Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007819.1 Hibiscus syriacus cultivar Beakdansim tig00110156_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3855360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2745 characters in sequence are not A, C, G, or T
File 10 of 17
Found at i:1910198 original size:2 final size:2
Alignment explanation
Indices: 1910191--1910216 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1910181 TCAAATAATT
1910191 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1910217 AAAGAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1916191 original size:21 final size:21
Alignment explanation
Indices: 1916167--1916241 Score: 123
Period size: 21 Copynumber: 3.6 Consensus size: 21
1916157 GAGTTACCGG
*
1916167 GACGGCCGCAATAACGTCCGC
1 GACGGCCGCAATAGCGTCCGC
1916188 GACGGCCGCAATAGCGTCCGC
1 GACGGCCGCAATAGCGTCCGC
*
1916209 GACGGCCGCAATAGCGTCCGT
1 GACGGCCGCAATAGCGTCCGC
*
1916230 GATGGCCGCAAT
1 GACGGCCGCAAT
1916242 CACGGTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.21, C:0.35, G:0.32, T:0.12
Consensus pattern (21 bp):
GACGGCCGCAATAGCGTCCGC
Found at i:1920298 original size:15 final size:17
Alignment explanation
Indices: 1920278--1920318 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
1920268 CATGATTAAA
1920278 ATAAC-ATAAA-ATAAC
1 ATAACAATAAATATAAC
*
1920293 ATAACAATAAATATAAT
1 ATAACAATAAATATAAC
*
1920310 ATAAAAATA
1 ATAACAATA
1920319 TTAGAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 12 0.55
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAACAATAAATATAAC
Found at i:1922227 original size:9 final size:9
Alignment explanation
Indices: 1922200--1922247 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
1922190 TCAGCATCAA
1922200 CATCA-TAT
1 CATCACTAT
*
1922208 CATCAATAT
1 CATCACTAT
*
1922217 CATCACCAT
1 CATCACTAT
* *
1922226 CACCACTAC
1 CATCACTAT
1922235 CATCACTAT
1 CATCACTAT
1922244 CATC
1 CATC
1922248 TTTATCATCG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
8 5 0.16
9 27 0.84
ACGTcount: A:0.35, C:0.38, G:0.00, T:0.27
Consensus pattern (9 bp):
CATCACTAT
Found at i:1924223 original size:22 final size:22
Alignment explanation
Indices: 1924191--1924242 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
1924181 GTTCATACTC
1924191 ATTC-AAATAAATAAATAAAG-T
1 ATTCAAAATAAATAAAT-AAGTT
1924212 ATTCAAAATAAATAAATAAGTT
1 ATTCAAAATAAATAAATAAGTT
1924234 ATTCAAAAT
1 ATTCAAAAT
1924243 CAATCAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.24
22 22 0.76
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.31
Consensus pattern (22 bp):
ATTCAAAATAAATAAATAAGTT
Found at i:1925357 original size:28 final size:28
Alignment explanation
Indices: 1925283--1925364 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 28
1925273 TTTAAGCACT
* *
1925283 AACTTAAAAGAGGATGTTTATTCTAAATATC
1 AACTTAAAAAAGGA--TTTATT-TAAATAGC
*
1925314 AACTTAAAAACA--ATTTATTTAGATAGC
1 AACTTAAAAA-AGGATTTATTTAAATAGC
1925341 AACTTAAAAAAGGATTTACTTTAA
1 AACTTAAAAAAGGATTTA-TTTAA
1925365 TTATCAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 1 0.02
27 16 0.37
28 11 0.26
29 4 0.09
30 1 0.02
31 9 0.21
32 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (28 bp):
AACTTAAAAAAGGATTTATTTAAATAGC
Found at i:1928850 original size:80 final size:77
Alignment explanation
Indices: 1928720--1928878 Score: 212
Period size: 80 Copynumber: 2.0 Consensus size: 77
1928710 AAAAAAATTA
*
1928720 TTAATAATATTAACATTTATGTATTGATTTTTTTAAATACAGTAAAATTTTCATATATTTAAGGT
1 TTAATAATATTAACATTTATGTATTGATTTTTTTAAAAACAGTAAAATTTTCATATATTTAAGGT
1928785 TCATG-TTTGAGT
66 TCA-GATTTGAGT
* * * * *
1928797 TTAATAATATTAATATTTATGTATTGATTTTTTTTTTAAAAATAGTAAGATTTTTATGTATTTAA
1 TTAATAATATTAACATTTATGTATTGA---TTTTTTTAAAAACAGTAAAATTTTCATATATTTAA
*
1928862 GGTTTAGATTTGAGT
63 GGTTCAGATTTGAGT
1928877 TT
1 TT
1928879 GAGGCTTCAA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
77 26 0.37
79 1 0.01
80 44 0.62
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (77 bp):
TTAATAATATTAACATTTATGTATTGATTTTTTTAAAAACAGTAAAATTTTCATATATTTAAGGT
TCAGATTTGAGT
Found at i:1930278 original size:15 final size:18
Alignment explanation
Indices: 1930235--1930279 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1930225 AATATCATCT
1930235 AAAATATTATTTTTATCG
1 AAAATATTATTTTTATCG
1930253 AAAATATTATTTTTATCG
1 AAAATATTATTTTTATCG
1930271 AAAATATTA
1 AAAATATTA
1930280 ATTTCACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (18 bp):
AAAATATTATTTTTATCG
Found at i:1936206 original size:60 final size:60
Alignment explanation
Indices: 1936139--1936256 Score: 191
Period size: 60 Copynumber: 2.0 Consensus size: 60
1936129 CTAAATTAGA
* **
1936139 TCTTCTGTTCCCAGTATCCACTTCTCCCTCCAATGCACCATCATCAGGCTACTTCCTATT
1 TCTTCTGTTCCCAGTATCCACTTCTCCATCCAACCCACCATCATCAGGCTACTTCCTATT
* *
1936199 TCTTCTGTTCCCAGTATCCCCTTCTCCATCCAACCCACCATCATCAGGCTCCTTCCTA
1 TCTTCTGTTCCCAGTATCCACTTCTCCATCCAACCCACCATCATCAGGCTACTTCCTA
1936257 GTCTTCGAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.18, C:0.42, G:0.08, T:0.33
Consensus pattern (60 bp):
TCTTCTGTTCCCAGTATCCACTTCTCCATCCAACCCACCATCATCAGGCTACTTCCTATT
Found at i:1938864 original size:27 final size:26
Alignment explanation
Indices: 1938811--1938864 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
1938801 GAGAAAAGAA
1938811 TAATAAAAAATATTAATATAATAATAT
1 TAATAAAAAATA-TAATATAATAATAT
1938838 TAATAAAAAATA-AATATATATATATAT
1 TAATAAAAAATATAATATA-ATA-ATAT
1938865 AAAACAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.24
26 3 0.12
27 16 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAAAAAATATAATATAATAATAT
Found at i:1938952 original size:14 final size:14
Alignment explanation
Indices: 1938929--1938961 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1938919 TATATAAAGT
1938929 AAAT-AAATAAAAA
1 AAATAAAATAAAAA
1938942 AAATAAAATAAAAA
1 AAATAAAATAAAAA
*
1938956 GAATAA
1 AAATAA
1938962 GTCAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (14 bp):
AAATAAAATAAAAA
Found at i:1939353 original size:11 final size:11
Alignment explanation
Indices: 1939334--1939378 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
1939324 CTGCAAAAAT
*
1939334 AATAAAATAAA
1 AATATAATAAA
1939345 AATATAATAATA
1 AATATAATAA-A
1939357 AATA-AATAAA
1 AATATAATAAA
*
1939367 TATATAATAAA
1 AATATAATAAA
1939378 A
1 A
1939379 TAAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 4 0.14
11 20 0.69
12 5 0.17
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATAATAAA
Found at i:1939353 original size:16 final size:16
Alignment explanation
Indices: 1939328--1939383 Score: 51
Period size: 22 Copynumber: 3.2 Consensus size: 16
1939318 CGGGGCCTGC
1939328 AAAA-ATAATAAAATA
1 AAAATATAATAAAATA
1939343 AAAATATAATAATAAATAAA
1 AAAATATAAT-A-AAAT--A
1939363 TAAATATATAATAAAATA
1 -AAA-ATATAATAAAATA
1939381 AAA
1 AAA
1939384 TATTTTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
15 4 0.12
16 5 0.15
17 4 0.12
18 5 0.15
20 5 0.15
21 4 0.12
22 7 0.21
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAATATAATAAAATA
Found at i:1939884 original size:84 final size:84
Alignment explanation
Indices: 1939714--1940408 Score: 596
Period size: 84 Copynumber: 8.4 Consensus size: 84
1939704 ATATGCCCTC
* * * * * * * *
1939714 GAGCTGAATGAAATCGAACTCGAAGGTCTTTG--G-CAGATATCCCTTCTTGTCCTGAGCTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGC
*
1939776 TGCAAATGATG-GCGCCTTT
66 TGCAAATGATGTGC-CCTTG
* * * *
1939795 GAGCTGAGTGGAGTCGAACTCGAAGGTCTTTGTTGACAGATAACCTTTCTAGCCTTAAGTTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGC
* * *
1939860 CGTAAATGATGTGCCCTCG
66 TGCAAATGATGTGCCCTTG
* * * * * *
1939879 AAGCTGAGTGTAATCAAACTCGAGGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGC
*
1939941 TGCAAATGATATG-CCTTG
66 TGCAAATGATGTGCCCTTG
* * * * * ** *
1939959 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTATCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATG
** * *
1940024 CTATAAATGATATGCCCTCG
65 CTGCAAATGATGTGCCCTTG
* * * * *
1940044 AAGCTGAGTGTAATTGAACTCG-AGG-GTTT-TTGGCAGATAACCCTTCTCA-ACTTAAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCT-AGACTTAAGTTATG
*
1940105 CTACAAATGATGTG-CCTTG
65 CTGCAAATGATGTGCCCTTG
* * *
1940124 GAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGA-AGATAAACCTTCTCGACTTAAGTTAT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTT-GACAGATAACCCTTCTAGACTTAAGTTAT
* *
1940188 ACTGCAAATGATATG-CCTTG
64 GCTGCAAATGATGTGCCCTTG
* * * * * * *
1940208 GAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTAGACTTAAGTTATG
* * *
1940273 CTGTAAATGATGTGCCATCG
65 CTGCAAATGATGTGCCCTTG
* * * * * * *
1940293 AAGATGAGTGTAATCGAACTCG-AGGATCTTTGGTTGGCAGATAACCTTTATTGATTTAAGTTAT
1 GAGCTGAGTGTAATCGAACTCGAAGG-TCTTT-GTTGACAGATAACCCTTCTAGACTTAAGTTAT
*
1940357 GCTGCAAATGACGTG-CCTTG
64 GCTGCAAATGATGTGCCCTTG
* * *
1940377 GAGCTGAGCGTAGTCGAACTCGAAGGCCTTTG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTG
1940409 GTGGGCACGA
Statistics
Matches: 486, Mismatches: 106, Indels: 42
0.77 0.17 0.07
Matches are distributed among these distances:
80 49 0.10
81 106 0.22
82 8 0.02
83 3 0.01
84 231 0.48
85 89 0.18
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (84 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGACTTAAGTTATGC
TGCAAATGATGTGCCCTTG
Found at i:1940001 original size:165 final size:165
Alignment explanation
Indices: 1939702--1940323 Score: 644
Period size: 165 Copynumber: 3.8 Consensus size: 165
1939692 GCAACGCGAT
* * * * * * *
1939702 TGATATGCCCTCG-AGCTGAATGAAATCGAACTCGAAGGTCTTTGGCAGATATCCCTTCTTGTCC
1 TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACT
* * * * * * *
1939766 TGAGCTATGCTGCAAATGATGGCGCCTTTGAGCTGAGTGGAGTCGAACTCGAAGGTC-TTTGTTG
66 TAAGCTATGCTGCAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTC
* *
1939830 ACAGATAACCTTTCTAGCCTTAAGTTATGCCGTAAA
130 ACAGATAACCCTTCTAGCCTTAAGTTATGCCATAAA
* * *
1939866 TGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACT
1 TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACT
* *
1939931 TAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCA
66 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCA
* * *
1939996 CAGATAACCCTTCTATCCTTGAGTTATGCTATAAA
131 CAGATAACCCTTCTAGCCTTAAGTTATGCCATAAA
* * *
1940031 TGATATGCCCTCGAAGCTGAGTGTAATTGAACTCGAGGGTTTTTGGCAGATAACCCTTCTCAACT
1 TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACT
* *
1940096 TAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGTTG
66 TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-T-
* * * * * ***
1940160 GA-AGATAAACCTTCTCGACTTAAGTTATACTGCAAA
129 CACAGATAACCCTTCTAGCCTTAAGTTATGCCATAAA
* * * * ** *
1940196 TGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCACAGATAACCCTTCTA
1 TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGG---CAGATAACCCTTCTC
* * * * * * * * *
1940260 GCCTTGAGTTATGCTGTAAATGATGTGCCATCGAAGATGAGTGTAATCGAACTCG-AGGATCTTT
62 GACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGG-TCTTT
1940324 GGTTGGCAGA
Statistics
Matches: 386, Mismatches: 61, Indels: 16
0.83 0.13 0.03
Matches are distributed among these distances:
164 72 0.19
165 248 0.64
166 1 0.00
168 40 0.10
169 23 0.06
170 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (165 bp):
TGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACT
TAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCA
CAGATAACCCTTCTAGCCTTAAGTTATGCCATAAA
Found at i:1940198 original size:249 final size:251
Alignment explanation
Indices: 1939799--1940410 Score: 772
Period size: 249 Copynumber: 2.4 Consensus size: 251
1939789 GCCTTTGAGC
* * * * * * **
1939799 TGAGTGGAGTCGAACTCGAAGGTCTTTGTTGACAGATAA-CCTT-TCTAGCCTTAAGTTATGCCG
1 TGAGTGTAATCGAACTCG-AGGACTTTGTTGGCAGATAACCCTTATC-A-ACTTAAGCTATGCTA
* * * * * * * **
1939862 TAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTC--T--TTGGCAGATAGCCCT
63 CAAATGATGTG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATAAACCT
*
1939923 TCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
127 TCTCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
* * *
1939988 TTTGGTCACAGATAACCCTTCTATCCTTGAGTTATGCTATAAATGATATGCCCTCGAAGC
192 TTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGCCATCGAAGA
* * *
1940048 TGAGTGTAATTGAACTCGAGG-GTTT-TTGGCAGATAACCCTTCTCAACTTAAGCTATGCTACAA
1 TGAGTGTAATCGAACTCGAGGACTTTGTTGGCAGATAACCCTTATCAACTTAAGCTATGCTACAA
1940111 ATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATAAACCTTCTC
66 ATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATAAACCTTCTC
* * *
1940176 GACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTG
131 GACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
* *
1940241 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCATCGAAGA
196 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGCCATCGAAGA
* ** * * *
1940297 TGAGTGTAATCGAACTCGAGGATCTTTGGTTGGCAGATAACCTTTATTGATTTAAGTTATGCTGC
1 TGAGTGTAATCGAACTCGAGGA-CTTT-GTTGGCAGATAACCCTTATCAACTTAAGCTATGCTAC
* * *
1940362 AAATGACGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGCCTTTGGT
64 AAATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGT
1940411 GGGCACGATT
Statistics
Matches: 314, Mismatches: 39, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
245 28 0.09
246 31 0.10
247 9 0.03
248 5 0.02
249 163 0.52
251 3 0.01
253 75 0.24
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (251 bp):
TGAGTGTAATCGAACTCGAGGACTTTGTTGGCAGATAACCCTTATCAACTTAAGCTATGCTACAA
ATGATGTGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTTGGAAGATAAACCTTCTC
GACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTG
GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATATGCCATCGAAGA
Found at i:1940354 original size:169 final size:168
Alignment explanation
Indices: 1939912--1940400 Score: 469
Period size: 165 Copynumber: 2.9 Consensus size: 168
1939902 GGGTCTTTGG
* * * * * * * *
1939912 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTCAACTTAAGCTATGCTACAAATGATGTGCCTCGAAGATGAGCGTAATCGAA
* * * * * ** *
1939977 CTCAAAGGTCTTTTGG-T-CACAGATAACCCTTCTATC--CTTGAGTTATGCTATAAATGATATG
66 CTCGAAGGTC-TTTGGTTGGA-AGATAAACC-T-TATCGACTTAAGTTATACTGCAAATGACATG
* * * * * **
1940038 CCCTCGAAGCTGAGTGTAATTGAACTCGAGGGT-TTTTGG---
127 -CCTTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCA
* * *
1940077 CAGATAACCCTTCTCAACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAATCGAA
1 CAGATAACCCTTCTCAACTTAAGCTATGCTACAAATGATGTGCCTCGAAGATGAGCGTAATCGAA
* *
1940142 CTCGAAGGTCTTTGGTTGGAAGATAAACCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTT
66 CTCGAAGGTCTTTGGTTGGAAGATAAACCTTATCGACTTAAGTTATACTGCAAATGACATGCCTT
1940207 GGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCA
131 GGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCA
* * * ** *
1940245 CAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGATGTGCCATCGAAGATGAGTGTAATCG
1 CAGATAACCCTTCTCA-ACTTAAGCTATGCTACAAATGATGTGCC-TCGAAGATGAGCGTAATCG
* * * * *
1940309 AACTCG-AGGATCTTTGGTTGGCAGAT-AACCTTTATTGATTTAAGTTATGCTGCAAATGACGTG
64 AACTCGAAGG-TCTTTGGTTGGAAGATAAACC-TTATCGACTTAAGTTATACTGCAAATGACATG
1940372 CCTTGGAGCTGAGCGTAGTCGAACTCGAA
127 CCTTGGAGCTGAGCGTAGTCGAACTCGAA
1940401 GGCCTTTGGT
Statistics
Matches: 276, Mismatches: 36, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
163 3 0.01
164 31 0.11
165 105 0.38
166 1 0.00
167 1 0.00
168 44 0.16
169 91 0.33
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (168 bp):
CAGATAACCCTTCTCAACTTAAGCTATGCTACAAATGATGTGCCTCGAAGATGAGCGTAATCGAA
CTCGAAGGTCTTTGGTTGGAAGATAAACCTTATCGACTTAAGTTATACTGCAAATGACATGCCTT
GGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTCA
Found at i:1940724 original size:110 final size:110
Alignment explanation
Indices: 1940532--1940841 Score: 484
Period size: 110 Copynumber: 2.9 Consensus size: 110
1940522 TGTTTCGAGG
* **
1940532 CCAATATCCTTCGCCGTGAAGTTGAAATTGACTC----TGAAACTGGAAAGTTGTTTGTTGACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGACAG
1940593 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCAAGT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCAAGT
* * *
1940638 CCAATATCCTTCGCTATGAAGTTGAAATTGACTCTGAATGAAACTATAAAGTTGTTTGTTAACAG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGACAG
*
1940703 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGT
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCAAGT
* * * *
1940748 CCAATATCATTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGACTG
1 CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGACAG
*
1940813 TCAGTCGCCCCTTCGCTGTGAAGTTGAGC
66 TCAGCCGCCCCTTCGCTGTGAAGTTGAGC
1940842 AACCACCATC
Statistics
Matches: 186, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
106 32 0.17
110 154 0.83
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (110 bp):
CCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTAAAAAGTTGTTTGTTGACAG
TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCAAGT
Found at i:1944512 original size:14 final size:14
Alignment explanation
Indices: 1944490--1944525 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1944480 GAAAAGAATA
1944490 ATAAAAATATTAAT
1 ATAAAAATATTAAT
*
1944504 ATAATAATATTAAT
1 ATAAAAATATTAAT
1944518 A-AAAAATA
1 ATAAAAATA
1944526 AAAAATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAATATTAAT
Found at i:1944951 original size:34 final size:34
Alignment explanation
Indices: 1944913--1944997 Score: 122
Period size: 33 Copynumber: 2.6 Consensus size: 34
1944903 TCCTACTTGG
* *
1944913 ACTCAAAATGC-TTCGGTTTTAGTGTTTCAATAGT
1 ACTCAAAATACGTT-GGTTTTAGTGTTTCAATAGA
1944947 ACTC-AAATACGTTGGTTTTAGTGTTTCAATAGA
1 ACTCAAAATACGTTGGTTTTAGTGTTTCAATAGA
1944980 ACTC-AAATACGTTGGTTT
1 ACTCAAAATACGTTGGTTT
1944998 ATTTTCTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
33 42 0.88
34 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (34 bp):
ACTCAAAATACGTTGGTTTTAGTGTTTCAATAGA
Found at i:1944968 original size:33 final size:33
Alignment explanation
Indices: 1944927--1944997 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
1944917 AAAATGCTTC
*
1944927 GGTTTTAGTGTTTCAATAGTACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
1944960 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
1 GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
1944993 GGTTT
1 GGTTT
1944998 ATTTTCTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (33 bp):
GGTTTTAGTGTTTCAATAGAACTCAAATACGTT
Found at i:1945059 original size:5 final size:5
Alignment explanation
Indices: 1945049--1945109 Score: 52
Period size: 5 Copynumber: 11.6 Consensus size: 5
1945039 CTGCAAAAAT
* *
1945049 AATAA AATAA AATAAA AATAT AATAA TAATAA TAAT-A AATAA ATATAT
1 AATAA AATAA AAT-AA AATAA AATAA -AATAA -AATAA AATAA A-ATAA
*
1945097 AATAT AATAA AAT
1 AATAA AATAA AAT
1945110 GTTTTTGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 3 0.06
5 27 0.56
6 18 0.38
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (5 bp):
AATAA
Found at i:1945076 original size:3 final size:3
Alignment explanation
Indices: 1945046--1945106 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
1945036 AGCCTGCAAA
*
1945046 AAT AAT AA- AAT AA- AAT AAA AAT -AT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
1945089 AAAT ATAT AAT -AT AAT AA
1 -AAT A-AT AAT AAT AAT AA
1945107 AATGTTTTTG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
2 8 0.16
3 32 0.64
4 10 0.20
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1945088 original size:27 final size:27
Alignment explanation
Indices: 1945046--1945109 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
1945036 AGCCTGCAAA
1945046 AATAATAAAATAAAATAAAAATATAAT
1 AATAATAAAATAAAATAAAAATATAAT
*
1945073 AATAATAATAAT-AAATAAATATATAAT
1 AATAATAA-AATAAAATAAAAATATAAT
1945100 -ATAATAAAAT
1 AATAATAAAAT
1945110 GTTTTTGTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 3 0.09
26 7 0.20
27 22 0.63
28 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
AATAATAAAATAAAATAAAAATATAAT
Found at i:1947993 original size:24 final size:25
Alignment explanation
Indices: 1947954--1948007 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
1947944 AAAATGACAA
* *
1947954 GGATAGCCGCAAGTATATATTGTCT
1 GGATAGACGCAAGTATAGATTGTCT
1947979 GGATAGACG-AAGTATAGATTGTCT
1 GGATAGACGCAAGTATAGATTGTCT
1948003 GGATA
1 GGATA
1948008 TACGTAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.31, C:0.11, G:0.28, T:0.30
Consensus pattern (25 bp):
GGATAGACGCAAGTATAGATTGTCT
Found at i:1948050 original size:19 final size:19
Alignment explanation
Indices: 1948026--1948068 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1948016 TAGTGCACAA
1948026 GGCACTTATGACTGACCAT
1 GGCACTTATGACTGACCAT
*
1948045 GGCACTTATGGCTGACCAT
1 GGCACTTATGACTGACCAT
1948064 GGCAC
1 GGCAC
1948069 AAGGCCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (19 bp):
GGCACTTATGACTGACCAT
Found at i:1950007 original size:18 final size:18
Alignment explanation
Indices: 1949984--1950018 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1949974 CTTCTCCCCT
1949984 CATTTG-TAATCATTTCAC
1 CATTTGTTAATC-TTTCAC
1950002 CATTTGTTAATCTTTCA
1 CATTTGTTAATCTTTCA
1950019 GAGTAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (18 bp):
CATTTGTTAATCTTTCAC
Found at i:1956066 original size:202 final size:202
Alignment explanation
Indices: 1955720--1956124 Score: 810
Period size: 202 Copynumber: 2.0 Consensus size: 202
1955710 TCAAGCAAGT
1955720 TTTATTTATGGAATACATGTTTCTAACAACATTCTCCTAGCTCAGGAGGTTATTCATAAAATTAA
1 TTTATTTATGGAATACATGTTTCTAACAACATTCTCCTAGCTCAGGAGGTTATTCATAAAATTAA
1955785 ACATTTCAAAGGGAAGAACATACTTGTTGTGATAAAAATTGATCTTGAGAAAGAATATGACAGGG
66 ACATTTCAAAGGGAAGAACATACTTGTTGTGATAAAAATTGATCTTGAGAAAGAATATGACAGGG
1955850 TTCGTTGGGTTTTCTTGAAGACACACATGTCCAATTTCGATTTCCTAGAATTTGGATTAACTTGA
131 TTCGTTGGGTTTTCTTGAAGACACACATGTCCAATTTCGATTTCCTAGAATTTGGATTAACTTGA
1955915 TACTACA
196 TACTACA
1955922 TTTATTTATGGAATACATGTTTCTAACAACATTCTCCTAGCTCAGGAGGTTATTCATAAAATTAA
1 TTTATTTATGGAATACATGTTTCTAACAACATTCTCCTAGCTCAGGAGGTTATTCATAAAATTAA
1955987 ACATTTCAAAGGGAAGAACATACTTGTTGTGATAAAAATTGATCTTGAGAAAGAATATGACAGGG
66 ACATTTCAAAGGGAAGAACATACTTGTTGTGATAAAAATTGATCTTGAGAAAGAATATGACAGGG
1956052 TTCGTTGGGTTTTCTTGAAGACACACATGTCCAATTTCGATTTCCTAGAATTTGGATTAACTTGA
131 TTCGTTGGGTTTTCTTGAAGACACACATGTCCAATTTCGATTTCCTAGAATTTGGATTAACTTGA
1956117 TACTACA
196 TACTACA
1956124 T
1 T
1956125 AGTGTTTGAA
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 203 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (202 bp):
TTTATTTATGGAATACATGTTTCTAACAACATTCTCCTAGCTCAGGAGGTTATTCATAAAATTAA
ACATTTCAAAGGGAAGAACATACTTGTTGTGATAAAAATTGATCTTGAGAAAGAATATGACAGGG
TTCGTTGGGTTTTCTTGAAGACACACATGTCCAATTTCGATTTCCTAGAATTTGGATTAACTTGA
TACTACA
Found at i:1957412 original size:36 final size:36
Alignment explanation
Indices: 1957367--1957537 Score: 274
Period size: 36 Copynumber: 4.7 Consensus size: 36
1957357 ACAAATCTAT
*
1957367 TTTTAGGTTGTAACTTATTTTTAGGTTATAATGAGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGAGA
*
1957403 TTTTAGGTTGTAACCTATTTTTAGGTTTTAAT-AGGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGA-GA
*
1957439 TTTTAGGTTGTAACCTATTTTTTAAGTTATAATGAGA
1 TTTTAGGTTGTAACCTA-TTTTTAGGTTATAATGAGA
1957476 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGAGA
1 TTTTAGGTTGTAACCTATTTTTAGGTTATAATGAGA
1957512 TTTTAGGTTGTAACC-ATATTTTAGGT
1 TTTTAGGTTGTAACCTAT-TTTTAGGT
1957538 AGTAACATAT
Statistics
Matches: 126, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
35 3 0.02
36 90 0.71
37 32 0.25
38 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.19, T:0.49
Consensus pattern (36 bp):
TTTTAGGTTGTAACCTATTTTTAGGTTATAATGAGA
Found at i:1957468 original size:73 final size:73
Alignment explanation
Indices: 1957367--1957533 Score: 275
Period size: 73 Copynumber: 2.3 Consensus size: 73
1957357 ACAAATCTAT
* * *
1957367 TTTTAGGTTGTAACTTA-TTTTTAGGTTATAATGAGATTTTAGGTTGTAACCTATTTTTAGGTTT
1 TTTTAGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTTAGGTTGTAACCTATTTTTAGGTTA
1957431 TAAT-AGGA
66 TAATGA-GA
1957439 TTTTAGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTTAGGTTGTAACCTATTTTTAGGTTA
1 TTTTAGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTTAGGTTGTAACCTATTTTTAGGTTA
1957504 TAATGAGA
66 TAATGAGA
1957512 TTTTAGGTTGTAACCATATTTT
1 TTTTAGGTTGTAACC-TATTTT
1957534 AGGTAGTAAC
Statistics
Matches: 89, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
72 16 0.18
73 66 0.74
74 7 0.08
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.50
Consensus pattern (73 bp):
TTTTAGGTTGTAACCTATTTTTTAAGTTATAATGAGATTTTAGGTTGTAACCTATTTTTAGGTTA
TAATGAGA
Found at i:1957598 original size:37 final size:36
Alignment explanation
Indices: 1957551--1957632 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 36
1957541 AACATATTTG
* *
1957551 TTTTAAGTTATAATGGGATTTAAGGTTATAACCTATT
1 TTTTAGGTTATAATGGGATTTAAGGTTATAACC-ATA
* *
1957588 TTTTAGGTTATAATGGGATTTTAGGTTGTAACCATA
1 TTTTAGGTTATAATGGGATTTAAGGTTATAACCATA
1957624 TTTTAGGTT
1 TTTTAGGTT
1957633 GAAACCTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 11 0.27
37 30 0.73
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.48
Consensus pattern (36 bp):
TTTTAGGTTATAATGGGATTTAAGGTTATAACCATA
Found at i:1957632 original size:55 final size:54
Alignment explanation
Indices: 1957568--1957690 Score: 167
Period size: 55 Copynumber: 2.2 Consensus size: 54
1957558 TTATAATGGG
* * * * *
1957568 ATTTAAGGTTATAACCTATTTTTTAGGTTATAATGGGATTTTAGGTTGTAACCAT
1 ATTTTAGGTTATAACCTATTTCTTAAGTTATAATGGAAATTTAGGTTGTAACC-T
1957623 ATTTTAGGTTGA-AACCTATTTCTTAAGTTATAATGGAAATTTAGGTTGTAACCT
1 ATTTTAGGTT-ATAACCTATTTCTTAAGTTATAATGGAAATTTAGGTTGTAACCT
1957677 ATTTTTAGGTTATA
1 A-TTTTAGGTTATA
1957691 TTGGGAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
54 3 0.05
55 56 0.93
56 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (54 bp):
ATTTTAGGTTATAACCTATTTCTTAAGTTATAATGGAAATTTAGGTTGTAACCT
Found at i:1957685 original size:18 final size:18
Alignment explanation
Indices: 1957363--1957687 Score: 125
Period size: 18 Copynumber: 17.7 Consensus size: 18
1957353 AGTTACAAAT
1957363 CTATTTTTAGGTTGTAAC
1 CTATTTTTAGGTTGTAAC
* *
1957381 TTATTTTTAGGTTATAA-
1 CTATTTTTAGGTTGTAAC
*
1957398 -TGAGATTTTAGGTTGTAAC
1 CT-A-TTTTTAGGTTGTAAC
*
1957417 CTATTTTTAGGTTTTAA-
1 CTATTTTTAGGTTGTAAC
*
1957434 -TAGGATTTTAGGTTGTAAC
1 CTA--TTTTTAGGTTGTAAC
* *
1957453 CTATTTTTTAAGTTATAA-
1 CTA-TTTTTAGGTTGTAAC
*
1957471 -TGAGATTTTAGGTTGTAAC
1 CT-A-TTTTTAGGTTGTAAC
*
1957490 CTATTTTTAGGTTATAA-
1 CTATTTTTAGGTTGTAAC
*
1957507 -TGAGATTTTAGGTTGTAAC
1 CT-A-TTTTTAGGTTGTAAC
*
1957526 C-ATATTTTAGGTAGTAAC
1 CTAT-TTTTAGGTTGTAAC
* * * *
1957544 ATATTTGTTTTAAGTTATAATG
1 CTA--T-TTTTAGGTTGTAA-C
** * *
1957566 GGA-TTTAAGGTTATAAC
1 CTATTTTTAGGTTGTAAC
* *
1957583 CTATTTTTTAGGTTATAATG
1 CTA-TTTTTAGGTTGTAA-C
**
1957603 GGA-TTTTAGGTTGTAAC
1 CTATTTTTAGGTTGTAAC
*
1957620 C-ATATTTTAGGTTGAAAC
1 CTAT-TTTTAGGTTGTAAC
* * *
1957638 CTATTTCTTAAGTTATAAT
1 CTATTT-TTAGGTTGTAAC
** **
1957657 GGAAATTTAGGTTGTAAC
1 CTATTTTTAGGTTGTAAC
1957675 CTATTTTTAGGTT
1 CTATTTTTAGGTT
1957688 ATATTGGGAA
Statistics
Matches: 222, Mismatches: 58, Indels: 54
0.66 0.17 0.16
Matches are distributed among these distances:
16 5 0.02
17 4 0.02
18 158 0.71
19 38 0.17
20 5 0.02
21 11 0.05
22 1 0.00
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.47
Consensus pattern (18 bp):
CTATTTTTAGGTTGTAAC
Found at i:1957700 original size:36 final size:37
Alignment explanation
Indices: 1957625--1957738 Score: 140
Period size: 37 Copynumber: 3.1 Consensus size: 37
1957615 GTAACCATAT
*
1957625 TTTAGGTTGAAACCTATTTCTTAAGTTATAATGGAAA
1 TTTAGGTTGTAACCTATTTCTTAAGTTATAATGGAAA
* * *
1957662 TTTAGGTTGTAACCTATTT-TTAGGTTATATTGGGAA
1 TTTAGGTTGTAACCTATTTCTTAAGTTATAATGGAAA
* * * * *
1957698 TTTATGTTGTAACATATTTCTTAAATTATAATAGAAT
1 TTTAGGTTGTAACCTATTTCTTAAGTTATAATGGAAA
1957735 TTTA
1 TTTA
1957739 AGTTATAATG
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 31 0.48
37 33 0.52
ACGTcount: A:0.32, C:0.06, G:0.15, T:0.46
Consensus pattern (37 bp):
TTTAGGTTGTAACCTATTTCTTAAGTTATAATGGAAA
Found at i:1957780 original size:36 final size:36
Alignment explanation
Indices: 1957734--1957820 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 36
1957724 TATAATAGAA
* * * *
1957734 TTTTAAGTTATAATGGGATTTT-ATGTTGTAACCTAT
1 TTTTAGGTTATAAT-GGATTTTGAGGTTATAACATAT
* *
1957770 TTTTAGGTTATAACTGGATTTTGGGGTTATAACATGT
1 TTTTAGGTTATAA-TGGATTTTGAGGTTATAACATAT
1957807 TTTTAGGTTATAAT
1 TTTTAGGTTATAAT
1957821 TGAACATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
36 20 0.47
37 23 0.53
ACGTcount: A:0.26, C:0.05, G:0.20, T:0.49
Consensus pattern (36 bp):
TTTTAGGTTATAATGGATTTTGAGGTTATAACATAT
Found at i:1957783 original size:18 final size:18
Alignment explanation
Indices: 1957752--1957819 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
1957742 TATAATGGGA
* *
1957752 TTTTATGTTGTAACCTAT
1 TTTTAGGTTATAACCTAT
1957770 TTTTAGGTTATAA-CTGGAT
1 TTTTAGGTTATAACCT--AT
** * *
1957789 TTTGGGGTTATAACATGT
1 TTTTAGGTTATAACCTAT
1957807 TTTTAGGTTATAA
1 TTTTAGGTTATAA
1957820 TTGAACATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 2 0.05
18 23 0.59
19 13 0.33
20 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (18 bp):
TTTTAGGTTATAACCTAT
Found at i:1957810 original size:19 final size:18
Alignment explanation
Indices: 1957770--1957819 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1957760 TGTAACCTAT
1957770 TTTTAGGTTATAACTGGA
1 TTTTAGGTTATAACTGGA
* *
1957788 TTTTGGGGTTATAACAT-GT
1 TTTT-AGGTTATAAC-TGGA
1957807 TTTTAGGTTATAA
1 TTTTAGGTTATAA
1957820 TTGAACATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
19 14 0.52
20 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (18 bp):
TTTTAGGTTATAACTGGA
Found at i:1961145 original size:2 final size:2
Alignment explanation
Indices: 1961140--1961170 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1961130 ATAGTGTGTG
1961140 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1961171 TTGTAGCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1961666 original size:60 final size:59
Alignment explanation
Indices: 1961529--1961666 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 59
1961519 TAAAGTATGT
* * *
1961529 AAATGGTCCATTGACTATAGAATATTATTTTATTAAGACTCTCGACTATTAAAAGTTATA
1 AAATAGTCC-TTGACTATAGAATATTACTTTATTAAGACCCTCGACTATTAAAAGTTATA
* * *
1961589 AAATAGTCCTCCT-ACTATAGAATGTTGCTTTGTTAAG-CCCATCGACTATTAAAAGTTATA
1 AAATAGTCCT--TGACTATAGAATATTACTTTATTAAGACCC-TCGACTATTAAAAGTTATA
1961649 AAAT-GATCACTTGACTAT
1 AAATAG-TC-CTTGACTAT
1961667 TTATTATTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
59 5 0.08
60 58 0.88
61 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (59 bp):
AAATAGTCCTTGACTATAGAATATTACTTTATTAAGACCCTCGACTATTAAAAGTTATA
Found at i:1962111 original size:23 final size:24
Alignment explanation
Indices: 1962070--1962114 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
1962060 AAATCTATTA
1962070 TATTAATTTTATTAATAATCATAT
1 TATTAATTTTATTAATAATCATAT
1962094 TATTAATTTT-TTAATAATCAT
1 TATTAATTTTATTAATAATCAT
1962115 TAAGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTAATTTTATTAATAATCATAT
Found at i:1966473 original size:2 final size:2
Alignment explanation
Indices: 1966462--1966508 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1966452 GGATAGCACA
1966462 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1966503 AT AT AT
1 AT AT AT
1966509 CTTTTCGACA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1971838 original size:15 final size:15
Alignment explanation
Indices: 1971818--1971855 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1971808 CAAAAATATT
*
1971818 TTATTATATTATTTA
1 TTATTATATAATTTA
1971833 TTATTAT-TAATTTA
1 TTATTATATAATTTA
1971847 TATATTATA
1 T-TATTATA
1971856 ATTAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTATATAATTTA
Found at i:1971841 original size:18 final size:18
Alignment explanation
Indices: 1971813--1971863 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1971803 GTCTACAAAA
1971813 ATATT-TTATT-ATATTAT
1 ATATTATTATTAAT-TTAT
*
1971830 TTATTATTATTAATTTAT
1 ATATTATTATTAATTTAT
*
1971848 ATATTATAATTAATTT
1 ATATTATTATTAATTT
1971864 TTTCAGGTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 4 0.14
18 23 0.79
19 2 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTATTATTAATTTAT
Found at i:1982027 original size:2 final size:2
Alignment explanation
Indices: 1982022--1982063 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
1982012 TGTGTATTAG
*
1982022 TA TA TA TA AA TGA -A TA TA TA TA TA T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1982063 T
1 T
1982064 TCTTATATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1985785 original size:23 final size:23
Alignment explanation
Indices: 1985725--1985779 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1985715 GATTCCCCTG
*
1985725 GGGGGAATTGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
1985748 GGGGGAATCGGTTCCCCTTC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
*
1985770 GGGGGTATCG
1 GGGGGAATCG
1985780 ATTTCCTCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:1991567 original size:19 final size:19
Alignment explanation
Indices: 1991543--1991580 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1991533 TTGAACAGTG
1991543 GGGGGGAATCGGTACCCTT
1 GGGGGGAATCGGTACCCTT
*
1991562 GGGGGGAATCGGTTCCCTT
1 GGGGGGAATCGGTACCCTT
1991581 CGAGCATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.42, T:0.24
Consensus pattern (19 bp):
GGGGGGAATCGGTACCCTT
Found at i:1992333 original size:24 final size:24
Alignment explanation
Indices: 1992263--1992333 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 24
1992253 CAATCTTATA
*
1992263 TGGCACTACGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* * *
1992286 CGACACTTCGGTGCAAATTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
*
1992310 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
1992334 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
23 11 0.28
24 28 0.72
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:1993224 original size:20 final size:19
Alignment explanation
Indices: 1993186--1993225 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1993176 CTGTTCACGA
*
1993186 TACTATTCATACAATATTT
1 TACTATTCATAAAATATTT
*
1993205 TACTGTTCATAAATATATTT
1 TACTATTCATAAA-ATATTT
1993225 T
1 T
1993226 TATCTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (19 bp):
TACTATTCATAAAATATTT
Found at i:1993943 original size:69 final size:69
Alignment explanation
Indices: 1993832--1993975 Score: 288
Period size: 69 Copynumber: 2.1 Consensus size: 69
1993822 TTGTCGTTTG
1993832 CGTTGCGAGGCAAAGCGATGGAAAAAAGCAGTGTTATTGTCACCGTGCTTAATCCAGTTAGCTCG
1 CGTTGCGAGGCAAAGCGATGGAAAAAAGCAGTGTTATTGTCACCGTGCTTAATCCAGTTAGCTCG
1993897 TGCT
66 TGCT
1993901 CGTTGCGAGGCAAAGCGATGGAAAAAAGCAGTGTTATTGTCACCGTGCTTAATCCAGTTAGCTCG
1 CGTTGCGAGGCAAAGCGATGGAAAAAAGCAGTGTTATTGTCACCGTGCTTAATCCAGTTAGCTCG
1993966 TGCT
66 TGCT
1993970 CGTTGC
1 CGTTGC
1993976 TCTCAGTATA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 75 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (69 bp):
CGTTGCGAGGCAAAGCGATGGAAAAAAGCAGTGTTATTGTCACCGTGCTTAATCCAGTTAGCTCG
TGCT
Found at i:2006565 original size:154 final size:154
Alignment explanation
Indices: 2006280--2006585 Score: 594
Period size: 154 Copynumber: 2.0 Consensus size: 154
2006270 CCTGGGGCAC
2006280 TCCCCTCATGTGGCTCCTACGCTTCGACTAGGGTAAGTCCTTATAGACCCAATGTGTTCCCTTAT
1 TCCCCTCATGTGGCTCCTACGCTTCGACTAGGGTAAGTCCTTATAGACCCAATGTGTTCCCTTAT
* *
2006345 GTTGGCTCTTAAGTCCAATGAACTTAGGGTAAGTCCTTATCGATGCAGTTTTGGGGAACTATATA
66 GTTGGCTCTTAAGTCCAATGAACTTAGGGTAAGTCCTTATAGATGCAGTTTTGGGGAACTACATA
2006410 TAGAGTGTTTAGGTGGAGGGTAAG
131 TAGAGTGTTTAGGTGGAGGGTAAG
2006434 TCCCCTCATGTGGCTCCTACGCTTCGACTAGGGTAAGTCCTTATAGACCCAATGTGTTCCCTTAT
1 TCCCCTCATGTGGCTCCTACGCTTCGACTAGGGTAAGTCCTTATAGACCCAATGTGTTCCCTTAT
2006499 GTTGGCTCTTAAGTCCAATGAACTTAGGGTAAGTCCTTATAGATGCAGTTTTGGGGAACTACATA
66 GTTGGCTCTTAAGTCCAATGAACTTAGGGTAAGTCCTTATAGATGCAGTTTTGGGGAACTACATA
2006564 TAGAGTGTTTAGGTGGAGGGTA
131 TAGAGTGTTTAGGTGGAGGGTA
2006586 TTATTGTGTT
Statistics
Matches: 150, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 150 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (154 bp):
TCCCCTCATGTGGCTCCTACGCTTCGACTAGGGTAAGTCCTTATAGACCCAATGTGTTCCCTTAT
GTTGGCTCTTAAGTCCAATGAACTTAGGGTAAGTCCTTATAGATGCAGTTTTGGGGAACTACATA
TAGAGTGTTTAGGTGGAGGGTAAG
Found at i:2022251 original size:2 final size:2
Alignment explanation
Indices: 2022244--2022296 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2022234 TAAGTAGAGA
2022244 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2022286 AT AT AT AT AT A
1 AT AT AT AT AT A
2022297 CTACCCTACA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2026699 original size:24 final size:23
Alignment explanation
Indices: 2026672--2026733 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
2026662 AAATTTTGGT
2026672 GTTTATTTTTATTATTGTGTTTTA
1 GTTTATTTTTATTATTGT-TTTTA
2026696 GTTT-TGTTTTAGTTTATTGTTTTTA
1 GTTTAT-TTTTA--TTATTGTTTTTA
2026721 -TTTATTTTT-TTAT
1 GTTTATTTTTATTAT
2026734 AATTTTGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
21 4 0.12
23 1 0.03
24 16 0.47
25 6 0.18
26 7 0.21
ACGTcount: A:0.15, C:0.00, G:0.11, T:0.74
Consensus pattern (23 bp):
GTTTATTTTTATTATTGTTTTTA
Found at i:2026732 original size:12 final size:13
Alignment explanation
Indices: 2026677--2026733 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
2026667 TTGGTGTTTA
2026677 TTTTTA-TTATTG
1 TTTTTATTTATTG
*
2026689 TGTTTTAGTT-TTG
1 T-TTTTATTTATTG
2026702 -TTTTAGTTTATTG
1 TTTTTA-TTTATTG
2026715 TTTTTATTTATT-
1 TTTTTATTTATTG
2026727 TTTTTAT
1 TTTTTAT
2026734 AATTTTGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 17 0.44
14 7 0.18
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (13 bp):
TTTTTATTTATTG
Found at i:2027296 original size:27 final size:27
Alignment explanation
Indices: 2027239--2027296 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2027229 CTTCTTTTGT
* * *
2027239 TTTAATAAAATTTAATATCGTTTCAAG
1 TTTAAAAAAATTTAATATCATTTCAAA
*
2027266 TTTAAAAAAATATTAATA-CATTTTAAA
1 TTTAAAAAAAT-TTAATATCATTTCAAA
2027293 TTTA
1 TTTA
2027297 TTAACAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (27 bp):
TTTAAAAAAATTTAATATCATTTCAAA
Found at i:2027810 original size:19 final size:19
Alignment explanation
Indices: 2027760--2027811 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
2027750 AATTCTGAAT
2027760 TTTTTATACTTTTTAAAAA
1 TTTTTATACTTTTTAAAAA
*
2027779 TATTTTA-A-TTTTTTAAAA
1 T-TTTTATACTTTTTAAAAA
2027797 TTTTTATGACTTTTT
1 TTTTTAT-ACTTTTT
2027812 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.18
18 10 0.36
19 3 0.11
20 10 0.36
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTATACTTTTTAAAAA
Found at i:2031882 original size:114 final size:114
Alignment explanation
Indices: 2031682--2031918 Score: 393
Period size: 114 Copynumber: 2.1 Consensus size: 114
2031672 TATGTTGAAA
* * * * *
2031682 AAGTTCCAGCTGAATGTGAAAATTCCAGTCAAGATGATCTACCTGGTCAAGAAAACCTTGCTAAT
1 AAGTTCAAGCTGAATGTGAAAATTCCAGTCAAGATGAGCTACCTGGTCAAGAAAACCATGATAAC
*
2031747 CAGATGTTAGATAATGATGATAATAATGACAATGATAATCATGCCGATG
66 CAGATGTTAGATAATGATGATAATAATGACAATGATAATCATGCCGAGG
* *
2031796 AAGTTCAAGCTGAATGTGAAAATTCCAGTCACGTTGAGCTACCTGGTCAAGAAAACCATGATAAC
1 AAGTTCAAGCTGAATGTGAAAATTCCAGTCAAGATGAGCTACCTGGTCAAGAAAACCATGATAAC
2031861 CAGATGTTAGATAATGATGATAATAATGACAATGATAATCATGCCGAGG
66 CAGATGTTAGATAATGATGATAATAATGACAATGATAATCATGCCGAGG
2031910 AAGATTCAA
1 AAG-TTCAA
2031919 AATGGTGGGA
Statistics
Matches: 114, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
114 109 0.96
115 5 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.26
Consensus pattern (114 bp):
AAGTTCAAGCTGAATGTGAAAATTCCAGTCAAGATGAGCTACCTGGTCAAGAAAACCATGATAAC
CAGATGTTAGATAATGATGATAATAATGACAATGATAATCATGCCGAGG
Found at i:2034610 original size:19 final size:19
Alignment explanation
Indices: 2034586--2034624 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2034576 TGACTACGAT
2034586 AGAGATGATAAGAAAAGAA
1 AGAGATGATAAGAAAAGAA
* * *
2034605 AGAGATTATATGTAAAGAA
1 AGAGATGATAAGAAAAGAA
2034624 A
1 A
2034625 AATTAAAACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.23, T:0.18
Consensus pattern (19 bp):
AGAGATGATAAGAAAAGAA
Found at i:2036154 original size:21 final size:22
Alignment explanation
Indices: 2036128--2036169 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2036118 TAAACTTAAA
2036128 AATTTTAAT-AAAAATAAAAAT
1 AATTTTAATAAAAAATAAAAAT
2036149 AATTTTAATAAAAAATAAAAA
1 AATTTTAATAAAAAATAAAAA
2036170 ATACTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATTTTAATAAAAAATAAAAAT
Found at i:2048739 original size:21 final size:21
Alignment explanation
Indices: 2048715--2048754 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2048705 AGTTTATTTT
2048715 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
2048736 TAAACTTTGTTTCAATTAT
1 TAAACTTTATTTCAATTAT
2048755 TGAACTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:2048809 original size:33 final size:32
Alignment explanation
Indices: 2048745--2048821 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 32
2048735 GTAAACTTTG
* *
2048745 TTTCAATTATTGAACTTGTAAGTTTTCAAGTA
1 TTTCAATTATCGAACTTGGAAGTTTTCAAGTA
*
2048777 TTTGAATTTATCGAACTTGGAAGTATTT-AAGTA
1 TTTCAA-TTATCGAACTTGGAAGT-TTTCAAGTA
2048810 TTTCAATTATCG
1 TTTCAATTATCG
2048822 TAAACTTTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 11 0.28
33 25 0.64
34 3 0.08
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.45
Consensus pattern (32 bp):
TTTCAATTATCGAACTTGGAAGTTTTCAAGTA
Found at i:2049402 original size:120 final size:120
Alignment explanation
Indices: 2049236--2049532 Score: 368
Period size: 120 Copynumber: 2.5 Consensus size: 120
2049226 TAAGTTTTGT
* * * * * * *
2049236 AAAAAATTGAAAGTTTAGATACTAAAACAGATCAAAAGTGATAGTTTAGATATTAAACGTGCTAA
1 AAAAAATTAAAAGTTTAGATACTAAAATAAATCAAAACTGAAAGTTTAGATAATAAACATGCTAA
* * *
2049301 GTTTTAAACGGTGGGTACT-AAAATGAAATCAAAACTAAACGTTAGGTATGATTTTA
66 GTTTTAAACGGTGGGTACTAAAAATAAAAT-AAAACTAAAAGTTAGGAATGA-TTTA
* * * * *
2049357 AAAAAATT-AAAGTTTAGGTACTAAAATGAACCAAAACTGAAAGTTTAGGTAATAAACATGTTAA
1 AAAAAATTAAAAGTTTAGATACTAAAATAAATCAAAACTGAAAGTTTAGATAATAAACATGCTAA
* *
2049421 GTTTTAAACGGTGTGTACTAAAAATAAAATAAAACTAAAAGTTATGAATGATTTA
66 GTTTTAAACGGTGGGTACTAAAAATAAAATAAAACTAAAAGTTAGGAATGATTTA
*
2049476 AAAAAATTAAAAGTTTA-ATTACTAAAATAAATCAAAACTGATAA-TTTAGATACTAAA
1 AAAAAATTAAAAGTTTAGA-TACTAAAATAAATCAAAACTGA-AAGTTTAGATAATAAA
2049533 TATATAATTT
Statistics
Matches: 151, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
119 12 0.08
120 120 0.79
121 19 0.13
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (120 bp):
AAAAAATTAAAAGTTTAGATACTAAAATAAATCAAAACTGAAAGTTTAGATAATAAACATGCTAA
GTTTTAAACGGTGGGTACTAAAAATAAAATAAAACTAAAAGTTAGGAATGATTTA
Found at i:2052695 original size:31 final size:31
Alignment explanation
Indices: 2052657--2052715 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2052647 GAACATTAAT
*
2052657 ATTATCGATTTGTGATAAAATGGTCACTAAC
1 ATTATCGATTTGTAATAAAATGGTCACTAAC
*
2052688 ATTATCGATTTGTAATAAAGTGGTCACT
1 ATTATCGATTTGTAATAAAATGGTCACT
2052716 CTACTATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (31 bp):
ATTATCGATTTGTAATAAAATGGTCACTAAC
Found at i:2054398 original size:16 final size:17
Alignment explanation
Indices: 2054369--2054415 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
2054359 AAAATATTTT
2054369 ATATATAATTAATATAAA
1 ATATATAA-TAATATAAA
* *
2054387 ATATATAA-AATATTAT
1 ATATATAATAATATAAA
2054403 ATATATATATAAT
1 ATATATA-ATAAT
2054416 CAGGGCGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 13 0.52
17 1 0.04
18 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATAATAATATAAA
Found at i:2055117 original size:89 final size:90
Alignment explanation
Indices: 2054966--2055151 Score: 311
Period size: 89 Copynumber: 2.0 Consensus size: 90
2054956 GTTGACAATT
*
2054966 ATGTATGCATGTGAAGTGCTGGTTTTGACCAGCATTCCGGTGGTTCGGTTCCATTACCCCCCCAA
1 ATGTATGCATGTGAAGTGCTGGTTTTGACCAGCATTCCGGTGGTTCGGTTCCATTACCCCCTCAA
2055031 TGATAG-TAAACCGTTGCATTAAAC
66 TGATAGATAAACCGTTGCATTAAAC
*
2055055 ATGTATGCATGTGAAGTGCTGGTTTTGACCAGCATTTCCTGTTGGTTCGGTTCCATTACCCCCTC
1 ATGTATGCATGTGAAGTGCTGGTTTTGACCAGCA-TTCC-GGTGGTTCGGTTCCATTACCCCCTC
2055120 AATGATAGTCATAAACCGTTGCATTAAAC
64 AATGATAG--ATAAACCGTTGCATTAAAC
2055149 ATG
1 ATG
2055152 GTTAATTGTG
Statistics
Matches: 90, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
89 34 0.38
90 4 0.04
91 31 0.34
94 21 0.23
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (90 bp):
ATGTATGCATGTGAAGTGCTGGTTTTGACCAGCATTCCGGTGGTTCGGTTCCATTACCCCCTCAA
TGATAGATAAACCGTTGCATTAAAC
Found at i:2055627 original size:21 final size:21
Alignment explanation
Indices: 2055588--2055630 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2055578 GAATTTAATA
2055588 TTAATAAAATATTTTAATTATT
1 TTAATAAAATA-TTTAATTATT
2055610 TTAATCAAAATA-TTAATTATT
1 TTAAT-AAAATATTTAATTATT
2055631 AAAATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATAAAATATTTAATTATT
Found at i:2055641 original size:12 final size:12
Alignment explanation
Indices: 2055626--2055656 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2055616 AAAATATTAA
2055626 TTATTAAAATAT
1 TTATTAAAATAT
2055638 TTATTAAAATAT
1 TTATTAAAATAT
2055650 TTATTAA
1 TTATTAA
2055657 TATTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTATTAAAATAT
Found at i:2055662 original size:18 final size:16
Alignment explanation
Indices: 2055616--2055686 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
2055606 TATTTTAATC
*
2055616 AAAATATTAAT-TATT
1 AAAATATTATTATATT
2055631 -AAA-A-TATT-TATT
1 AAAATATTATTATATT
2055643 AAAATATTTATTAATATT
1 AAAATA-TTATT-ATATT
2055661 AAAATATTATTATATT
1 AAAATATTATTATATT
**
2055677 TTAATATTAT
1 AAAATATTAT
2055687 AATAAAGAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 7 0.15
13 4 0.09
14 4 0.09
16 17 0.36
17 5 0.11
18 10 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAAATATTATTATATT
Found at i:2055689 original size:8 final size:8
Alignment explanation
Indices: 2055639--2055690 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
2055629 TTAAAATATT
*
2055639 TATTAAAA
1 TATTATAA
2055647 TATTTATTAA
1 TA-TTA-TAA
*
2055657 TATTAAAA
1 TATTATAA
*
2055665 TATTATTA
1 TATTATAA
*
2055673 TATTTTAA
1 TATTATAA
2055681 TATTATAA
1 TATTATAA
2055689 TA
1 TA
2055691 AAGAATCAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
8 25 0.71
9 6 0.17
10 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TATTATAA
Found at i:2055759 original size:27 final size:28
Alignment explanation
Indices: 2055703--2055767 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
2055693 GAATCAATTA
* * *
2055703 TATTTAATAA-ATAAGATATTATTTTTT
1 TATTTAATAATATAAGAAATTATTATAT
*
2055730 TATTTAATAATATAATAAATT-TTATAT
1 TATTTAATAATATAAGAAATTATTATAT
*
2055757 TATTTATTAAT
1 TATTTAATAAT
2055768 TTCGTAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTTAATAATATAAGAAATTATTATAT
Found at i:2057712 original size:2 final size:2
Alignment explanation
Indices: 2057705--2057739 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2057695 TAGTCAAAAC
2057705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2057740 GAACGAGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2065571 original size:133 final size:134
Alignment explanation
Indices: 2065333--2065595 Score: 519
Period size: 133 Copynumber: 2.0 Consensus size: 134
2065323 ATTATACCAG
2065333 AGGCTAATGGCAACCGGTTAACATGATATGAAACCATTTGTACTCATCGATCTTCCGGTTCCGAA
1 AGGCTAATGGCAACCGGTTAACATGATATGAAACCATTTGTACTCATCGATCTTCCGGTTCCGAA
2065398 CATCGTCGATCCATATCTGGCTACAAACCGGGACCTGAATCGGTCC-GGAAGATCGATGAATTCA
66 CATCGTCGATCCATATCTGGCTACAAACCGGGACCTGAATCGGTCCGGGAAGATCGATGAATTCA
2065462 TACC
131 TACC
2065466 AGGCTAATGGCAACCGGTTAACATGATATGAAACCATTTGTACTCATCGATCTTCCGGTTCCGAA
1 AGGCTAATGGCAACCGGTTAACATGATATGAAACCATTTGTACTCATCGATCTTCCGGTTCCGAA
2065531 CATCGTCGATCCATATCTGGCTACAAACCGGGACCTGAATCGGTCCGGGAAGATCGATGAATTCA
66 CATCGTCGATCCATATCTGGCTACAAACCGGGACCTGAATCGGTCCGGGAAGATCGATGAATTCA
2065596 CACTTAACAT
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
133 111 0.86
134 18 0.14
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (134 bp):
AGGCTAATGGCAACCGGTTAACATGATATGAAACCATTTGTACTCATCGATCTTCCGGTTCCGAA
CATCGTCGATCCATATCTGGCTACAAACCGGGACCTGAATCGGTCCGGGAAGATCGATGAATTCA
TACC
Found at i:2067564 original size:33 final size:33
Alignment explanation
Indices: 2067519--2067582 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
2067509 TGCTACTATA
*
2067519 TACATACCCAATAACAACTTTTGGGTGAAAAAC
1 TACATACACAATAACAACTTTTGGGTGAAAAAC
2067552 TACATACACAATAACAACTTTTGGGTGAAAA
1 TACATACACAATAACAACTTTTGGGTGAAAA
2067583 GCGCCACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (33 bp):
TACATACACAATAACAACTTTTGGGTGAAAAAC
Found at i:2067665 original size:43 final size:43
Alignment explanation
Indices: 2067571--2067668 Score: 108
Period size: 43 Copynumber: 2.3 Consensus size: 43
2067561 AATAACAACT
** * * *
2067571 TTTGGGTGAAAAGCGCCACTATATATAATGAATTTTAACGGTG
1 TTTGGGTGAAAATTGTCACTATATATAATGAATATTAACGGCG
* * *
2067614 TTTGGGTGAAAATTGTCACTATATATCATGACTATTACCGGCG
1 TTTGGGTGAAAATTGTCACTATATATAATGAATATTAACGGCG
2067657 TTAT-GGTGAAAA
1 TT-TGGGTGAAAA
2067669 GACGCAATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (43 bp):
TTTGGGTGAAAATTGTCACTATATATAATGAATATTAACGGCG
Found at i:2067987 original size:2 final size:2
Alignment explanation
Indices: 2067980--2068024 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
2067970 CCCATTAAAA
2067980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
2068023 AT
1 AT
2068025 GCTGCATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2073660 original size:24 final size:24
Alignment explanation
Indices: 2073627--2073683 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2073617 CCCAATTAAT
*
2073627 TTTATATTCATTCAT-TTACGTTCG
1 TTTATGTTCATTCATATT-CGTTCG
*
2073651 TTTATGTTCATTTATATTCGTTCG
1 TTTATGTTCATTCATATTCGTTCG
*
2073675 TTTGTGTTC
1 TTTATGTTC
2073684 GTTTATCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 27 0.93
25 2 0.07
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTATGTTCATTCATATTCGTTCG
Found at i:2073688 original size:24 final size:25
Alignment explanation
Indices: 2073645--2073694 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
2073635 CATTCATTTA
2073645 CGTTCGTTTATGTTCATTTAT-ATT
1 CGTTCGTTTATGTTCATTTATCATT
* *
2073669 CGTTCGTTTGTGTTCGTTTATCATT
1 CGTTCGTTTATGTTCATTTATCATT
2073694 C
1 C
2073695 AAACAGACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (25 bp):
CGTTCGTTTATGTTCATTTATCATT
Found at i:2075409 original size:21 final size:21
Alignment explanation
Indices: 2075368--2075409 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
2075358 ATAATAAGTT
2075368 AGTTTTTAATTAGTTAAGGATC
1 AGTTTTTAATTAGTT-AGGATC
2075390 AGTTTTGTAATTAGTT-GGAT
1 AGTTTT-TAATTAGTTAGGAT
2075410 ATCAGTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.29, C:0.02, G:0.21, T:0.48
Consensus pattern (21 bp):
AGTTTTTAATTAGTTAGGATC
Found at i:2076061 original size:2 final size:2
Alignment explanation
Indices: 2076054--2076083 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2076044 TAAATTAATA
2076054 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2076084 TATTAAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2076379 original size:39 final size:40
Alignment explanation
Indices: 2076297--2076394 Score: 157
Period size: 39 Copynumber: 2.5 Consensus size: 40
2076287 TCAGGTGTTT
*
2076297 CATG-CGTCTTCAAGCTAGATATGAAAATTTTTATGACTG
1 CATGACGTCTTCAAGCTAAATATGAAAATTTTTATGACTG
*
2076336 CATGACGTCTTCAAGCTAAATATGAAGA-TTTTATGACTG
1 CATGACGTCTTCAAGCTAAATATGAAAATTTTTATGACTG
2076375 CATGACGTCTTCAAG-TAAAT
1 CATGACGTCTTCAAGCTAAAT
2076395 GAAAAATACC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
38 5 0.09
39 30 0.54
40 21 0.38
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (40 bp):
CATGACGTCTTCAAGCTAAATATGAAAATTTTTATGACTG
Found at i:2084515 original size:11 final size:11
Alignment explanation
Indices: 2084499--2084537 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
2084489 CCCACCTGTG
*
2084499 AAACCAACCCA
1 AAACCAAACCA
2084510 AAACCAAAACCA
1 AAACC-AAACCA
2084522 AAACCAAAACCA
1 AAACC-AAACCA
2084534 AAAC
1 AAAC
2084538 ATATACATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (11 bp):
AAACCAAACCA
Found at i:2084518 original size:6 final size:6
Alignment explanation
Indices: 2084507--2084537 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
2084497 TGAAACCAAC
2084507 CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA C
1 CCAAAA CCAAAA CCAAAA CCAAAA CCAAAA C
2084538 ATATACATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.65, C:0.35, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAAAA
Found at i:2088161 original size:16 final size:16
Alignment explanation
Indices: 2088119--2088164 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
2088109 AGTAATTAAA
* *
2088119 TTATTTTTTTATTTTT
1 TTATTTTTTAAATTTT
*
2088135 TTATTACTTTAAATTTT
1 TTATT-TTTTAAATTTT
2088152 TTATTTTTTAAAT
1 TTATTTTTTAAAT
2088165 CAGATTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTTTAAATTTT
Found at i:2104471 original size:24 final size:24
Alignment explanation
Indices: 2104444--2104520 Score: 145
Period size: 24 Copynumber: 3.2 Consensus size: 24
2104434 GCAGTATATT
*
2104444 GATACACCAGTGAAGGGATGTATC
1 GATACACCAGTGAAGGGATGTACC
2104468 GATACACCAGTGAAGGGATGTACC
1 GATACACCAGTGAAGGGATGTACC
2104492 GATACACCAGTGAAGGGATGTACC
1 GATACACCAGTGAAGGGATGTACC
2104516 GATAC
1 GATAC
2104521 CCTATAGAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (24 bp):
GATACACCAGTGAAGGGATGTACC
Found at i:2105858 original size:23 final size:23
Alignment explanation
Indices: 2105832--2105896 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
2105822 TTTATATGGA
* *
2105832 ACTTTGGTGCATTTTTACGCGGC
1 ACTTCGGTGCATTTATACGCGGC
* ** *
2105855 ACTTCGGTGCAATCCTACGTGGC
1 ACTTCGGTGCATTTATACGCGGC
2105878 ACTTCGGTGCATTTATACG
1 ACTTCGGTGCATTTATACG
2105897 AGCTATGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
ACTTCGGTGCATTTATACGCGGC
Found at i:2110705 original size:23 final size:23
Alignment explanation
Indices: 2110653--2110713 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
2110643 ACATTTTATA
* * *
2110653 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATCCTAAG
* *
2110676 CGACACTTCGGTGCAATCCTAAG
1 TGGCACTTCGGTGCAATCCTAAG
*
2110699 TGGCACTTCAGTGCA
1 TGGCACTTCGGTGCA
2110714 TTTATACGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATCCTAAG
Found at i:2112191 original size:3 final size:3
Alignment explanation
Indices: 2112183--2112211 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2112173 ATCTTTACTC
2112183 TCA TCA TCA TCA TCA -CA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2112212 GGAGCAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:2112203 original size:14 final size:14
Alignment explanation
Indices: 2112184--2112211 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2112174 TCTTTACTCT
2112184 CATCATCATCATCA
1 CATCATCATCATCA
2112198 CATCATCATCATCA
1 CATCATCATCATCA
2112212 GGAGCAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CATCATCATCATCA
Found at i:2114265 original size:15 final size:15
Alignment explanation
Indices: 2114242--2114285 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2114232 AAATGTAATA
*
2114242 AAAAATTAATACAAT
1 AAAAATTAATAAAAT
*
2114257 AAAATTTAATAAAAT
1 AAAAATTAATAAAAT
*
2114272 AATAAATTATTAAA
1 AA-AAATTAATAAA
2114286 TACTTATAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAAATTAATAAAAT
Found at i:2118846 original size:16 final size:18
Alignment explanation
Indices: 2118827--2118870 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
2118817 TAATTAATTA
2118827 TTTTAAATAT-TA-CTAT
1 TTTTAAATATCTATCTAT
*
2118843 TTTTAAATTATCTATTTAT
1 TTTTAAA-TATCTATCTAT
2118862 TTTTAAATA
1 TTTTAAATA
2118871 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 3 0.12
18 4 0.17
19 10 0.42
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAAATATCTATCTAT
Found at i:2118929 original size:23 final size:23
Alignment explanation
Indices: 2118901--2118960 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2118891 ATACGTTTGG
2118901 TAATATTATTTTAAATAAATAAA
1 TAATATTATTTTAAATAAATAAA
*
2118924 TAATATGATTTTAAA-AAATAAA
1 TAATATTATTTTAAATAAATAAA
*
2118946 TAA-A-TATTTAAAATA
1 TAATATTATTTTAAATA
2118961 TTTTCATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 7 0.21
21 2 0.06
22 10 0.30
23 14 0.42
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATATTATTTTAAATAAATAAA
Found at i:2122750 original size:163 final size:164
Alignment explanation
Indices: 2122534--2122879 Score: 464
Period size: 163 Copynumber: 2.1 Consensus size: 164
2122524 CCAAATAATG
* * *
2122534 GTGGTGTATTATCATATTCTGCAACTTTTCAAATGTCATTAAATACATAATTTAAACAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTAAATACATAATTTAAACAACTTTTC
* * *
2122599 AGAATACAGGTGACATAATGGTGCATTATCATCTTCTGCAA-CTCTTCAAATGTCATTCAATGCA
66 AGAAAACAGGTGAAATAATGGTGCATTATCATCTTCTGCAACCT-TTCAAAGGTCATTCAATGCA
* * *
2122663 TAATTTAAAT-A-TTTTTCAGAAAACTGGTGAAATA
130 TAATTTAAATAACTTTAT-AGAAAACGGGTAAAATA
* * * * * * *
2122697 GTGGTGCATTATCATCTTTTGCAACTTTTCAGAGGTTATTCAATGCATAATTTAAACTACTTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTAAATACATAATTTAAACAACTTTTC
** * * *
2122762 AGAAAATGGGTGAAATAGTGGTGCATTATCATCTTTTGCAACCTTTCAGAGGTCATTCAATGCAT
66 AGAAAACAGGTGAAATAATGGTGCATTATCATCTTCTGCAACCTTTCAAAGGTCATTCAATGCAT
2122827 AATTTAAATAACTTTATAGAAAACGGGTAAAATA
131 AATTTAAATAACTTTATAGAAAACGGGTAAAATA
2122861 GTGGTGCATTATCATCTTC
1 GTGGTGCATTATCATCTTC
2122880 AATAACTTTT
Statistics
Matches: 158, Mismatches: 22, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
163 118 0.75
164 36 0.23
165 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (164 bp):
GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTAAATACATAATTTAAACAACTTTTC
AGAAAACAGGTGAAATAATGGTGCATTATCATCTTCTGCAACCTTTCAAAGGTCATTCAATGCAT
AATTTAAATAACTTTATAGAAAACGGGTAAAATA
Found at i:2122795 original size:82 final size:81
Alignment explanation
Indices: 2122534--2122879 Score: 442
Period size: 82 Copynumber: 4.2 Consensus size: 81
2122524 CCAAATAATG
* * * * * * *
2122534 GTGGTGTATTATCATATTCTGCAACTTTTCAAATGTCATTAAATACATAATTTAAACAACTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAA-TACTTTTT
* * *
2122599 AGAATACAGGTGACATA
65 AGAAAACGGGTGAAATA
* * *
2122616 ATGGTGCATTATCATCTTCTGCAACTCTTCAAATGTCATTCAATGCATAATTTAAATA-TTTTTC
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAATACTTTTT-
*
2122680 AGAAAACTGGTGAAATA
65 AGAAAACGGGTGAAATA
* * *
2122697 GTGGTGCATTATCATCTTTTGCAACTTTTCAGAGGTTATTCAATGCATAATTTAAACTACTTTTT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAA-TACTTTTT
*
2122762 AGAAAATGGGTGAAATA
65 AGAAAACGGGTGAAATA
* * * *
2122779 GTGGTGCATTATCATCTTTTGCAACCTTTCAGAGGTCATTCAATGCATAATTTAAATAACTTTAT
1 GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAAT-ACTTTTT
*
2122844 AGAAAACGGGTAAAATA
65 AGAAAACGGGTGAAATA
2122861 GTGGTGCATTATCATCTTC
1 GTGGTGCATTATCATCTTC
2122880 AATAACTTTT
Statistics
Matches: 235, Mismatches: 25, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
80 4 0.02
81 66 0.28
82 160 0.68
83 5 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (81 bp):
GTGGTGCATTATCATCTTCTGCAACTTTTCAAAGGTCATTCAATGCATAATTTAAATACTTTTTA
GAAAACGGGTGAAATA
Found at i:2125672 original size:31 final size:31
Alignment explanation
Indices: 2125637--2125719 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
2125627 CTTTTAAAAC
** *
2125637 TTGCAATACAGTCCCCCAACATTTAGTCTGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
2125668 TTGCAATATGGTCCCCCAACATTTAGTCCGT
1 TTGCAATATGGTCCCCCAACATTTAGTCCGT
2125699 TTGCAATATGGTCCCCCAACA
1 TTGCAATATGGTCCCCCAACA
2125720 GTTACGTCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCCGT
Found at i:2127790 original size:31 final size:31
Alignment explanation
Indices: 2127752--2127811 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2127742 ATAATATCCG
* *
2127752 ACATTTAGTCCGTTTGCAATATGGTCCCTCA
1 ACATTTAGTCCATTTGCAATATGATCCCTCA
* *
2127783 ACATTTAGTTCATTTTCAATATGATCCCT
1 ACATTTAGTCCATTTGCAATATGATCCCT
2127812 GAAGTAACTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (31 bp):
ACATTTAGTCCATTTGCAATATGATCCCTCA
Found at i:2133260 original size:163 final size:161
Alignment explanation
Indices: 2132993--2133317 Score: 616
Period size: 163 Copynumber: 2.0 Consensus size: 161
2132983 TGTTCCATTT
2132993 CCCAATCCCTGCCAAATTCAGCGAGGAGCTTTAAATTGTTAGCAGCTGCATCTCGAATAGAGTAA
1 CCCAATCCCTGCCAAATTCAGCGAGGAGCTTTAAATTGTTAGCAGCTGCATCTCGAATAGAGTAA
2133058 ACCTGTAACAATATCCATGCAAAAATAGTGCCTAGTTGAGAAGTAATATCA-TGTTTCACAATCA
66 ACCTGTAACAATATCCATGCAAAAATAGTGCCTAGTTGAGAAGTAATATCATTGTTTCACAATCA
2133122 GTAAATAAAATATTAACAAAACAGTGGATGG
131 GTAAATAAAATATTAACAAAACAGTGGATGG
2133153 CCCAATCCCTGCCAAATTCTTCAGCGAGGAGCTTTAAATTGTTAGCAGCTGCATCTCGAATAGAG
1 CCCAATCCCTGCCAAA---TTCAGCGAGGAGCTTTAAATTGTTAGCAGCTGCATCTCGAATAGAG
2133218 TAAACCTGTAACAATATCCATGCAAAAATAGTGCCTAGTTGAGAAGTAATATCATTGTTTCACAA
63 TAAACCTGTAACAATATCCATGCAAAAATAGTGCCTAGTTGAGAAGTAATATCATTGTTTCACAA
2133283 TCAGTAAATAAAATATTAACAAAACAGTGGATGG
128 TCAGTAAATAAAATATTAACAAAACAGTGGATGG
2133317 C
1 C
2133318 GCATTCACTT
Statistics
Matches: 161, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
160 16 0.10
163 100 0.62
164 45 0.28
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (161 bp):
CCCAATCCCTGCCAAATTCAGCGAGGAGCTTTAAATTGTTAGCAGCTGCATCTCGAATAGAGTAA
ACCTGTAACAATATCCATGCAAAAATAGTGCCTAGTTGAGAAGTAATATCATTGTTTCACAATCA
GTAAATAAAATATTAACAAAACAGTGGATGG
Found at i:2136533 original size:63 final size:63
Alignment explanation
Indices: 2136434--2136560 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
2136424 ACCATCAGCA
2136434 TGTCATCTTGACACAATTGACTGTATATTGACCTTAATTCTGTTTTCAACATCTCAGGGGCAC
1 TGTCATCTTGACACAATTGACTGTATATTGACCTTAATTCTGTTTTCAACATCTCAGGGGCAC
2136497 TGTCATCTTGACACAATTGACTGTATATTGACCTTAATTCTGTTTTCAACATCTCAGGGGCAC
1 TGTCATCTTGACACAATTGACTGTATATTGACCTTAATTCTGTTTTCAACATCTCAGGGGCAC
2136560 T
1 T
2136561 TGGATAAGCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (63 bp):
TGTCATCTTGACACAATTGACTGTATATTGACCTTAATTCTGTTTTCAACATCTCAGGGGCAC
Found at i:2136994 original size:77 final size:77
Alignment explanation
Indices: 2136912--2137068 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 77
2136902 ATAATATGAA
2136912 AAAAAAAAATTAATTTAAATAATATAAAATTAAGAAACAAACAACTAACCTTTACTAGAGGAACA
1 AAAAAAAAATTAATTTAAATAATATAAAATTAAGAAACAAACAACTAACCTTTACTAGAGGAACA
2136977 AACGAATCAATC
66 AACGAATCAATC
*
2136989 AAAAAAACATTAATTTAAATAATATAAAATTAAGAAACAAACAACTAACCTTTACTAGAGGAACA
1 AAAAAAAAATTAATTTAAATAATATAAAATTAAGAAACAAACAACTAACCTTTACTAGAGGAACA
2137054 AACGAATCAATC
66 AACGAATCAATC
2137066 AAA
1 AAA
2137069 TCATTCTCCC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.59, C:0.13, G:0.06, T:0.22
Consensus pattern (77 bp):
AAAAAAAAATTAATTTAAATAATATAAAATTAAGAAACAAACAACTAACCTTTACTAGAGGAACA
AACGAATCAATC
Found at i:2150650 original size:15 final size:15
Alignment explanation
Indices: 2150630--2150682 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
2150620 AACCGGGTAT
2150630 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
2150645 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
*
2150662 CGGGTACCCTATTAC
1 CGGGTACCCGATTAC
2150677 CGGGTA
1 CGGGTA
2150683 TCCGTAACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 17 0.55
16 4 0.13
17 10 0.32
ACGTcount: A:0.23, C:0.32, G:0.26, T:0.19
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:2150676 original size:32 final size:32
Alignment explanation
Indices: 2150630--2150698 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
2150620 AACCGGGTAT
2150630 CGGGTACCCGATTACCGGGTACCCGCAAAATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
* * * *
2150662 CGGGTACCCTATTACCGGGTATCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGCAAAATC
2150694 CGGGT
1 CGGGT
2150699 CGGGATACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.20
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGCAAAATC
Found at i:2150833 original size:21 final size:21
Alignment explanation
Indices: 2150806--2150860 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
2150796 ATTCTTCTAT
* *
2150806 ATATTATTTTTTTCAATTAAA
1 ATATTATTTTTTTAAATAAAA
*
2150827 TTATTATTTTTATTAAATAAAA
1 ATATTATTTTT-TTAAATAAAA
*
2150849 ATAATATTTTTT
1 ATATTATTTTTT
2150861 ATTATTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTATTTTTTTAAATAAAA
Found at i:2152128 original size:2 final size:2
Alignment explanation
Indices: 2152112--2152152 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2152102 ATAAAGATTT
2152112 TA TA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2152152 T
1 T
2152153 CGTCTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2152254 original size:16 final size:16
Alignment explanation
Indices: 2152233--2152265 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2152223 TAATAAATAA
2152233 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
*
2152249 ACGAACATAAACGAAC
1 ACGAACATAAACAAAC
2152265 A
1 A
2152266 AATTTTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.24, G:0.09, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:2152356 original size:23 final size:23
Alignment explanation
Indices: 2152329--2152385 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
2152319 CATTTAAATG
* **
2152329 ATAAACGAACATAATAAATTAAC
1 ATAAACGAACACAATAAACAAAC
*
2152352 ATAAACGAACACAGTAAACAAAC
1 ATAAACGAACACAATAAACAAAC
*
2152375 ATAAACTAACA
1 ATAAACGAACA
2152386 ACACAAACAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (23 bp):
ATAAACGAACACAATAAACAAAC
Found at i:2152393 original size:23 final size:23
Alignment explanation
Indices: 2152349--2152394 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2152339 ATAATAAATT
*
2152349 AACATAAACGAACACAGTAAACA
1 AACATAAACGAACACAGCAAACA
*
2152372 AACATAAACTAACAACA-CAAACA
1 AACATAAACGAAC-ACAGCAAACA
2152395 CAAACACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.63, C:0.24, G:0.04, T:0.09
Consensus pattern (23 bp):
AACATAAACGAACACAGCAAACA
Found at i:2152682 original size:10 final size:10
Alignment explanation
Indices: 2152664--2152721 Score: 71
Period size: 10 Copynumber: 5.4 Consensus size: 10
2152654 ATAAATGAAC
2152664 GAACATAAAT
1 GAACATAAAT
*
2152674 GAGCATAAAT
1 GAACATAAAT
2152684 GAACATAAAT
1 GAACATAAAT
2152694 GAACGGATATAAAT
1 GAAC----ATAAAT
2152708 GAACATAAAT
1 GAACATAAAT
2152718 GAAC
1 GAAC
2152722 GAACATATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 32 0.76
14 10 0.24
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.19
Consensus pattern (10 bp):
GAACATAAAT
Found at i:2152694 original size:34 final size:34
Alignment explanation
Indices: 2152651--2152721 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
2152641 TATCTGTTTA
*
2152651 AACATAAATGAACGAACATAAATGAGCATAAATG
1 AACATAAATGAACGAACATAAATGAACATAAATG
* *
2152685 AACATAAATGAACGGATATAAATGAACATAAATG
1 AACATAAATGAACGAACATAAATGAACATAAATG
2152719 AAC
1 AAC
2152722 GAACATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.18
Consensus pattern (34 bp):
AACATAAATGAACGAACATAAATGAACATAAATG
Found at i:2152737 original size:16 final size:14
Alignment explanation
Indices: 2152651--2152738 Score: 56
Period size: 14 Copynumber: 7.0 Consensus size: 14
2152641 TATCTGTTTA
2152651 AACATAAATGAACG
1 AACATAAATGAACG
2152665 AACATAAATG-A-G
1 AACATAAATGAACG
2152677 --CATAAAT----G
1 AACATAAATGAACG
2152685 AACATAAATGAACG
1 AACATAAATGAACG
* *
2152699 GATATAAAT----G
1 AACATAAATGAACG
2152709 AACATAAATGAACG
1 AACATAAATGAACG
2152723 AACATATAATCGAACG
1 AACATA-AAT-GAACG
2152739 TTCACGAACG
Statistics
Matches: 58, Mismatches: 4, Indels: 22
0.69 0.05 0.26
Matches are distributed among these distances:
8 1 0.02
10 22 0.38
12 1 0.02
13 1 0.02
14 25 0.43
15 3 0.05
16 5 0.09
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.18
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:2160023 original size:13 final size:14
Alignment explanation
Indices: 2160007--2160037 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2159997 ATATTATGCA
2160007 AAAAATTGTTC-AT
1 AAAAATTGTTCAAT
2160020 AAAAATTGTTCAAT
1 AAAAATTGTTCAAT
2160034 AAAA
1 AAAA
2160038 TATAGGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (14 bp):
AAAAATTGTTCAAT
Found at i:2161289 original size:253 final size:251
Alignment explanation
Indices: 2160914--2161406 Score: 814
Period size: 253 Copynumber: 2.0 Consensus size: 251
2160904 AATATATCAT
* *
2160914 AATCTTACTTTAAGAAAAATAAGATATTTTGAAAATTTTACAATTGAATTTATTTTACACTAATT
1 AATCTTACTATAAGAAAAATAAGATATTTTGAAAATTTTACAATTGAATTGATTTTACACTAATT
*
2160979 CGATTTATCATTTAATAATTATAGACACGATAATAATAATAGAGATAATTAAAAGGTAT-AAATC
66 CGATTTATCATTTAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAAAAT-
2161043 CTATAATAACAAATCATAAATATAGACGTAGGACTAGAATGGTATTAGA-TCTAATGTAGCAAAA
130 CTATAATAACAAATCATAAATATAGACGTAGGACTAGAATGGTATTA-ACTCTAATGTAGCAAAA
*
2161107 GTGTCAATTTGAAATAAATAAATAAAGGGTAAATTACGTGTTTAGTACTTAAAATGTC
194 GTGTCAATTTAAAATAAATAAATAAAGGGTAAATTACGTGTTTAGTACTTAAAATGTC
*
2161165 AATCTTACTATAAGAAAAA-AA-ATATTTTGAAATTTTTACAATTGAATTGATTTTAACACTAAT
1 AATCTTACTATAAGAAAAATAAGATATTTTGAAAATTTTACAATTGAATTGATTTT-ACACTAAT
*
2161228 TTGATTTATCATTTAATAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAA
65 TCGATTTATCA-TT--TAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAA
* *
2161293 AATCTATAATAATAAATCATAAATATAGACGTAGGACTAGAATGGTATTAACTCTAATGTAGTAA
127 AATCTATAATAACAAATCATAAATATAGACGTAGGACTAGAATGGTATTAACTCTAATGTAGCAA
**
2161358 AAGTGTCAATTTAAAATAAATAAATAAAGGGTAAATTTTGTGTTTAGTA
192 AAGTGTCAATTTAAAATAAATAAATAAAGGGTAAATTACGTGTTTAGTA
2161407 TCTAAACTAT
Statistics
Matches: 226, Mismatches: 10, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
249 31 0.14
250 20 0.09
251 20 0.09
252 1 0.00
253 150 0.66
254 4 0.02
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (251 bp):
AATCTTACTATAAGAAAAATAAGATATTTTGAAAATTTTACAATTGAATTGATTTTACACTAATT
CGATTTATCATTTAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAAAATC
TATAATAACAAATCATAAATATAGACGTAGGACTAGAATGGTATTAACTCTAATGTAGCAAAAGT
GTCAATTTAAAATAAATAAATAAAGGGTAAATTACGTGTTTAGTACTTAAAATGTC
Found at i:2163834 original size:13 final size:14
Alignment explanation
Indices: 2163818--2163848 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
2163808 ATATTATGCA
2163818 AAAAATTGTTC-AT
1 AAAAATTGTTCAAT
2163831 AAAAATTGTTCAAT
1 AAAAATTGTTCAAT
2163845 AAAA
1 AAAA
2163849 TATTATAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (14 bp):
AAAAATTGTTCAAT
Found at i:2165181 original size:251 final size:253
Alignment explanation
Indices: 2164729--2165210 Score: 837
Period size: 251 Copynumber: 1.9 Consensus size: 253
2164719 TTATTTTAAG
*
2164729 AAAAATAAGATATTTTGAAAATTTTACAATTGAATTTATTTTTAACACTAATTCGATTTATCATT
1 AAAAATAAGATATTTTGAAAATTTTACAATTGAATTGATTTTTAACACTAATTCGATTTATCATT
*
2164794 TAATAATAATTATAGACACGATAATAATAATAGAGATAATTAAAAGGTATAAATCCTATAATAAC
66 TAATAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAAATCCTATAATAAC
*
2164859 AAATCATAAATATAGACGTAGGACTAGAATGGTATTAGATCTAATGTAGCAAAAGTGTCAATTTG
131 AAATCATAAATATAGACGTAGGACTAGAATGGTATTAGATCTAATGTAGCAAAAGTGTCAATTTA
2164924 AAATAAATAAATAAAGGGTAAATTACGTGTTTAGTACTTAAAATGTCAATCTTACTAT
196 AAATAAATAAATAAAGGGTAAATTACGTGTTTAGTACTTAAAATGTCAATCTTACTAT
* *
2164982 AAAAA-AA-ATATTTTGAAATTTTTACAATTGAATTGATTTTTAACACTAATTTGATTTATCATT
1 AAAAATAAGATATTTTGAAAATTTTACAATTGAATTGATTTTTAACACTAATTCGATTTATCATT
2165045 TAATAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAAAAT-CTATAATAA
66 TAATAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTAT-AAATCCTATAATAA
* *
2165109 TAAATCATAAATATAGACGTAGGACTAGAATGGTATTA-ACTCTAATGTAGTAAAAGTGTCAATT
130 CAAATCATAAATATAGACGTAGGACTAGAATGGTATTAGA-TCTAATGTAGCAAAAGTGTCAATT
**
2165173 TAAAATAAATAAATAAAGGGTAAATTTTGTGTTTAGTA
194 TAAAATAAATAAATAAAGGGTAAATTACGTGTTTAGTA
2165211 TCTAAACTAT
Statistics
Matches: 218, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
250 1 0.00
251 206 0.94
252 6 0.03
253 5 0.02
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.35
Consensus pattern (253 bp):
AAAAATAAGATATTTTGAAAATTTTACAATTGAATTGATTTTTAACACTAATTCGATTTATCATT
TAATAATAATTATAGACACGATAATAATAATAAAGATAATTAAAAGGTATAAATCCTATAATAAC
AAATCATAAATATAGACGTAGGACTAGAATGGTATTAGATCTAATGTAGCAAAAGTGTCAATTTA
AAATAAATAAATAAAGGGTAAATTACGTGTTTAGTACTTAAAATGTCAATCTTACTAT
Found at i:2168478 original size:29 final size:30
Alignment explanation
Indices: 2168439--2168500 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
2168429 AAATTATCTC
*
2168439 TTTATTCTTGTTTTAAATTATTAAATAT-T
1 TTTATTCTTGTCTTAAATTATTAAATATAT
* *
2168468 TTTATTTTTGTCTTAATTTATTAAATATAT
1 TTTATTCTTGTCTTAAATTATTAAATATAT
2168498 TTT
1 TTT
2168501 GTATATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTATTCTTGTCTTAAATTATTAAATATAT
Found at i:2168698 original size:29 final size:29
Alignment explanation
Indices: 2168640--2168733 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 29
2168630 TAATATTTTT
* *
2168640 AATATATTTTAAAAAGTTAAGATAATAATAA
1 AATATATTTT--AAAGTAAAGATAAGAATAA
*
2168671 AATATATTTTAAATTGAAA-ATAAGAATAA
1 AATATATTTTAAAGT-AAAGATAAGAATAA
* *
2168700 TATATATTTTTAAGTAAAGATAAGAATAA
1 AATATATTTTAAAGTAAAGATAAGAATAA
2168729 AATAT
1 AATAT
2168734 TAAATATTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
28 3 0.06
29 39 0.72
30 2 0.04
31 10 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.36
Consensus pattern (29 bp):
AATATATTTTAAAGTAAAGATAAGAATAA
Found at i:2169272 original size:2 final size:2
Alignment explanation
Indices: 2169267--2169314 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
2169257 ACTTTTTTAA
2169267 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2169309 AT AT AT
1 AT AT AT
2169315 TGAAATCCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2170423 original size:37 final size:38
Alignment explanation
Indices: 2170344--2170451 Score: 111
Period size: 37 Copynumber: 3.0 Consensus size: 38
2170334 AAGTATTAAA
** *
2170344 ATGGTTTTC-AAGTTTGGTAACCA--ACTTTGAAAAA-
1 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
2170378 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
* * * *
2170416 A-GTTTTTCAAAGTTTGGTAGATGTTT-GTTGAAAAAT
1 ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
2170452 GATAATGAGA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
34 9 0.14
35 12 0.19
36 9 0.14
37 32 0.51
38 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (38 bp):
ATGGTTTTCAAAGTTTGGTAAATATTTCTTTGAAAAAT
Found at i:2174964 original size:37 final size:36
Alignment explanation
Indices: 2174865--2174984 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
2174855 TGGTAACCAA
2174865 CTTTGAAAAGATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
*
2174902 ATTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
2174937 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
*
2174974 -GTTGAAAAATG
1 CTTTGAAAAATG
2174985 ATAATGAGAT
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 32 0.42
36 17 0.22
37 27 0.36
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:2177828 original size:2 final size:2
Alignment explanation
Indices: 2177821--2177855 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2177811 TTAAAATTAC
2177821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2177856 AACTTTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2180671 original size:17 final size:17
Alignment explanation
Indices: 2180649--2180687 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2180639 AAAAAAGAAG
2180649 GGAAATCTGGAAATAAA
1 GGAAATCTGGAAATAAA
2180666 GGAAATCTGGAAATAAA
1 GGAAATCTGGAAATAAA
2180683 GGAAA
1 GGAAA
2180688 AGGAAGATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (17 bp):
GGAAATCTGGAAATAAA
Found at i:2187767 original size:12 final size:12
Alignment explanation
Indices: 2187750--2187775 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2187740 ACATTCTTTT
2187750 CGATGAAGTTGC
1 CGATGAAGTTGC
2187762 CGATGAAGTTGC
1 CGATGAAGTTGC
2187774 CG
1 CG
2187776 CCCCCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.35, T:0.23
Consensus pattern (12 bp):
CGATGAAGTTGC
Found at i:2195270 original size:12 final size:11
Alignment explanation
Indices: 2195241--2195276 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2195231 GTAGTAAAAT
2195241 AAAATATTTTA
1 AAAATATTTTA
2195252 AAAATATTTTA
1 AAAATATTTTA
*
2195263 TCAAATATTTTA
1 -AAAATATTTTA
2195275 AA
1 AA
2195277 GTGAAATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATATTTTA
Done.