Indices: 112785182--112785241 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
112785172 AAATATATAG
*
112785182 TATTATTTATATTTTTATTAAATATTCTTAAAT
1 TATTATTTATAATTTTA-TAAATATT-TTAAAT
112785215 TATTATTTA-AATTTTA-AAATATTTTAA
1 TATTATTTATAATTTTATAAATATTTTAA
112785242 TTAAGTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
32 6 0.23
33 9 0.35
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (31 bp):
TATTATTTATAATTTTATAAATATTTTAAAT
Found at i:112785578 original size:29 final size:30
Alignment explanation
Indices: 112785540--112785596 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
112785530 TGGCCTGATA
*
112785540 TGTAATTTTATACATG-AATTTTGATTTTG
1 TGTAATTTTATACATGAAATTTTAATTTTG
112785569 TGTAATTTTATACATGAAATTTTAATTT
1 TGTAATTTTATACATGAAATTTTAATTT
112785597 GATCAAATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.54
Consensus pattern (30 bp):
TGTAATTTTATACATGAAATTTTAATTTTG
Found at i:112796298 original size:22 final size:23
Alignment explanation
Indices: 112796273--112796318 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
112796263 CAACCAAATC
112796273 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
112796295 AATTCATACATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
112796318 A
1 A
112796319 CGTCATCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 15 0.68
24 1 0.05
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:112796324 original size:23 final size:24
Alignment explanation
Indices: 112796279--112796331 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
112796269 AATCAATTCA
*
112796279 ACATATTTTCAAGATAAATTCAT-
1 ACATATTTTCAAGATAAAGTCATC
*
112796302 ACATATTTAT-AAGATAACGTCATC
1 ACATATTT-TCAAGATAAAGTCATC
112796326 ACATAT
1 ACATAT
112796332 CTAAAACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.43, C:0.15, G:0.06, T:0.36
Consensus pattern (24 bp):
ACATATTTTCAAGATAAAGTCATC
Found at i:112803358 original size:30 final size:30
Alignment explanation
Indices: 112803322--112803378 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
112803312 ATGGCCATGA
*
112803322 CACACGGGCGTGTGGCCTACCCGTGTGTCT
1 CACACGGGCGTGTGGACTACCCGTGTGTCT
* *
112803352 CACACGGGTGTGTGGATTACCCGTGTG
1 CACACGGGCGTGTGGACTACCCGTGTG
112803379 GAAGTGGGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.28, G:0.35, T:0.25
Consensus pattern (30 bp):
CACACGGGCGTGTGGACTACCCGTGTGTCT
Found at i:112808392 original size:23 final size:22
Alignment explanation
Indices: 112808366--112808417 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
112808356 TAAAAGAACA
112808366 TATATAAATAATAAGAAAAATAT-
1 TATATAAATAAT-A-AAAAATATC
* *
112808389 TATAATAAGTACTAAAAAATATC
1 TAT-ATAAATAATAAAAAATATC
112808412 TATATA
1 TATATA
112808418 TATACATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 11 0.44
23 7 0.28
24 7 0.28
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
TATATAAATAATAAAAAATATC
Found at i:112808838 original size:17 final size:16
Alignment explanation
Indices: 112808795--112808843 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
112808785 ATAATACTTC
*
112808795 ATAAATATATATACGTA
1 ATAAA-ATATATACATA
*
112808812 CTAAAA-ATATACATA
1 ATAAAATATATACATA
112808827 ATAATAATATATACATA
1 ATAA-AATATATACATA
112808844 CAAAGTACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.41
16 3 0.11
17 13 0.48
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (16 bp):
ATAAAATATATACATA
Found at i:112808905 original size:16 final size:16
Alignment explanation
Indices: 112808881--112808911 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
112808871 AATAGTAAAC
*
112808881 ATAATATTAATATTAA
1 ATAAAATTAATATTAA
112808897 ATAAAATTAATATTA
1 ATAAAATTAATATTA
112808912 CAAATTTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTAATATTAA
Found at i:112823018 original size:127 final size:127
Alignment explanation
Indices: 112822792--112823058 Score: 525
Period size: 127 Copynumber: 2.1 Consensus size: 127
112822782 GGGAACAAGC
112822792 TTGCCTTTATTTAAAATTAATGTATTTTAACTTCTTTTAAAAGGATATTCGGTTAGTTAGGGTGA
1 TTGCCTTTATTTAAAATTAATGTATTTTAACTTCTTTTAAAAGGATATTCGGTTAGTTAGGGTGA
112822857 ACGAGGAAAATCAAAACCCAGTAAGTTAAGGTACGTTTCTTCGAATTTTCGAACACCGAATA
66 ACGAGGAAAATCAAAACCCAGTAAGTTAAGGTACGTTTCTTCGAATTTTCGAACACCGAATA
112822919 TTGCCTTTATTTAAAATTAATGTATTTTAACTTCTTTTAAAAGGATATTCGGTTAGTTAGGGTGA
1 TTGCCTTTATTTAAAATTAATGTATTTTAACTTCTTTTAAAAGGATATTCGGTTAGTTAGGGTGA
112822984 ACGAGGAAAATCAAAACCCAGTAAGTTAAGGTACGTTTCTTCGAATTTTCGAACACCGAATA
66 ACGAGGAAAATCAAAACCCAGTAAGTTAAGGTACGTTTCTTCGAATTTTCGAACACCGAATA
*
112823046 TTGCCTTTGTTTA
1 TTGCCTTTATTTA
112823059 CGAAAAAACC
Statistics
Matches: 139, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
127 139 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (127 bp):
TTGCCTTTATTTAAAATTAATGTATTTTAACTTCTTTTAAAAGGATATTCGGTTAGTTAGGGTGA
ACGAGGAAAATCAAAACCCAGTAAGTTAAGGTACGTTTCTTCGAATTTTCGAACACCGAATA
Found at i:112824111 original size:22 final size:23
Alignment explanation
Indices: 112824058--112824111 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
112824048 TAATAATACG
112824058 TATATATAACGTAGTATTAAAATA
1 TATATATAAC-TAGTATTAAAATA
* *
112824082 TATGTATAA-TAGTATTTAAATA
1 TATATATAACTAGTATTAAAATA
*
112824104 TGTATATA
1 TATATATA
112824112 TATGTTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 18 0.69
24 8 0.31
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (23 bp):
TATATATAACTAGTATTAAAATA
Found at i:112824113 original size:24 final size:24
Alignment explanation
Indices: 112824052--112824113 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
112824042 TAAATATAAT
*
112824052 AATACGTATATATAACGTAGTATTA
1 AATATGTATATATAAC-TAGTATTA
* *
112824077 AA-ATATATGTATAA-TAGTATTTA
1 AATATGTATATATAACTAGTA-TTA
112824100 AATATGTATATATA
1 AATATGTATATATA
112824114 TGTTTGTTAG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
22 5 0.17
23 5 0.17
24 18 0.60
25 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (24 bp):
AATATGTATATATAACTAGTATTA
Found at i:112825399 original size:32 final size:32
Alignment explanation
Indices: 112825308--112825401 Score: 83
Period size: 32 Copynumber: 3.0 Consensus size: 32
112825298 TTGGGCTATG
112825308 TGTGTTTGGGTCAAAAGTTGT--AATGGGTCTT
1 TGTGTTTGGGTCAAAAGTTGTAAAATGGGT-TT
* * *
112825339 AGT-TTTGGGT---AGGTTTGTTTAAATTGGGTTT
1 TGTGTTTGGGTCAAAAG-TTG--TAAAATGGGTTT
112825370 TGTGTTTGGGTCAAAAGTTGTAAAATGGGTTT
1 TGTGTTTGGGTCAAAAGTTGTAAAATGGGTTT
112825402 AGGTTTAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 17
0.68 0.08 0.24
Matches are distributed among these distances:
27 2 0.04
28 3 0.06
30 8 0.17
31 6 0.12
32 24 0.50
34 3 0.06
35 2 0.04
ACGTcount: A:0.20, C:0.03, G:0.32, T:0.45
Consensus pattern (32 bp):
TGTGTTTGGGTCAAAAGTTGTAAAATGGGTTT
Found at i:112825425 original size:62 final size:62
Alignment explanation
Indices: 112825308--112825428 Score: 147
Period size: 62 Copynumber: 2.0 Consensus size: 62
112825298 TTGGGCTATG
* * * * * *
112825308 TGTGTTTGGGTCAAAAGTTGTAATGGGTCTTAGTTTTGGGTAGGTTTGTTTAAATTGGGTTT
1 TGTGTTTGGGTCAAAAGTTGTAATGGGTCTTAGGTTTGAGTAGGCTGGGTGAAATTGGGTTT
*
112825370 TGTGTTTGGGTCAAAAGTTGTAAAATGGGT-TTAGGTTT-AGTGGGCTGGGTGAAATTGGG
1 TGTGTTTGGGTCAAAAGTTGT--AATGGGTCTTAGGTTTGAGTAGGCTGGGTGAAATTGGG
112825429 CTTGTACAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
62 36 0.72
63 7 0.14
64 7 0.14
ACGTcount: A:0.20, C:0.03, G:0.36, T:0.41
Consensus pattern (62 bp):
TGTGTTTGGGTCAAAAGTTGTAATGGGTCTTAGGTTTGAGTAGGCTGGGTGAAATTGGGTTT
Found at i:112826169 original size:16 final size:15
Alignment explanation
Indices: 112826143--112826198 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
112826133 ATACGTTAGC
112826143 AAATAAAATATATAT
1 AAATAAAATATATAT
*
112826158 AAATATAAATATAAAT
1 AAATA-AAATATATAT
**
112826174 AAAT-ATTTATATAT
1 AAATAAAATATATAT
112826188 AAAATAAAATA
1 -AAATAAAATA
112826199 AAAATAGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 7 0.22
15 9 0.28
16 16 0.50
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAAATATATAT
Found at i:112826187 original size:30 final size:32
Alignment explanation
Indices: 112826151--112826222 Score: 96
Period size: 30 Copynumber: 2.3 Consensus size: 32
112826141 GCAAATAAAA
* *
112826151 TATATATAAATAT-AAATATAAATA-AATATT
1 TATATATAAATATAAAATAAAAATAGAATAAT
112826181 TATATATAAA-ATAAAATAAAAATAGAATAAT
1 TATATATAAATATAAAATAAAAATAGAATAAT
*
112826212 TATATTTAAAT
1 TATATATAAAT
112826223 TGTCAAATAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 2 0.06
30 20 0.56
31 14 0.39
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
TATATATAAATATAAAATAAAAATAGAATAAT
Found at i:112831568 original size:14 final size:14
Alignment explanation
Indices: 112831549--112831575 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
112831539 GTAAGTCATT
112831549 GGAGAGTAGTTTGG
1 GGAGAGTAGTTTGG
112831563 GGAGAGTAGTTTG
1 GGAGAGTAGTTTG
112831576 TTGAAGATTG
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:0.22, C:0.00, G:0.48, T:0.30
Consensus pattern (14 bp):
GGAGAGTAGTTTGG
Found at i:112844506 original size:17 final size:19
Alignment explanation
Indices: 112844484--112844522 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
112844474 CCTTGTAATA
112844484 TTATAAT-TTA-AGATTTT
1 TTATAATATTATAGATTTT
*
112844501 TTATAATATTATATATTTT
1 TTATAATATTATAGATTTT
112844520 TTA
1 TTA
112844523 AACATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 3 0.16
19 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTATAATATTATAGATTTT
Found at i:112844867 original size:31 final size:31
Alignment explanation
Indices: 112844832--112844892 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
112844822 AGATAAAATA
* *
112844832 AAATTTTGATTGTATTTCAAATC-TATACATG
1 AAATTTTAATTGTAATTC-AATCGTATACATG
*
112844863 AAATTTTAATTTTAATTCAATCGTATACAT
1 AAATTTTAATTGTAATTCAATCGTATACAT
112844893 TTACAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (31 bp):
AAATTTTAATTGTAATTCAATCGTATACATG
Found at i:112847450 original size:12 final size:12
Alignment explanation
Indices: 112847435--112847459 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112847425 CTGATTCAGC
112847435 TAGATCATGCAT
1 TAGATCATGCAT
112847447 TAGATCATGCAT
1 TAGATCATGCAT
112847459 T
1 T
112847460 TTACATGTTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TAGATCATGCAT
Found at i:112847497 original size:51 final size:51
Alignment explanation
Indices: 112847437--112847538 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
112847427 GATTCAGCTA
* * *
112847437 GATCATGCATTAGATCATGCATTTTACATGTTAGTCCTTCCC-CTGGATATC
1 GATCATGCATTAAATCATGCATTTTACATCTTAATCCTTCCCTC-GGATATC
112847488 GATCATGCATTAAATCATGCATTTTACATCTTAATCCTTCCCTCGGATATC
1 GATCATGCATTAAATCATGCATTTTACATCTTAATCCTTCCCTCGGATATC
112847539 TTTTTCCTAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.37
Consensus pattern (51 bp):
GATCATGCATTAAATCATGCATTTTACATCTTAATCCTTCCCTCGGATATC
Found at i:112861798 original size:19 final size:19
Alignment explanation
Indices: 112861756--112861798 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
112861746 TTATCAAAAG
* *
112861756 AAAATAAGAATTATATTAA
1 AAAATAAGAATTAAATAAA
* *
112861775 TAAATGAGAATTAAATAAA
1 AAAATAAGAATTAAATAAA
112861794 AAAAT
1 AAAAT
112861799 TACAAACTTA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAATAAGAATTAAATAAA
Found at i:112865310 original size:30 final size:32
Alignment explanation
Indices: 112865276--112865335 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
112865266 CTCAAAGACA
*
112865276 TTTTA-TTTTCTACTTAATACCC-AAAAAATC
1 TTTTATTTTTCTACTTAAAACCCTAAAAAATC
112865306 TTTTATTTTTCTACTTAAAACCCTAAAAAA
1 TTTTATTTTTCTACTTAAAACCCTAAAAAA
112865336 AATCCTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 5 0.19
31 16 0.59
32 6 0.22
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.43
Consensus pattern (32 bp):
TTTTATTTTTCTACTTAAAACCCTAAAAAATC
Found at i:112879405 original size:21 final size:21
Alignment explanation
Indices: 112879379--112879419 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
112879369 AGACAAACGA
*
112879379 TACTCCACAACACGTGGAGTG
1 TACTCCAAAACACGTGGAGTG
*
112879400 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACACGTGGAGT
112879420 TTGAGTAGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACACGTGGAGTG
Found at i:112881348 original size:22 final size:22
Alignment explanation
Indices: 112881320--112881361 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
112881310 CAAGGTGGAG
112881320 ATTGTTGACAATTGCATGGTAA
1 ATTGTTGACAATTGCATGGTAA
112881342 ATTGTTGACAATTGCATGGT
1 ATTGTTGACAATTGCATGGT
112881362 TTTGCAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.38
Consensus pattern (22 bp):
ATTGTTGACAATTGCATGGTAA
Found at i:112889511 original size:77 final size:77
Alignment explanation
Indices: 112889421--112889574 Score: 299
Period size: 77 Copynumber: 2.0 Consensus size: 77
112889411 AATAATATTG
*
112889421 TTAGTGATTTGAAAAAAAATGAATTAATGAAATTAAAAATTACACAAAATCGAAATTCATTTATA
1 TTAGTGATTTGAAAAAAAATGAATTAATAAAATTAAAAATTACACAAAATCGAAATTCATTTATA
112889486 ATATTGCATTAA
66 ATATTGCATTAA
112889498 TTAGTGATTTGAAAAAAAATGAATTAATAAAATTAAAAATTACACAAAATCGAAATTCATTTATA
1 TTAGTGATTTGAAAAAAAATGAATTAATAAAATTAAAAATTACACAAAATCGAAATTCATTTATA
112889563 ATATTGCATTAA
66 ATATTGCATTAA
112889575 CATATAATTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.34
Consensus pattern (77 bp):
TTAGTGATTTGAAAAAAAATGAATTAATAAAATTAAAAATTACACAAAATCGAAATTCATTTATA
ATATTGCATTAA
Found at i:112892439 original size:16 final size:17
Alignment explanation
Indices: 112892420--112892451 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
112892410 AAAAAAATTG
112892420 AATTA-ATAAAATTAAA
1 AATTACATAAAATTAAA
112892436 AATTACATAAAATTAA
1 AATTACATAAAATTAA
112892452 TTTTCATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTACATAAAATTAAA
Found at i:112892735 original size:10 final size:10
Alignment explanation
Indices: 112892722--112892746 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
112892712 TATATTTATA
112892722 TTTTTTAAAC
1 TTTTTTAAAC
112892732 TTTTTTAAAC
1 TTTTTTAAAC
112892742 TTTTT
1 TTTTT
112892747 GAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAAAC
Found at i:112895819 original size:40 final size:43
Alignment explanation
Indices: 112895764--112895843 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 43
112895754 GTTTGCTCTT
112895764 TGTATTTCTATTATAT-TAT-TAT-TATT-ATTATATAGTAGTG
1 TGTATTTCTATTATATGTATATATATATTGA-TATATAGTAGTG
112895804 TGTATTTGC-ATTATATGTATATATATATTGATATATAGTA
1 TGTATTT-CTATTATATGTATATATATATTGATATATAGTA
112895844 TTATTTTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
40 14 0.40
41 4 0.11
42 3 0.09
43 13 0.37
44 1 0.03
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.54
Consensus pattern (43 bp):
TGTATTTCTATTATATGTATATATATATTGATATATAGTAGTG
Found at i:112902233 original size:88 final size:88
Alignment explanation
Indices: 112902113--112902312 Score: 337
Period size: 88 Copynumber: 2.3 Consensus size: 88
112902103 TGACCTTCCC
*
112902113 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGGAGGAGAGCAGATCAAAGACATAGCTG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGAGGAGAGCAGATCAAAGACATAGCTG
*
112902178 ATTTGGCTTTCACGTGTTTACGT
66 ATTTGGCTTTCACGTGTTTACAT
* * *
112902201 TGAAACAGATCCAAGATGATTTGGCATCTCTGTATCAGGCGGGGAGCAGATCAAAGACATAGCTG
1 TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGAGGAGAGCAGATCAAAGACATAGCTG
112902266 ATTTGGCTTTCACGTGTTTACAT
66 ATTTGGCTTTCACGTGTTTACAT
* *
112902289 TGAAGCAAATCCAAGATAATTTGG
1 TGAAGCAGATCCAAGATGATTTGG
112902313 GGTCTTTGTA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 104 1.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (88 bp):
TGAAGCAGATCCAAGATGATTTGGCATCTCTGTATCAGGAGGAGAGCAGATCAAAGACATAGCTG
ATTTGGCTTTCACGTGTTTACAT
Found at i:112902395 original size:44 final size:44
Alignment explanation
Indices: 112902338--112903138 Score: 524
Period size: 44 Copynumber: 18.4 Consensus size: 44
112902328 GGAGAGCAGG
* * *
112902338 TCGAAGATTGCAGATTTGGCATCCCTATGTTTATAGGGAACAGA
1 TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * * * *
112902382 TCAAAGATAGCAGATCTGACATTCCC-GTGCTTACAGTGAATCAGA
1 TCGAAGATAGCAGATTTGGCA-TCCCTGTGCTTATAGGGAA-CAGA
***
112902427 TCGAAGATTTTAGCA--TGGCATCCCTGTGCTTATAGGGAACA-A
1 TCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA
* *
112902469 GTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
1 -TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * * * * * * * * *
112902514 TCGAAGATAACAGATCTGACATTCTTATACTTACAGTGAAGTAGA
1 TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGA
**
112902559 TCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAACA-A
1 TCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA
* *
112902601 GTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
1 -TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * * * * *
112902646 TCGAAGATAACAGATCTGACATTCCTGTGCTTACAGTGAAGCAGA
1 TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGA
*** *
112902691 TCGAAGATTTTAGCA--TGGCATCCCTGTGCTGATAGGGAACA-A
1 TCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * *
112902733 GTTGAAAATAACAGATTTGGCATCCC--TG----T---GAACAGA
1 -TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * ** * * * *
112902769 TCGAAGATAGCAAATCTAACATTCCTGTGCTTACAGTGAAGTAGA
1 TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGA
** * *
112902814 TCGAAGATTTCAGCA--TGGCATCCCTATGCTTATAGAGAACA-A
1 TCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA
* *
112902856 GTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
1 -TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * * * * * *
112902901 TCGAAGATAGCAGATCTGACATTCCTATGCTTACAGTGAAGCAAA
1 TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGA
**
112902946 TCGAAGATTTCAGCA--TGGCATCCCTGTGCTTATAGGGAACA-A
1 TCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * **
112902988 GTTGAAAATAGCAGATTTGGCATCCCTGTAATTATAGGGAACAGA
1 -TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
* * *** * *
112903033 TCGAAGATAGCAGATCTGACATTATTGTGCTTACAGTGAAGCAGA
1 TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAA-CAGA
* ** *
112903078 TTGAAGATTTCAGCA--TGGCATCCCTGTGTTTATAGGGAACA-A
1 TCGAAGATAGCAG-ATTTGGCATCCCTGTGCTTATAGGGAACAGA
*
112903120 GTTGAAGATAGCAGATTTG
1 -TCGAAGATAGCAGATTTG
112903139 ACCCCCTAAG
Statistics
Matches: 573, Mismatches: 138, Indels: 92
0.71 0.17 0.11
Matches are distributed among these distances:
35 22 0.04
36 1 0.00
37 2 0.00
38 1 0.00
42 14 0.02
43 68 0.12
44 369 0.64
45 90 0.16
46 6 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
TCGAAGATAGCAGATTTGGCATCCCTGTGCTTATAGGGAACAGA
Found at i:112902511 original size:132 final size:132
Alignment explanation
Indices: 112902347--112903138 Score: 1260
Period size: 132 Copynumber: 6.1 Consensus size: 132
112902337 GTCGAAGATT
* * * *
112902347 GCAGATTTGGCATCCCTATGTTTATAGGGAACAGATCAAAGATAGCAGATCTGACATTCCCGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* *
112902412 TTACAGTGAATCAGATCGAAGATTTTAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
112902477 TA
131 TA
* * * *
112902479 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCTTATAC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
*
112902544 TTACAGTGAAGTAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
112902609 TA
131 TA
*
112902611 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* *
112902676 TTACAGTGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGCTGATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
112902741 TA
131 TA
* * *
112902743 ACAGATTTGGCATCCC--TG----T---GAACAGATCGAAGATAGCAAATCTAACATTCCTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
112902799 TTACAGTGAAGTAGATCGAAGATTTCAGCATGGCATCCCTATGCTTATAGAGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
112902864 TA
131 TA
*
112902866 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTATGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
*
112902931 TTACAGTGAAGCAAATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
112902996 TA
131 TA
** **
112902998 GCAGATTTGGCATCCCTGTAATTATAGGGAACAGATCGAAGATAGCAGATCTGACATTATTGTGC
1 GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
* * *
112903063 TTACAGTGAAGCAGATTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGA
66 TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
112903128 TA
131 TA
112903130 GCAGATTTG
1 GCAGATTTG
112903139 ACCCCCTAAG
Statistics
Matches: 608, Mismatches: 43, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
123 111 0.18
125 2 0.00
126 1 0.00
129 1 0.00
130 2 0.00
132 491 0.81
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (132 bp):
GCAGATTTGGCATCCCTGTGCTTATAGGGAACAGATCGAAGATAGCAGATCTGACATTCCTGTGC
TTACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAA
TA
Found at i:112903095 original size:387 final size:387
Alignment explanation
Indices: 112902375--112903138 Score: 1305
Period size: 387 Copynumber: 2.0 Consensus size: 387
112902365 TGTTTATAGG
* * *
112902375 GAACAGATCAAAGATAGCAGATCTGACATTCCCGTGCTTACAGTGAATCAGATCGAAGATTTTAG
1 GAACAGATCAAAGATAGCAAATCTAACATTCCCGTGCTTACAGTGAATCAGATCGAAGATTTCAG
* *
112902440 CATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATA
66 CATGGCATCCCTATGCTTATAGAGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATA
* * *
112902505 GGGAACAGATCGAAGATAACAGATCTGACATTCTTATACTTACAGTGAAGTAGATCGAAGATTTC
131 GGGAACAGATCGAAGATAACAGATCTGACATTCCTATACTTACAGTGAAGCAAATCGAAGATTTC
**
112902570 AGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTA
196 AGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTAATTA
*
112902635 TAGGGAACAGATCGAAGATAACAGATCTGACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATT
261 TAGGGAACAGATCGAAGATAACAGATCTGACATTACTGTGCTTACAGTGAAGCAGATCGAAGATT
*
112902700 TTAGCATGGCATCCCTGTGCTGATAGGGAACAAGTTGAAAATAACAGATTTGGCATCCCTGT
326 TCAGCATGGCATCCCTGTGCTGATAGGGAACAAGTTGAAAATAACAGATTTGGCATCCCTGT
* *
112902762 GAACAGATCGAAGATAGCAAATCTAACATTCCTGTGCTTACAGTGAAGT-AGATCGAAGATTTCA
1 GAACAGATCAAAGATAGCAAATCTAACATTCCCGTGCTTACAGTGAA-TCAGATCGAAGATTTCA
112902826 GCATGGCATCCCTATGCTTATAGAGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTAT
65 GCATGGCATCCCTATGCTTATAGAGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTAT
* *
112902891 AGGGAACAGATCGAAGATAGCAGATCTGACATTCCTATGCTTACAGTGAAGCAAATCGAAGATTT
130 AGGGAACAGATCGAAGATAACAGATCTGACATTCCTATACTTACAGTGAAGCAAATCGAAGATTT
112902956 CAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTAATT
195 CAGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTAATT
* * *
112903021 ATAGGGAACAGATCGAAGATAGCAGATCTGACATTATTGTGCTTACAGTGAAGCAGATTGAAGAT
260 ATAGGGAACAGATCGAAGATAACAGATCTGACATTACTGTGCTTACAGTGAAGCAGATCGAAGAT
* * * *
112903086 TTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTG
325 TTCAGCATGGCATCCCTGTGCTGATAGGGAACAAGTTGAAAATAACAGATTTG
112903139 ACCCCCTAAG
Statistics
Matches: 353, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
387 352 1.00
388 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (387 bp):
GAACAGATCAAAGATAGCAAATCTAACATTCCCGTGCTTACAGTGAATCAGATCGAAGATTTCAG
CATGGCATCCCTATGCTTATAGAGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTGCTTATA
GGGAACAGATCGAAGATAACAGATCTGACATTCCTATACTTACAGTGAAGCAAATCGAAGATTTC
AGCATGGCATCCCTGTGCTTATAGGGAACAAGTTGAAAATAGCAGATTTGGCATCCCTGTAATTA
TAGGGAACAGATCGAAGATAACAGATCTGACATTACTGTGCTTACAGTGAAGCAGATCGAAGATT
TCAGCATGGCATCCCTGTGCTGATAGGGAACAAGTTGAAAATAACAGATTTGGCATCCCTGT
Found at i:112903278 original size:44 final size:44
Alignment explanation
Indices: 112903222--112903723 Score: 331
Period size: 44 Copynumber: 11.6 Consensus size: 44
112903212 ATTTATAGAT
* *
112903222 CTTAACCCCCTAAGCAGTAGGGAAATAGATCGAAGGCGATGAAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
* * * **
112903266 CTTAAACCCCTAAGCAGTAGGGTAATAGGT-TTA--C-A-G--C
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
* *
112903303 TCTTAACCCCCTAAGCAATAGGGAAACAGATCGAAGGCGATGAAC
1 -CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
* * * ** *
112903348 CTTAAACCCCTAAGCAGTAGGGTAACAGGTTGGAATTTAC-A-G-AT
1 CTTAAACCCCTAAGCAGTAGGGAAACA-GATCGAA--GGCGATGAAC
*
112903392 CTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAA-
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
* * * *** *
112903435 CTTCAAACCCCTAAGCAGTAGGGTAACAGGTTGGATTTAC-A-G-AT
1 CTT-AAACCCCTAAGCAGTAGGGAAACA-GATCGA-AGGCGATGAAC
* * * *
112903479 CTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAAGCGATGGAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
* * * **** * *
112903523 CTTAAACCCCTAAGCAGTAGGGTAATAGGT-GAAATTTA-CAGAT
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGA-AC
* * * *
112903566 CTTAACCCCCTAAGCAGTAGGGAATCAGATCAAAGGCGATGGAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
* * * ** *
112903610 CTTAAACCCCTAAGCAGTAGGGTAACAGGTGGAATTTAC-A-G-AT
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAA--GGCGATGAAC
* * *
112903653 TTTAACCCCCTAAGCAGTAGGGAAATAGATCGAAGGCGATGAAC
1 CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
*
112903697 CTTAAACCCCTAAGCAGTAGGGTAACA
1 CTTAAACCCCTAAGCAGTAGGGAAACA
112903724 TGCTGAATTT
Statistics
Matches: 341, Mismatches: 88, Indels: 58
0.70 0.18 0.12
Matches are distributed among these distances:
37 1 0.00
38 25 0.07
39 2 0.01
40 1 0.00
41 5 0.01
42 7 0.02
43 95 0.28
44 188 0.55
45 13 0.04
46 3 0.01
47 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.20
Consensus pattern (44 bp):
CTTAAACCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGAAC
Found at i:112903817 original size:88 final size:86
Alignment explanation
Indices: 112903131--112903818 Score: 895
Period size: 87 Copynumber: 8.0 Consensus size: 86
112903121 TTGAAGATAG
* * * * * * *
112903131 CAGAT-TTGACCCCCTAAGCAGTAGGGAAACAAATCGAAAGCGACGGGCCTT-AACTTCCTAAGT
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAAC-CCCTAAGC
* *
112903194 AGTAGGGTAATAGGCTAAATTTA
65 AGTAGGGTAACAGG-TGAATTTA
* * *
112903217 TAGATCTTAACCCCCTAAGCAGTAGGGAAATAGATCGAAGGCGATGAACCTTAAACCCCTAAGCA
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGCA
*
112903282 GTAGGGTAATA-G-G--TTTA
66 GTAGGGTAACAGGTGAATTTA
* * *
112903299 CAGCTCTTAACCCCCTAAGCAATAGGGAAACAGATCGAAGGCGATGAACCTTAAACCCCTAAGCA
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGCA
112903364 GTAGGGTAACAGGTTGGAATTTA
66 GTAGGGTAACAGG-T-GAATTTA
*
112903387 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGAT-GAACTTCAAACCCCTAAGC
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTT-AAACCCCTAAGC
*
112903451 AGTAGGGTAACAGGTTGGATTTA
65 AGTAGGGTAACAGG-TGAATTTA
* *
112903474 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCAAAAGCGATGGACCTTAAACCCCTAAGCA
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGCA
*
112903539 GTAGGGTAATAGGTGAAATTTA
66 GTAGGGTAACAGGTG-AATTTA
* *
112903561 CAGATCTTAACCCCCTAAGCAGTAGGGAATCAGATCAAAGGCGATGGACCTTAAACCCCTAAGCA
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGCA
112903626 GTAGGGTAACAGGTGGAATTTA
66 GTAGGGTAACAGGT-GAATTTA
* * *
112903648 CAGATTTTAACCCCCTAAGCAGTAGGGAAATAGATCGAAGGCGATGAACCTTAAACCCCTAAGCA
1 CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGCA
*
112903713 GTAGGGTAACATGCTGAATTTA
66 GTAGGGTAACA-GGTGAATTTA
* * * * * * * *
112903735 CAAGATCTTAACCCCCTAAGCAGTAAGGAAATAAATAGAAGGTGATGGGCCTTAAACCCCAAAGT
1 C-AGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGC
* *
112903800 AATAGGGTAATAGGCTGAA
65 AGTAGGGTAACAGG-TGAA
112903819 AATTATAGAT
Statistics
Matches: 540, Mismatches: 47, Indels: 28
0.88 0.08 0.05
Matches are distributed among these distances:
82 75 0.14
83 1 0.00
86 8 0.01
87 302 0.56
88 154 0.29
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (86 bp):
CAGATCTTAACCCCCTAAGCAGTAGGGAAACAGATCGAAGGCGATGGACCTTAAACCCCTAAGCA
GTAGGGTAACAGGTGAATTTA
Found at i:112905515 original size:3 final size:3
Alignment explanation
Indices: 112905507--112905548 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
112905497 ACTTTCTGCA
112905507 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
112905549 CAGTGTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:112905654 original size:3 final size:3
Alignment explanation
Indices: 112905646--112905675 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
112905636 TGTATTTCTA
112905646 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
112905676 ATAGTAGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:112911900 original size:14 final size:14
Alignment explanation
Indices: 112911881--112911910 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
112911871 TTTATTTTTT
112911881 AAAAAAGAAAACAA
1 AAAAAAGAAAACAA
*
112911895 AAAAAAGAAAAGAA
1 AAAAAAGAAAACAA
112911909 AA
1 AA
112911911 GAGTCAAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.87, C:0.03, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAACAA
Found at i:112912845 original size:14 final size:13
Alignment explanation
Indices: 112912807--112912856 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
112912797 GTTTCCACTC
112912807 TTGTATT-TTTTT
1 TTGTATTATTTTT
*
112912819 TT-TAGTATTTTT
1 TTGTATTATTTTT
*
112912831 TTGTATTATTCTT
1 TTGTATTATTTTT
*
112912844 TTGCACTTATTTT
1 TTGTA-TTATTTT
112912857 ACATGCATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 3 0.10
12 9 0.30
13 12 0.40
14 6 0.20
ACGTcount: A:0.14, C:0.06, G:0.08, T:0.72
Consensus pattern (13 bp):
TTGTATTATTTTT
Found at i:112912920 original size:21 final size:21
Alignment explanation
Indices: 112912894--112912936 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
112912884 CATTATATCG
*
112912894 TTATTATTAATATTATTACTA
1 TTATTATTAATATTAGTACTA
* *
112912915 TTATTATTCATGTTAGTACTA
1 TTATTATTAATATTAGTACTA
112912936 T
1 T
112912937 AATGTCTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (21 bp):
TTATTATTAATATTAGTACTA
Found at i:112917085 original size:27 final size:26
Alignment explanation
Indices: 112917047--112917100 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
112917037 TCACGCAAGA
*
112917047 AGAAAATAAAAGAATAATAACAAAATC
1 AGAAAATAAAAGAA-AATAAAAAAATC
*
112917074 AGAAAA-AGAAAGAAACTAAAAAAATC
1 AGAAAATA-AAAGAAAATAAAAAAATC
112917100 A
1 A
112917101 CCTTTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.72, C:0.07, G:0.09, T:0.11
Consensus pattern (26 bp):
AGAAAATAAAAGAAAATAAAAAAATC
Found at i:112919252 original size:34 final size:34
Alignment explanation
Indices: 112919209--112919277 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
112919199 TATTGGAAGA
112919209 GAAAATCAACAGCCAATAATATTTCCTCAATTAT
1 GAAAATCAACAGCCAATAATATTTCCTCAATTAT
112919243 GAAAATCAACAGCCAATAATATTTCCTCAATTAT
1 GAAAATCAACAGCCAATAATATTTCCTCAATTAT
112919277 G
1 G
112919278 CTTCAGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.29
Consensus pattern (34 bp):
GAAAATCAACAGCCAATAATATTTCCTCAATTAT
Found at i:112927524 original size:12 final size:12
Alignment explanation
Indices: 112927507--112927531 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
112927497 TAACATGTAA
112927507 AATGCATGATTT
1 AATGCATGATTT
112927519 AATGCATGATTT
1 AATGCATGATTT
112927531 A
1 A
112927532 GCAGAATTTG
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:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
AATGCATGATTT
Found at i:112933476 original size:4 final size:4
Alignment explanation
Indices: 112933462--112933500 Score: 69
Period size: 4 Copynumber: 9.5 Consensus size: 4
112933452 GACCGGGCTG
112933462 TAAA CTAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
112933501 TGCATTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:112935097 original size:30 final size:31
Alignment explanation
Indices: 112935057--112935123 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
112935047 TATATTCAAA
*
112935057 TTATATTTTATTATATAACATTTATTATATT
1 TTATATTTTATTATATAACACTTATTATATT
* ** *
112935088 TTAT-TTTTATTCTATATTACTTATTATTTT
1 TTATATTTTATTATATAACACTTATTATATT
112935118 TTATAT
1 TTATAT
112935124 ATGTTATGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (31 bp):
TTATATTTTATTATATAACACTTATTATATT
Found at i:112935544 original size:33 final size:33
Alignment explanation
Indices: 112935505--112935574 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
112935495 TTGTATTACT
*
112935505 CTTTTTTGTATATCATATATTATTTAATTATTA
1 CTTTTTTGTATATCATACATTATTTAATTATTA
*
112935538 CTTTTTTGTATATCATGCATTATTTAATTATTA
1 CTTTTTTGTATATCATACATTATTTAATTATTA
112935571 CTTT
1 CTTT
112935575 GTATGTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (33 bp):
CTTTTTTGTATATCATACATTATTTAATTATTA
Found at i:112939157 original size:59 final size:59
Alignment explanation
Indices: 112939065--112939185 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
112939055 CTTCTTTACA
112939065 AAAGCTGGGGCACTAGCAGCCTTGGAATAAACTTTGTCGACTTGAACCTTTGGACAACG
1 AAAGCTGGGGCACTAGCAGCCTTGGAATAAACTTTGTCGACTTGAACCTTTGGACAACG
112939124 AAAGCTGGGGCACTAGCAGCCTTGGAATAAACTTTGTCGACTTGAACCTTTGGACAACG
1 AAAGCTGGGGCACTAGCAGCCTTGGAATAAACTTTGTCGACTTGAACCTTTGGACAACG
112939183 AAA
1 AAA
112939186 CAAAGCCGTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (59 bp):
AAAGCTGGGGCACTAGCAGCCTTGGAATAAACTTTGTCGACTTGAACCTTTGGACAACG
Found at i:112953774 original size:144 final size:144
Alignment explanation
Indices: 112953539--112953813 Score: 426
Period size: 144 Copynumber: 1.9 Consensus size: 144
112953529 AAATTAACAA
* ** *
112953539 TAGGAGATTGCAAGGAGGTTGATTTCGTGGGCATGCAATGGGAACTCCTTACGAATCTCTCTCAT
1 TAGGAGATTGCAAGGAGGTTGATTTAGAAGGCATGCAATGGGAACTCCTTAAGAATCTCTCTCAT
* ** * *
112953604 TTGGAGATTAATAATAATCCGCAGCTGCTGTCTCTCCCCTTTTGGCTTCAACATCTTGTTCAATT
66 TTGGAGATTAAGAATAATCCAAAGCTGCTGTCTCTCCCCATTGGGCTTCAACATCTTGTTCAATT
112953669 GAAAGGATTAATAG
131 GAAAGGATTAATAG
*
112953683 TAGGAGATTGCAAGGAGGTTGATTTAGAAGGCATGCAATGGGAAGC-CCTTAAGAATCTCTCTCG
1 TAGGAGATTGCAAGGAGGTTGATTTAGAAGGCATGCAATGGGAA-CTCCTTAAGAATCTCTCTCA
* *
112953747 TTTGGAGATTAAGAATATTCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCTTGTTCAAT
65 TTTGGAGATTAAGAATAATCCAAAGCTGCTGTCTCTCCCCATTGGGCTTCAACATCTTGTTCAAT
112953812 TG
130 TG
112953814 GAAACATTAG
Statistics
Matches: 118, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
144 117 0.99
145 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (144 bp):
TAGGAGATTGCAAGGAGGTTGATTTAGAAGGCATGCAATGGGAACTCCTTAAGAATCTCTCTCAT
TTGGAGATTAAGAATAATCCAAAGCTGCTGTCTCTCCCCATTGGGCTTCAACATCTTGTTCAATT
GAAAGGATTAATAG
Found at i:112961180 original size:35 final size:35
Alignment explanation
Indices: 112961134--112961205 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
112961124 TTGCATAACT
112961134 AAAGTAAGTTGAAAGAGTGTTTACTTAATTGTACA
1 AAAGTAAGTTGAAAGAGTGTTTACTTAATTGTACA
112961169 AAAGTAAGTTGAAAGAGTGTTTACTTAATTGTACA
1 AAAGTAAGTTGAAAGAGTGTTTACTTAATTGTACA
112961204 AA
1 AA
112961206 GGTGAGGTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (35 bp):
AAAGTAAGTTGAAAGAGTGTTTACTTAATTGTACA
Found at i:112964280 original size:22 final size:23
Alignment explanation
Indices: 112964253--112964307 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 23
112964243 CGATTTACAT
112964253 AAAAAATTTGAATCAACCA-A-AA
1 AAAAAATTTGAATCAA-CAGAGAA
*
112964275 AGAAAA-TT-AATCAACAGAGAA
1 AAAAAATTTGAATCAACAGAGAA
112964296 AAAAAATTTGAA
1 AAAAAATTTGAA
112964308 ATCACCTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.07
20 7 0.26
21 9 0.33
22 7 0.26
23 2 0.07
ACGTcount: A:0.64, C:0.09, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAAATTTGAATCAACAGAGAA
Found at i:112972083 original size:53 final size:53
Alignment explanation
Indices: 112972008--112972115 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 53
112971998 TGCTCTAATG
* * * *
112972008 AGATTGAAACCAATAATAACAACGACGACGATGACGATAATAATAATAAGATT
1 AGATTGAAAACAATAATAACAACGACGAAGACGACAATAATAATAATAAGATT
* *
112972061 AGATTGAAAATAATAATGACAACGACGAAGACGACAATAATAATAATAAGATT
1 AGATTGAAAACAATAATAACAACGACGAAGACGACAATAATAATAATAAGATT
112972114 AG
1 AG
112972116 CTGATGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.20
Consensus pattern (53 bp):
AGATTGAAAACAATAATAACAACGACGAAGACGACAATAATAATAATAAGATT
Found at i:112972345 original size:47 final size:47
Alignment explanation
Indices: 112972272--112972407 Score: 254
Period size: 47 Copynumber: 2.9 Consensus size: 47
112972262 TTAACCCTTA
* *
112972272 AACTTGCATTCTCTGTCAAATTATCTCAAAATGGATGGAAAAGTTTG
1 AACTTGCATTCTCTATCAAATCATCTCAAAATGGATGGAAAAGTTTG
112972319 AACTTGCATTCTCTATCAAATCATCTCAAAATGGATGGAAAAGTTTG
1 AACTTGCATTCTCTATCAAATCATCTCAAAATGGATGGAAAAGTTTG
112972366 AACTTGCATTCTCTATCAAATCATCTCAAAATGGATGGAAAA
1 AACTTGCATTCTCTATCAAATCATCTCAAAATGGATGGAAAA
112972408 ATTAAATAGA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 87 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (47 bp):
AACTTGCATTCTCTATCAAATCATCTCAAAATGGATGGAAAAGTTTG
Found at i:112973281 original size:24 final size:24
Alignment explanation
Indices: 112973232--112973281 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
112973222 ATTTACAATA
**
112973232 AAAAAAATAAATGTATATTATTAT
1 AAAAAAATAAATGTATATTAAAAT
112973256 AAAAAAATAAATGTATATTAAAAT
1 AAAAAAATAAATGTATATTAAAAT
112973280 AA
1 AA
112973282 TTAAAATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (24 bp):
AAAAAAATAAATGTATATTAAAAT
Found at i:112976344 original size:25 final size:25
Alignment explanation
Indices: 112976316--112976365 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
112976306 TTAGGTTGAT
112976316 TATATACAATATTCATAGTAGTAAA
1 TATATACAATATTCATAGTAGTAAA
112976341 TATATACAATATTCATAGTAGTAAA
1 TATATACAATATTCATAGTAGTAAA
112976366 CAAATCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (25 bp):
TATATACAATATTCATAGTAGTAAA
Found at i:112977145 original size:45 final size:40
Alignment explanation
Indices: 112977078--112977166 Score: 99
Period size: 45 Copynumber: 2.1 Consensus size: 40
112977068 AACAATGAAC
*
112977078 ATATATACATAATAATGATATTAAGAATATGTACGTAATATATA
1 ATATATAAATAATAATGATATT-AGAA-ATGTAC--AATATATA
*
112977122 TATATATAAATAGTAAT-AGTATTAGAAATGTACAATATATA
1 -ATATATAAATAATAATGA-TATTAGAAATGTACAATATATA
112977163 ATAT
1 ATAT
112977167 TCGCAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
40 4 0.10
41 8 0.20
43 6 0.15
44 5 0.12
45 18 0.44
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.37
Consensus pattern (40 bp):
ATATATAAATAATAATGATATTAGAAATGTACAATATATA
Found at i:112986272 original size:15 final size:15
Alignment explanation
Indices: 112986252--112986281 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
112986242 GCCACATATC
112986252 AATTAATCCTTCATT
1 AATTAATCCTTCATT
112986267 AATTAATCCTTCATT
1 AATTAATCCTTCATT
112986282 TAAGGGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAATCCTTCATT
Found at i:112990913 original size:3 final size:3
Alignment explanation
Indices: 112990905--112990929 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
112990895 TACCATTACA
112990905 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
112990930 CCCAATGTCT
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:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:112993140 original size:15 final size:15
Alignment explanation
Indices: 112993120--112993149 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
112993110 AAAATTTGAG
112993120 TCCTAGATTAATCTA
1 TCCTAGATTAATCTA
112993135 TCCTAGATTAATCTA
1 TCCTAGATTAATCTA
112993150 ACTTTTACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
TCCTAGATTAATCTA
Found at i:112994809 original size:16 final size:17
Alignment explanation
Indices: 112994790--112994826 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
112994780 TCATCTTTCT
112994790 ATTTTTCTATC-CCTCA
1 ATTTTTCTATCTCCTCA
*
112994806 A-TTTTCTATCTTCTCA
1 ATTTTTCTATCTCCTCA
112994822 ATTTT
1 ATTTT
112994827 CTCTCCTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 6 0.33
17 3 0.17
ACGTcount: A:0.19, C:0.24, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTCTATCTCCTCA
Found at i:112994810 original size:15 final size:16
Alignment explanation
Indices: 112994792--112994828 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
112994782 ATCTTTCTAT
112994792 TTTTCTATC-CCTCAA
1 TTTTCTATCTCCTCAA
*
112994807 TTTTCTATCTTCTCAA
1 TTTTCTATCTCCTCAA
112994823 TTTTCT
1 TTTTCT
112994829 CTCCTGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTCTATCTCCTCAA
Found at i:113000321 original size:18 final size:18
Alignment explanation
Indices: 113000298--113000368 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
113000288 CCCAACTACT
* *
113000298 GTATACGTGAACAGTACC
1 GTATACGTAAATAGTACC
*
113000316 GTATACGTAAATAGTGCC
1 GTATACGTAAATAGTACC
* *
113000334 GTATATGTAAATAGTACT
1 GTATACGTAAATAGTACC
*
113000352 GTATACGTGAATAGTAC
1 GTATACGTAAATAGTAC
113000369 AGTAAACGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (18 bp):
GTATACGTAAATAGTACC
Found at i:113014141 original size:22 final size:21
Alignment explanation
Indices: 113014123--113014164 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
113014113 TCCTTTTTTG
*
113014123 ATTTTTTTATATATTTTTTTAA
1 ATTTTATTAT-TATTTTTTTAA
*
113014145 ATTTTATTATTATTTATTTA
1 ATTTTATTATTATTTTTTTA
113014165 CTTAGGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTATTATTATTTTTTTAA
Found at i:113014428 original size:118 final size:118
Alignment explanation
Indices: 113014268--113014498 Score: 390
Period size: 118 Copynumber: 2.0 Consensus size: 118
113014258 TATTTTTGGT
113014268 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
* *
113014333 CCTACCCCGGTTACTCAGTCAGTCACGATTTGAGCCATACTCATAACCTCGGC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
****
113014386 TAGCGGAGTTTTACTTGTCACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
1 TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
**
113014451 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCTGTACTCATAACC
66 CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACC
113014499 ATGGAAAACA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (118 bp):
TAGCGGAGTTTTACCCAACACGTCACACAACCTTTTGACGCGAAGTAGAATGACAACCCAAGCAC
CCTACCCCGGTTACTCAGTCAGTCACGATCTAAGCCATACTCATAACCTCGGC
Found at i:113015347 original size:42 final size:42
Alignment explanation
Indices: 113015288--113015392 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
113015278 GGGATTCTAA
* * * *
113015288 GGCTGAAATAGGACTGTTTGGCTGCAGAGATGTAGCATTCTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATAGCATTCTG
* *
113015330 GGCTGGAATAGAACTGTTTGGCAGCAGGGATATAGCATTTTG
1 GGCTGGAATAGAACTGTTTGGCAGCAGAGATATAGCATTCTG
*
113015372 GGTTGGAATAGAACTGTTTGG
1 GGCTGGAATAGAACTGTTTGG
113015393 TACCATGGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.25, C:0.11, G:0.34, T:0.30
Consensus pattern (42 bp):
GGCTGGAATAGAACTGTTTGGCAGCAGAGATATAGCATTCTG
Found at i:113015510 original size:10 final size:10
Alignment explanation
Indices: 113015497--113015551 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
113015487 ATTAATATTT
113015497 AAATAAAATA
1 AAATAAAATA
113015507 AAATAAAATAA
1 AAATAAAAT-A
113015518 TAAATAATAA-A
1 -AAATAA-AATA
*
113015529 AGATAAAAT-
1 AAATAAAATA
113015538 AAATAAAAATA
1 AAAT-AAAATA
113015549 AAA
1 AAA
113015552 AGAAAGATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
9 5 0.14
10 19 0.51
11 5 0.14
12 6 0.16
13 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (10 bp):
AAATAAAATA
Found at i:113015517 original size:15 final size:15
Alignment explanation
Indices: 113015497--113015551 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
113015487 ATTAATATTT
113015497 AAATAAAATAAAATA
1 AAATAAAATAAAATA
113015512 AAATAATAAATAATAA-A
1 AAAT-A-AAATAA-AATA
*
113015529 AGATAAAAT-AAATAA
1 AAATAAAATAAAAT-A
113015544 AAATAAAA
1 AAATAAAA
113015552 AGAAAGATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 16 0.48
16 2 0.06
17 10 0.30
18 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAAAATAAAATA
Found at i:113015521 original size:22 final size:21
Alignment explanation
Indices: 113015496--113015556 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
113015486 TATTAATATT
*
113015496 TAAATAAAATAAAATAAAATAA
1 TAAATAAAATAAAAGAAAA-AA
*
113015518 TAAAT--AATAAAAGATAAAA
1 TAAATAAAATAAAAGAAAAAA
113015537 TAAATAAAAATAAAAAGAAA
1 TAAAT-AAAAT-AAAAGAAA
113015557 GATTGGGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 7 0.22
20 10 0.31
22 8 0.25
23 7 0.22
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (21 bp):
TAAATAAAATAAAAGAAAAAA
Found at i:113015559 original size:27 final size:27
Alignment explanation
Indices: 113015496--113015552 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
113015486 TATTAATATT
*
113015496 TAAATAAA-ATAAAATAAAATAATAAA
1 TAAAAAAAGATAAAATAAAATAATAAA
*
113015522 TAATAAAAGATAAAAT-AAATAA-AAA
1 TAAAAAAAGATAAAATAAAATAATAAA
113015547 TAAAAA
1 TAAAAA
113015553 GAAAGATTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.30
26 12 0.44
27 7 0.26
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (27 bp):
TAAAAAAAGATAAAATAAAATAATAAA
Found at i:113045750 original size:161 final size:161
Alignment explanation
Indices: 113045565--113045894 Score: 464
Period size: 171 Copynumber: 2.0 Consensus size: 161
113045555 CAAAGAACTT
*
113045565 ATCAATAGCATAGGTACCATCTGAGC-TTGGCATATATATTTTATAACTCTTGAAATACTCCATT
1 ATCAATAGCATAGGTACCATCTGAGCATTGGCATATATATCTTATAACTCTTGAAATACTCCATT
* * *
113045629 TTTATCATATCAATTGGAAACTACAAGGAAATTTGTGACATATATTACAAGGAAATTTATAGACA
66 TTTATCATATCAATTGGAAACTACAAGGAAATCTATGACATATATTACAAGGAAATTTATACACA
113045694 CATGTCAGCAGATATTTGGGATTTAATTTTCA
131 CATGTCAGCAGATATTTGGG-TTTAATTTTCA
* *
113045726 ATCAATAGCATAGGTACTATCTGAGCTAGTAATAAGTTGGCATTTATATCTTATAACTCTTGAAA
1 ATCAATAGCATAGGTACCATCTGAGC--------A-TTGGCATATATATCTTATAACTCTTGAAA
* * * *
113045791 TACTCCATTTTTATCCTATCAATTGGAAATTACAAGGAAATCTATGACATATGTTATAAGGAAAT
57 TACTCCATTTTTATCATATCAATTGGAAACTACAAGGAAATCTATGACATATATTACAAGGAAAT
*
113045856 TTATACATACATGTCAGCAGATATTTGGGTTTAATTTTC
122 TTATACACACATGTCAGCAGATATTTGGGTTTAATTTTC
113045895 GATTATAGTA
Statistics
Matches: 148, Mismatches: 11, Indels: 11
0.87 0.06 0.06
Matches are distributed among these distances:
161 25 0.17
170 10 0.07
171 113 0.76
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (161 bp):
ATCAATAGCATAGGTACCATCTGAGCATTGGCATATATATCTTATAACTCTTGAAATACTCCATT
TTTATCATATCAATTGGAAACTACAAGGAAATCTATGACATATATTACAAGGAAATTTATACACA
CATGTCAGCAGATATTTGGGTTTAATTTTCA
Found at i:113046356 original size:106 final size:106
Alignment explanation
Indices: 113046171--113046385 Score: 430
Period size: 106 Copynumber: 2.0 Consensus size: 106
113046161 ACTATGAAAC
113046171 ATTGGTGGATTAACAACATCCACTCACTTAGCTCCACTCCTAACAATTGTGAGATTATTATTATC
1 ATTGGTGGATTAACAACATCCACTCACTTAGCTCCACTCCTAACAATTGTGAGATTATTATTATC
113046236 ATTTAAAAGTGTATACACAACTGTATAGATTTTGTCTTGAA
66 ATTTAAAAGTGTATACACAACTGTATAGATTTTGTCTTGAA
113046277 ATTGGTGGATTAACAACATCCACTCACTTAGCTCCACTCCTAACAATTGTGAGATTATTATTATC
1 ATTGGTGGATTAACAACATCCACTCACTTAGCTCCACTCCTAACAATTGTGAGATTATTATTATC
113046342 ATTTAAAAGTGTATACACAACTGTATAGATTTTGTCTTGAA
66 ATTTAAAAGTGTATACACAACTGTATAGATTTTGTCTTGAA
113046383 ATT
1 ATT
113046386 AATAGAAGAG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 109 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (106 bp):
ATTGGTGGATTAACAACATCCACTCACTTAGCTCCACTCCTAACAATTGTGAGATTATTATTATC
ATTTAAAAGTGTATACACAACTGTATAGATTTTGTCTTGAA
Found at i:113046957 original size:22 final size:21
Alignment explanation
Indices: 113046932--113046972 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
113046922 TTTACCCAAT
113046932 AAATCAATTAAATCGAAAATGA
1 AAATCAATTAAATC-AAAATGA
*
113046954 AAATCGATTAAATCAAAAT
1 AAATCAATTAAATCAAAAT
113046973 TTTCTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.59, C:0.10, G:0.07, T:0.24
Consensus pattern (21 bp):
AAATCAATTAAATCAAAATGA
Found at i:113050523 original size:29 final size:30
Alignment explanation
Indices: 113050476--113050532 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
113050466 GAATTTCTAT
*
113050476 TTTCTTTTTAAAATTTTCATTTATTTAAAA
1 TTTCTTTTTAAAATTTTCATTCATTTAAAA
*
113050506 TTTCTTTTTCAAA-TTTCATTCATTTAA
1 TTTCTTTTTAAAATTTTCATTCATTTAA
113050533 TATTCTTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTCTTTTTAAAATTTTCATTCATTTAAAA
Found at i:113051371 original size:15 final size:15
Alignment explanation
Indices: 113051353--113051403 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
113051343 ATTTTATTCT
113051353 ATTAGGATAATTAAA
1 ATTAGGATAATTAAA
*
113051368 ATTAAGATAATT---
1 ATTAGGATAATTAAA
*
113051380 ATTAGGATTATTAAA
1 ATTAGGATAATTAAA
113051395 ATTTAGGAT
1 A-TTAGGAT
113051404 TTTATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 10 0.34
15 12 0.41
16 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (15 bp):
ATTAGGATAATTAAA
Found at i:113052902 original size:118 final size:118
Alignment explanation
Indices: 113052681--113052916 Score: 382
Period size: 118 Copynumber: 2.0 Consensus size: 118
113052671 TGTTTTCCAT
* *
113052681 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
* *
113052746 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACATGACAAGTAAAACTCCGCTAACCGA
**
113052799 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
****
113052864 CTACTTCGCGTCAAAAGGTTGTGTGACATGTTGGGTAAAACTCCGCTAACCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACATGACAAGTAAAACTCCGCTAACCGA
113052917 AAATAAATAA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 108 1.00
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACATGACAAGTAAAACTCCGCTAACCGA
Found at i:113054140 original size:422 final size:422
Alignment explanation
Indices: 113053356--113054192 Score: 1631
Period size: 422 Copynumber: 2.0 Consensus size: 422
113053346 GGGGAGAATT
113053356 TGATAATACTCTAAAATGACGTGTTTTTATATATTAATCATGTGTTTATTTTGAGCTTGAGCCTA
1 TGATAATACTCTAAAATGACGTGTTTTTATATATTAATCATGTGTTTATTTTGAGCTTGAGCCTA
113053421 CTAATTTGAGCTATTTATGTCTTTTTATCTTTTAGGGACTAAATTGGAGGCGAAAAGTAAATTCA
66 CTAATTTGAGCTATTTATGTCTTTTTATCTTTTAGGGACTAAATTGGAGGCGAAAAGTAAATTCA
113053486 AGGGAAAAAGCGTCAATTCGGAGATTAAATGGGCCAATATGCAACGTGGGACAAATATGGTGCCA
131 AGGGAAAAAGCGTCAATTCGGAGATTAAATGGGCCAATATGCAACGTGGGACAAATATGGTGCCA
*
113053551 AAAGTGCGAACATGGAAGGCACAAGGACTTAAAAGCAAATAGAAGAGATTTTATTTTGGAAGACT
196 AAAGTGCGAACATGGAAGGCACAAGAACTTAAAAGCAAATAGAAGAGATTTTATTTTGGAAGACT
113053616 CTATTTTATTTTATTCTATTAGGATAATTAATATTAAGATAATTATTAGGATTATTCAAATTTAG
261 CTATTTTATTTTATTCTATTAGGATAATTAATATTAAGATAATTATTAGGATTATTCAAATTTAG
113053681 GATTTTATTTTAATTATCTTTGTTTATATTTAATTAAATGTATTTATCTTTTTAGAATTTAAGTT
326 GATTTTATTTTAATTATCTTTGTTTATATTTAATTAAATGTATTTATCTTTTTAGAATTTAAGTT
113053746 CAATTAGACTATCTCCCTAG-ACTATAAATAGG
391 CAATTAGACTATCT-CCTAGCACTATAAATAGG
113053778 TGATAATACTCTAAAATGACGTGTTTTTATATATTAATCATGTGTTTATTTTGAGCTTGAGCCTA
1 TGATAATACTCTAAAATGACGTGTTTTTATATATTAATCATGTGTTTATTTTGAGCTTGAGCCTA
113053843 CTAATTTGAGCTATTTATGTCTTTTTATCTTTTAGGGACTAAATTGGAGGCGAAAAGTAAATTCA
66 CTAATTTGAGCTATTTATGTCTTTTTATCTTTTAGGGACTAAATTGGAGGCGAAAAGTAAATTCA
*
113053908 AGGGAAAAAGCGTCAATTCGGAGATTAAATGGGCCAATATGCAACGTGGGACAAATATTGTGCCA
131 AGGGAAAAAGCGTCAATTCGGAGATTAAATGGGCCAATATGCAACGTGGGACAAATATGGTGCCA
113053973 AAAGTGCGAACATGGAAGGCACAAGAACTTAAAAGCAAATAGAAGAGATTTTATTTTGGAAGACT
196 AAAGTGCGAACATGGAAGGCACAAGAACTTAAAAGCAAATAGAAGAGATTTTATTTTGGAAGACT
113054038 CTATTTTATTTTATTCTATTAGGATAATTAATATTAAGATAATTATTAGGATTATTCAAATTTAG
261 CTATTTTATTTTATTCTATTAGGATAATTAATATTAAGATAATTATTAGGATTATTCAAATTTAG
*
113054103 GATTTTATTTTAATTATCTTTGTTTATCTTTAATTAAATGTATTTATCTTTTTAGAATTTAAGTT
326 GATTTTATTTTAATTATCTTTGTTTATATTTAATTAAATGTATTTATCTTTTTAGAATTTAAGTT
113054168 CAATTAGACTATCTCCTAGCACTAT
391 CAATTAGACTATCTCCTAGCACTAT
113054193 NNNNNNNNNN
Statistics
Matches: 411, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
421 5 0.01
422 406 0.99
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.38
Consensus pattern (422 bp):
TGATAATACTCTAAAATGACGTGTTTTTATATATTAATCATGTGTTTATTTTGAGCTTGAGCCTA
CTAATTTGAGCTATTTATGTCTTTTTATCTTTTAGGGACTAAATTGGAGGCGAAAAGTAAATTCA
AGGGAAAAAGCGTCAATTCGGAGATTAAATGGGCCAATATGCAACGTGGGACAAATATGGTGCCA
AAAGTGCGAACATGGAAGGCACAAGAACTTAAAAGCAAATAGAAGAGATTTTATTTTGGAAGACT
CTATTTTATTTTATTCTATTAGGATAATTAATATTAAGATAATTATTAGGATTATTCAAATTTAG
GATTTTATTTTAATTATCTTTGTTTATATTTAATTAAATGTATTTATCTTTTTAGAATTTAAGTT
CAATTAGACTATCTCCTAGCACTATAAATAGG
Found at i:113072883 original size:3 final size:3
Alignment explanation
Indices: 113072875--113072923 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
113072865 TGACTTGTCG
* * *
113072875 TCA TCA TCA TCA TCA TTA CCA TCA TCA TTA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
113072923 T
1 T
113072924 TCCATACTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:113076121 original size:35 final size:36
Alignment explanation
Indices: 113076043--113076122 Score: 101
Period size: 35 Copynumber: 2.2 Consensus size: 36
113076033 TTAAATAATG
113076043 AATTTAAAAGATTAAATTTAATTTTTATTATTTAAA
1 AATTTAAAAGATTAAATTTAATTTTTATTATTTAAA
* * *
113076079 AAATTAAAATA-TAATTTTAA-TTTTATTAATTTAAA
1 AATTTAAAAGATTAAATTTAATTTTTATT-ATTTAAA
*
113076114 ATTTTAAAA
1 AATTTAAAA
113076123 ATTTCAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
34 7 0.18
35 22 0.58
36 9 0.24
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (36 bp):
AATTTAAAAGATTAAATTTAATTTTTATTATTTAAA
Found at i:113082042 original size:3 final size:3
Alignment explanation
Indices: 113082036--113082075 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
113082026 CTTGTCGTCG
* * *
113082036 TCA TCA TCA TCA TTA CCA TCA TCA TTA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
113082076 AATTCCATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:113086412 original size:29 final size:29
Alignment explanation
Indices: 113086371--113086446 Score: 66
Period size: 31 Copynumber: 2.6 Consensus size: 29
113086361 ACAATTTGAT
**
113086371 ACATGAATTTTGATTTGGTGCA-ATTATAC
1 ACATGAAACTTGATTTGGTGCATA-TATAC
* *
113086400 ACATGAAACTTGAATTCTGGTTCATATATAT
1 ACATGAAACTTG-ATT-TGGTGCATATATAC
113086431 ACAT-AAACTTTGATTT
1 ACATGAAAC-TTGATTT
113086447 TAATTCAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
29 11 0.28
30 10 0.26
31 17 0.44
32 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (29 bp):
ACATGAAACTTGATTTGGTGCATATATAC
Found at i:113103233 original size:11 final size:11
Alignment explanation
Indices: 113103217--113103278 Score: 56
Period size: 11 Copynumber: 5.4 Consensus size: 11
113103207 GTGATTGTTT
113103217 TTTTCTAAATG
1 TTTTCTAAATG
113103228 TTTTCTCAAGTTAATG
1 TTTTCT--A---AATG
113103244 TTTTCTAAATG
1 TTTTCTAAATG
113103255 TTTT-TAAAT-
1 TTTTCTAAATG
*
113103264 TTCTCTAAATG
1 TTTTCTAAATG
113103275 TTTT
1 TTTT
113103279 AATAATACGT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
9 3 0.07
10 10 0.24
11 17 0.40
13 1 0.02
14 1 0.02
16 10 0.24
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (11 bp):
TTTTCTAAATG
Done.