Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003577.1 Hibiscus syriacus cultivar Beakdansim tig00007550_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: 203375
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:285 original size:8 final size:8
Alignment explanation
Indices: 269--320 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
259 ATCAAAGGGA
*
269 AAAAAAAT
1 AAAATAAT
277 AAAATAAT
1 AAAATAAT
*
285 AAAA-ACT
1 AAAATAAT
*
292 GAAAATAAA
1 -AAAATAAT
301 AAAATAAGT
1 AAAATAA-T
310 AAAATAAT
1 AAAATAAT
318 AAA
1 AAA
321 TAAATCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
7 2 0.06
8 26 0.72
9 8 0.22
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (8 bp):
AAAATAAT
Found at i:312 original size:12 final size:12
Alignment explanation
Indices: 269--354 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
259 ATCAAAGGGA
269 AAAAAAATAAAAT
1 AAAAAAAT-AAAT
282 AATAAAAACTGAAAAT
1 AA-AAAAA-T--AAAT
*
298 AAAAAAATAAGT
1 AAAAAAATAAAT
*
310 AAAATAATAAAT
1 AAAAAAATAAAT
* *
322 AAATCAAAGAAAT
1 AAA-AAAATAAAT
* *
335 CAAAGAA-AAAT
1 AAAAAAATAAAT
346 AAAAAAATA
1 AAAAAAATA
355 TTAAATATTA
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
11 9 0.16
12 19 0.33
13 10 0.18
14 6 0.11
15 6 0.11
16 7 0.12
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAAATAAAT
Found at i:1772 original size:37 final size:36
Alignment explanation
Indices: 1722--1901 Score: 254
Period size: 37 Copynumber: 4.9 Consensus size: 36
1712 TATATATATA
1722 TTGAAAACTTATATAATATATGGTTTTTAAAAACATT
1 TTGAAAA-TTATATAATATATGGTTTTTAAAAACATT
*
1759 TTGAAAATATATATAATATATGGTTTTAAAAAACATT
1 TTGAAAAT-TATATAATATATGGTTTTTAAAAACATT
1796 TTGAAAACTTATATAATATAT-GTTTTTAAAAACATTT
1 TTGAAAA-TTATATAATATATGGTTTTTAAAAACA-TT
* *
1833 TTGAAAAAATATATAATATATGGTTTTTAAAAAACTTT
1 TTG-AAAATTATATAATATATGGTTTTT-AAAAACATT
* *
1871 TTGAAAATTATATAATATATAGTTTTGAAAA
1 TTGAAAATTATATAATATATGGTTTTTAAAA
1902 CTTTTTAATA
Statistics
Matches: 130, Mismatches: 7, Indels: 13
0.87 0.05 0.09
Matches are distributed among these distances:
36 17 0.13
37 91 0.70
38 16 0.12
39 6 0.05
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.43
Consensus pattern (36 bp):
TTGAAAATTATATAATATATGGTTTTTAAAAACATT
Found at i:1806 original size:74 final size:74
Alignment explanation
Indices: 1722--1925 Score: 299
Period size: 74 Copynumber: 2.8 Consensus size: 74
1712 TATATATATA
1722 TTGAAAACTTATATAATATATGGTTTTTAAAAACATTTTGAAAATATATATAATATATGG-TTTT
1 TTGAAAACTTATATAATATAT-GTTTTTAAAAACATTTTGAAAATATATATAATATATGGTTTTT
1786 AAAAAACATT
65 AAAAAACATT
*
1796 TTGAAAACTTATATAATATATGTTTTTAAAAACATTTTTGAAAAAATATATAATATATGGTTTTT
1 TTGAAAACTTATATAATATATGTTTTTAAAAACA-TTTTGAAAATATATATAATATATGGTTTTT
*
1861 AAAAAACTTT
65 AAAAAACATT
* * * *
1871 TTGAAAA-TTATATAATATATAG-TTTTGAAAAC-TTTTTAATATATATATTATATAT
1 TTGAAAACTTATATAATATAT-GTTTTTAAAAACATTTTGAAAATATATATAATATAT
1926 ATATATATTT
Statistics
Matches: 120, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
72 19 0.16
73 13 0.11
74 67 0.56
75 21 0.17
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (74 bp):
TTGAAAACTTATATAATATATGTTTTTAAAAACATTTTGAAAATATATATAATATATGGTTTTTA
AAAAACATT
Found at i:1901 original size:24 final size:24
Alignment explanation
Indices: 1869--1915 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1859 TTAAAAAACT
1869 TTTTGAAAA-TTATATAATATATAG
1 TTTTGAAAACTT-TATAATATATAG
*
1893 TTTTGAAAACTTTTTAATATATA
1 TTTTGAAAACTTTATAATATATA
1916 TATTATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (24 bp):
TTTTGAAAACTTTATAATATATAG
Found at i:1916 original size:2 final size:2
Alignment explanation
Indices: 1909--1958 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
1899 AAACTTTTTA
* *
1909 AT AT AT AT AT -T AT AT AT AT AT AT AT TT A- AA 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
1949 AT AT AT AT AT
1 AT AT AT AT AT
1959 TAAAAAAGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1933 original size:19 final size:19
Alignment explanation
Indices: 1909--1957 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1899 AAACTTTTTA
*
1909 ATATATATATTATATATAT
1 ATATATATATAATATATAT
* *
1928 ATATATTTAAAATATATAT
1 ATATATATATAATATATAT
1947 ATATATATATA
1 ATATATATATA
1958 TTAAAAAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATATATATAATATATAT
Found at i:1955 original size:25 final size:26
Alignment explanation
Indices: 1913--1964 Score: 88
Period size: 25 Copynumber: 2.0 Consensus size: 26
1903 TTTTTAATAT
*
1913 ATATATTATATATATATATATTTAAA
1 ATATATTATATATATATATATTAAAA
1939 ATATA-TATATATATATATATTAAAA
1 ATATATTATATATATATATATTAAAA
1964 A
1 A
1965 AGTTTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATATTATATATATATATATTAAAA
Found at i:1988 original size:36 final size:37
Alignment explanation
Indices: 1941--2290 Score: 368
Period size: 36 Copynumber: 9.6 Consensus size: 37
1931 TATTTAAAAT
* * * * *
1941 ATATATATATATATATATTAAAAAAG-TTTTCAAAACT
1 ATATAT-TATATATATTTTCAAAATGTTTTTAAAAACC
*
1978 ATATATTATATA-ATTTTCAAAAAGTTTTTAAAAACC
1 ATATATTATATATATTTTCAAAATGTTTTTAAAAACC
*
2014 ATATATTATATATTTTTTTCAAAAATGTTTTTAAAAA-C
1 ATATATTATATA-TATTTTC-AAAATGTTTTTAAAAACC
*
2052 ATATGTTATATA-AGTTTTCAAAATGTTTTTTAAAAACC
1 ATATATTATATATA-TTTTCAAAATG-TTTTTAAAAACC
2090 ATATA-TATATATA-TTTCAAAATGTTTTTAAAAACC
1 ATATATTATATATATTTTCAAAATGTTTTTAAAAACC
* *
2125 ATATATTATATA-GTTTTCAAAATATTTTTTAAAAACC
1 ATATATTATATATATTTTCAAAAT-GTTTTTAAAAACC
* *
2162 ACATA-TATATAT-TTTT-AAAATGTTTTTAAAAATC
1 ATATATTATATATATTTTCAAAATGTTTTTAAAAACC
*
2196 ATATA-TATA-A-GTTTTCAAAATGTTTTTTAAAAAACC
1 ATATATTATATATATTTTCAAAATG-TTTTT-AAAAACC
* * *
2232 ATATATTATATATGTTTTCAAAATGTTTTCAAAAAAC
1 ATATATTATATATATTTTCAAAATGTTTTTAAAAACC
* *
2269 -TATATAATATACATTTTCAAAA
1 ATATATTATATATATTTTCAAAA
2291 CTATATATAT
Statistics
Matches: 273, Mismatches: 21, Indels: 39
0.82 0.06 0.12
Matches are distributed among these distances:
33 5 0.02
34 25 0.09
35 37 0.14
36 98 0.36
37 53 0.19
38 28 0.10
39 27 0.10
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATTATATATATTTTCAAAATGTTTTTAAAAACC
Found at i:2000 original size:25 final size:25
Alignment explanation
Indices: 1952--1999 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1942 TATATATATA
1952 TATATATTAAAAAAGTTTTCAAAAC
1 TATATATTAAAAAAGTTTTCAAAAC
* *
1977 TATATATTATATAA-TTTTCAAAA
1 TATATATTAAAAAAGTTTTCAAAA
2000 AGTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
TATATATTAAAAAAGTTTTCAAAAC
Found at i:2313 original size:23 final size:23
Alignment explanation
Indices: 2264--2307 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
2254 ATGTTTTCAA
2264 AAAACTATATAATATACATTTTC
1 AAAACTATATAATATACATTTTC
*
2287 AAAACTATAT-ATATATATTTT
1 AAAACTATATAATATACATTTT
2308 TTAAAATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAACTATATAATATACATTTTC
Found at i:2340 original size:57 final size:59
Alignment explanation
Indices: 2226--2346 Score: 185
Period size: 57 Copynumber: 2.1 Consensus size: 59
2216 TGTTTTTTAA
2226 AAAACCATATATTATATATGTTTTCAAAATGTTTTCAAAAAACTATATAATATACATTTTC
1 AAAACCATATATTATATATGTTTTCAAAATGTTTTC-AAAAACTATATAATATACA-TTTC
* *
2287 AAAACTATATA-TATATAT-TTTTTAAAATGTTTTC-AAAACTATATAATATACATTTC
1 AAAACCATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATATAATATACATTTC
2343 AAAA
1 AAAA
2347 ATGATTTTTA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
56 8 0.14
57 18 0.31
59 15 0.26
60 7 0.12
61 10 0.17
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (59 bp):
AAAACCATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATATAATATACATTTC
Found at i:2348 original size:34 final size:35
Alignment explanation
Indices: 2281--2359 Score: 99
Period size: 34 Copynumber: 2.3 Consensus size: 35
2271 TATAATATAC
* **
2281 ATTTTCAAAACTATATATATATATTTTTTAAAATG
1 ATTTTCAAAACTATATATATATAATTTCAAAAATG
2316 -TTTTCAAAACTATATA-ATATACATTTCAAAAATG
1 ATTTTCAAAACTATATATATATA-ATTTCAAAAATG
*
2350 ATTTTTAAAA
1 ATTTTCAAAA
2360 ACAAAAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 5 0.13
34 25 0.66
35 8 0.21
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (35 bp):
ATTTTCAAAACTATATATATATAATTTCAAAAATG
Found at i:10821 original size:15 final size:14
Alignment explanation
Indices: 10794--10835 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
10784 TAACTTAATT
10794 AATATATTTTATTA
1 AATATATTTTATTA
10808 AATATATCTTTATTA
1 AATATAT-TTTATTA
*
10823 AATTTATTTTATT
1 AATATATTTTATT
10836 TTTATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
AATATATTTTATTA
Found at i:11720 original size:18 final size:19
Alignment explanation
Indices: 11694--11735 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
11684 GTTAAAAATT
*
11694 TAATAAAAT-AATATTTTA
1 TAATTAAATAAATATTTTA
11712 TAATTAAATAAATATTTTA
1 TAATTAAATAAATATTTTA
11731 TAATT
1 TAATT
11736 TTTAATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTAAATAAATATTTTA
Found at i:19486 original size:38 final size:38
Alignment explanation
Indices: 19404--19516 Score: 131
Period size: 38 Copynumber: 3.0 Consensus size: 38
19394 AGTGACGGTG
* * *
19404 AGGGTGTCTCGGACAAATCCCAAGCTC--AATCTATTC
1 AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
*
19440 AGGCTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
1 AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
** * **
19478 AGGGTGTCTCAGATGAATCCTGAGTTCATTGTCTATTC
1 AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
19516 A
1 A
19517 TTGATTTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 23 0.35
38 42 0.65
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (38 bp):
AGGGTGTCTCAGACAAATCCCGAGTTCATAATCTATTC
Found at i:28855 original size:18 final size:18
Alignment explanation
Indices: 28829--28863 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28819 ACCATAATTA
* *
28829 CCACTACCATATCCACCG
1 CCACCACCATAGCCACCG
28847 CCACCACCATAGCCACC
1 CCACCACCATAGCCACC
28864 ACCGCCATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.54, G:0.06, T:0.11
Consensus pattern (18 bp):
CCACCACCATAGCCACCG
Found at i:28912 original size:15 final size:15
Alignment explanation
Indices: 28847--28915 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
28837 ATATCCACCG
*
28847 CCACCACCATAGCCA
1 CCACCTCCATAGCCA
*
28862 CCACCGCCATAGCCA
1 CCACCTCCATAGCCA
* *
28877 CCACCTCCATACCCG
1 CCACCTCCATAGCCA
*
28892 CCGCCTCCATAGCCA
1 CCACCTCCATAGCCA
*
28907 CCGCCTCCA
1 CCACCTCCA
28916 AAGTTACGAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.23, C:0.57, G:0.10, T:0.10
Consensus pattern (15 bp):
CCACCTCCATAGCCA
Found at i:31533 original size:11 final size:11
Alignment explanation
Indices: 31519--31559 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
31509 ATCATTAAAT
*
31519 TTATTAAACAG
1 TTATTAAACAA
* *
31530 TTATAAAAGAA
1 TTATTAAACAA
31541 TTATTAAACAA
1 TTATTAAACAA
31552 TTATTAAA
1 TTATTAAA
31560 TTTTATCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (11 bp):
TTATTAAACAA
Found at i:36434 original size:22 final size:22
Alignment explanation
Indices: 36359--36435 Score: 59
Period size: 22 Copynumber: 3.4 Consensus size: 22
36349 TGCGAACGTA
*
36359 TTCGTTTATATGTTCA-TAATCGTG
1 TTCGTTTAT-TGTTCATTTATC--G
* *
36383 TTCGTTTAATATTCATTTAGT-G
1 TTCGTTTATTGTTCATTTA-TCG
**
36405 TTTATTTATTGTTCATTTATCG
1 TTCGTTTATTGTTCATTTATCG
36427 TTCGTTTAT
1 TTCGTTTAT
36436 ATATTCAATT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
21 1 0.02
22 24 0.59
23 5 0.12
24 10 0.24
25 1 0.02
ACGTcount: A:0.19, C:0.10, G:0.13, T:0.57
Consensus pattern (22 bp):
TTCGTTTATTGTTCATTTATCG
Found at i:36913 original size:23 final size:23
Alignment explanation
Indices: 36883--36929 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
36873 TCACTCTACG
36883 TTAAAAAGGAATATTTGAACACT
1 TTAAAAAGGAATATTTGAACACT
36906 TTAAAAAGGAATATTTGAACACT
1 TTAAAAAGGAATATTTGAACACT
36929 T
1 T
36930 GAAGGAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (23 bp):
TTAAAAAGGAATATTTGAACACT
Found at i:37935 original size:22 final size:24
Alignment explanation
Indices: 37892--37940 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
37882 TGGGTAATCA
37892 AATTTTGCATCTATATAAATTTAT
1 AATTTTGCATCTATATAAATTTAT
* *
37916 AATTTTGTAT-TAT-TAAATTTTT
1 AATTTTGCATCTATATAAATTTAT
37938 AAT
1 AAT
37941 ATAACTTACT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 3 0.13
24 9 0.39
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (24 bp):
AATTTTGCATCTATATAAATTTAT
Found at i:40365 original size:2 final size:2
Alignment explanation
Indices: 40358--40401 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
40348 TATATGTTTA
40358 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
40400 AT
1 AT
40402 TAATCTAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41368 original size:12 final size:12
Alignment explanation
Indices: 41335--41370 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41325 TGAACAGTAA
*
41335 TGAACAGTACCG
1 TGAACAGTATCG
*
41347 TGAATAGTATCG
1 TGAACAGTATCG
41359 TGAACAGTATCG
1 TGAACAGTATCG
41371 AATGCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (12 bp):
TGAACAGTATCG
Found at i:43802 original size:24 final size:23
Alignment explanation
Indices: 43729--43802 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
43719 TATCCCGAAT
* *
43729 GACCACGTAGAATTGTCCCGAAG
1 GACCACATAGAATTGTCCCAAAG
*
43752 GACCACATA-ACATTGTCCCAAAA
1 GACCACATAGA-ATTGTCCCAAAG
*
43775 GACCACATAGAATTTTTCCCAAAG
1 GACCACATAGAA-TTGTCCCAAAG
43799 GACC
1 GACC
43803 GCGTACCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.02
23 28 0.65
24 14 0.33
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.19
Consensus pattern (23 bp):
GACCACATAGAATTGTCCCAAAG
Found at i:53901 original size:13 final size:13
Alignment explanation
Indices: 53883--53907 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53873 TTCCGTTAAA
53883 TTTTTATTTTTAC
1 TTTTTATTTTTAC
53896 TTTTTATTTTTA
1 TTTTTATTTTTA
53908 TTTGATCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:56904 original size:18 final size:18
Alignment explanation
Indices: 56855--56907 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
56845 GTTGTTCGAA
* *
56855 AAAGAAAAGAAAAAAAAAG
1 AAAGAAGAG-AAAAAGAAG
56874 AAAGAAGAG-AAAAGAAG
1 AAAGAAGAGAAAAAGAAG
* *
56891 AAAGACGTGAAAAAGAA
1 AAAGAAGAGAAAAAGAA
56908 TTGAGCAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 14 0.48
18 7 0.24
19 8 0.28
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.02
Consensus pattern (18 bp):
AAAGAAGAGAAAAAGAAG
Found at i:62452 original size:17 final size:16
Alignment explanation
Indices: 62421--62454 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
62411 CACGTGAGGA
62421 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
62437 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
62454 T
1 T
62455 ACTTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:72711 original size:17 final size:16
Alignment explanation
Indices: 72680--72713 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
72670 CACGTGAGGA
72680 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
72696 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
72713 T
1 T
72714 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:73125 original size:22 final size:23
Alignment explanation
Indices: 73110--73154 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
73100 AAAGGCATAA
73110 AAAACGTGCCATAAAGACAGAAG
1 AAAACGTGCCATAAAGACAGAAG
* * *
73133 AATACGTGTCATAAAGAAAGAA
1 AAAACGTGCCATAAAGACAGAA
73155 TTATTAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.20, T:0.13
Consensus pattern (23 bp):
AAAACGTGCCATAAAGACAGAAG
Found at i:78251 original size:207 final size:208
Alignment explanation
Indices: 77895--78307 Score: 677
Period size: 207 Copynumber: 2.0 Consensus size: 208
77885 GTGTATCCAT
*
77895 ATTGCCAACTGATGAGCTATCAAATAGTTGACAGGTATTGAGATTCTGCAGCTGCTTTTTGACAA
1 ATTGCCAACTGATGAGCTATCAAATAGTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
*
77960 TTCTCATAACTGACAGGATTAGGCGTTTCCTGCTTGTTTTCTAACTACTGTGTTTCAAATAAAGA
66 TTCTCATAACTGACAGGATTAGGCGTTTCCTGCTTGGTTTCTAACTACTGTGTTTCAAATAAAGA
* * *
78025 GGCCGGGATGTCTCTAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTATCTTGAA
131 GGCCGGGATGTCTCTAGATCTATCAGACTTAACCATATGATACTCATTGGATTCATTATCTTGAA
*
78090 AATGAGCACCTAC
196 AATGAACACCTAC
* *
78103 ATTGCCAACTGATGAGCTATC-AATAGTTGACAGGTGTTGAGGTTCTGCAGCTGCTTCTTGACAA
1 ATTGCCAACTGATGAGCTATCAAATAGTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
* * *
78167 TTCTCATAACTGACAGGATTAGGGGTTTCCTGCTTGGTTTCTAAC-AGGTGTGTTTCAAATGAAG
66 TTCTCATAACTGACAGGATTAGGCGTTTCCTGCTTGGTTTCTAACTA-CTGTGTTTCAAATAAAG
* *
78231 AGGCCGGGATGTCTCTAGATCTATCGGATTTAACCATATGATACTCATTGGATTCATTATCTTGA
130 AGGCCGGGATGTCTCTAGATCTATCAGACTTAACCATATGATACTCATTGGATTCATTATCTTGA
*
78296 TAATGAACACCT
195 AAATGAACACCT
78308 CCACCACCAG
Statistics
Matches: 190, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
206 1 0.01
207 168 0.88
208 21 0.11
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (208 bp):
ATTGCCAACTGATGAGCTATCAAATAGTTGACAGGTATTGAGATTCTGCAGCTGCTTCTTGACAA
TTCTCATAACTGACAGGATTAGGCGTTTCCTGCTTGGTTTCTAACTACTGTGTTTCAAATAAAGA
GGCCGGGATGTCTCTAGATCTATCAGACTTAACCATATGATACTCATTGGATTCATTATCTTGAA
AATGAACACCTAC
Found at i:79008 original size:435 final size:431
Alignment explanation
Indices: 78162--79023 Score: 1233
Period size: 432 Copynumber: 2.0 Consensus size: 431
78152 GCTGCTTCTT
* *
78162 GACAATTCTCATAACTGACAGGATTAGGGGTTTCCTGCTTGGTTTCTAACAGGTGTGTTTCAAAT
1 GACAATTCTCATAACTGAAAGGATTAGGCGTTTCCTGCTTGGTTTCTAACAGGTGTGTTTCAAAT
* * *
78227 GAAGAGGCCGGGATGTCTCTAGATCTATCGGATTTAACCATATGATACTCATTGGATTCATTATC
66 AAAGAGGCCGGGATGTCTCTAGATCTATCAGACTTAACCATATGATACTCATTGGATTCATTATC
* * *
78292 TTGATAATGAACACCTCCACCACCAGAATCTTCTCTTTTCTCCGAACTCTGCCTGATCTCTTCAC
131 TTGATAATGAACACCTACACCACAAGAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCAC
* * *
78357 AAGCATTATTAGTCCTAGGAACATGAGGCAACTCCATACACTGTTGTTCACTCCTTTTCCACCTA
196 AAGCATTATTAGTCCTAGGAACATGAGGCAACTCCAGACACTGCTGTTCACTCCTTTCCCACCTA
* *
78422 GATTCATAAATCTTCCCAGAATCATGGTGCAGATAGCGACAAAACACTCCACGGTAACACCTGCC
261 GATTCATAAATCCTCCCAGAATCATGGTGCAGATAACGACAAAACACTCCACGGTAACACCTGCC
* * *
78487 TCGACGGAAGTGAAAACAGAATGGCATCTGTCCCTTCACCCGTCTCTTATTATCACCACTGGATT
326 TCGACGGAAGTCAAAACAGAATGGAATCTGTCCCTTCACCCGTCTCTTATTATCACCACTGAATT
*
78552 CATCTGTACACTTAAAACTGGGAGATCTACTCCTGCTTATCC
391 CATCTGTACACTTAAAACTGGGA-ACCTACTCCTGCTTATCC
* * * *
78594 GACAATTCTCATAACTGAAAGGATTATGCTTTTCCTGCTTGTTTTCTAACATGTGTGTTTCAAAT
1 GACAATTCTCATAACTGAAAGGATTAGGCGTTTCCTGCTTGGTTTCTAACAGGTGTGTTTCAAAT
** * * * *
78659 AAAGAGGTTGGGATGTCTCTAGATCTATCAGACTTAACCATGTGATACTCATTTGATTGATTATT
66 AAAGAGGCCGGGATGTCTCTAGATCTATCAGACTTAACCATATGATACTCATTGGATTCATTATC
* * * *
78724 TTGA-ACATGAGCACCTACATCACAAGAATCTTCTCTTTTCTCAGAGCTCTGCTTGATCTCTTCA
131 TTGATA-ATGAACACCTACACCACAAGAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCA
* * * * **
78788 CGAGCATTATTAGTCCTCCTA-GAAGCATTAGGTAACTCCAGATACTGCTGTTTGCTCCTTTCCC
195 CAAGCATTATTAG---TCCTAGGAA-CATGAGGCAACTCCAGACACTGCTGTTCACTCCTTTCCC
* * * * *
78852 ACCTTGATTCATAACTCCTGCCAGAATCATGGTGCAGATAACGACAAGACCCTCCACGGTAACAC
256 ACCTAGATTCATAAATCCTCCCAGAATCATGGTGCAGATAACGACAAAACACTCCACGGTAACAC
*
78917 CTGCCTCGACGGAAGTCAAAACAGAATGGAATCTGTCCCTTCACCCGTCTCTTATTTTCACCACT
321 CTGCCTCGACGGAAGTCAAAACAGAATGGAATCTGTCCCTTCACCCGTCTCTTATTATCACCACT
*** *
78982 GAATTCATCTGTATTGTTAAAACTGGGAACCTGCTCCTGCTT
386 GAATTCATCTGTACACTTAAAACTGGGAACCTACTCCTGCTT
79024 CTCCAGTTTC
Statistics
Matches: 378, Mismatches: 47, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
431 1 0.00
432 182 0.48
434 15 0.04
435 180 0.48
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (431 bp):
GACAATTCTCATAACTGAAAGGATTAGGCGTTTCCTGCTTGGTTTCTAACAGGTGTGTTTCAAAT
AAAGAGGCCGGGATGTCTCTAGATCTATCAGACTTAACCATATGATACTCATTGGATTCATTATC
TTGATAATGAACACCTACACCACAAGAATCTTCTCTTTTCTCAGAACTCTGCCTGATCTCTTCAC
AAGCATTATTAGTCCTAGGAACATGAGGCAACTCCAGACACTGCTGTTCACTCCTTTCCCACCTA
GATTCATAAATCCTCCCAGAATCATGGTGCAGATAACGACAAAACACTCCACGGTAACACCTGCC
TCGACGGAAGTCAAAACAGAATGGAATCTGTCCCTTCACCCGTCTCTTATTATCACCACTGAATT
CATCTGTACACTTAAAACTGGGAACCTACTCCTGCTTATCC
Found at i:79049 original size:30 final size:30
Alignment explanation
Indices: 79004--79454 Score: 460
Period size: 30 Copynumber: 15.3 Consensus size: 30
78994 ATTGTTAAAA
79004 CTGGGA-ACCTGCTCCTGCTTCTCCAGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* * * *
79033 CTAGAAGACGTGCTCCTGCTTCTCC-GACTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAG-TTT
*
79063 CTGGGAGACCTGCTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* *
79093 CAGGGAGACCTGCTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* *
79123 CT-GGAGACCTGTTCCTGCTTCTCCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
*
79152 CTGGGAGACCTGCTCCTGCTTCTCCTGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
*
79182 CTGGGAGACCTGCTCCTGCTTCT-CTGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAG-TTT
* * * * *
79212 CTGGGAGATCTGCTGCTGCTTCTGCAATTA
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* *
79242 CTGGGAGATCTACTCCTGCTTCTCCAGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* * * *
79272 ATGGGAGATCTGCTCCTGCTTCTTCGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* * *
79302 CTCGGACA-CAGCTCCTGCTTCT-CAGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCA-GTTT
* *
79331 CTCGGAGACCTACTCCTGC-TC-CCA-TTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
79358 CTGGGAGACCTGCTCCTGCTTCTCC-GATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAG-TTT
* * * * *
79388 CTTGGAGATCAGCTCCTGC-TC-CAATTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
* **
79416 AT-GGAGACCTGCTCCTGCTTCTCTGGTTT
1 CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
79445 CTGGGAGACC
1 CTGGGAGACC
79455 AACTAAAAAA
Statistics
Matches: 356, Mismatches: 49, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
27 34 0.10
28 10 0.03
29 73 0.21
30 237 0.67
31 2 0.01
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.34
Consensus pattern (30 bp):
CTGGGAGACCTGCTCCTGCTTCTCCAGTTT
Found at i:79316 original size:149 final size:148
Alignment explanation
Indices: 79014--79455 Score: 504
Period size: 149 Copynumber: 3.0 Consensus size: 148
79004 CTGGGAACCT
* * *
79014 GCTCCTGCTTCTCCAGTTTCTAGAAGACGTGCTCCTGCTTCTCCGACTTCTGGGAGACCTGCTCC
1 GCTCCTGCTTCTCCAGTTTCTAGGAGACCTGCTCCTGCTTCT-CGATTTCTGGGAGACCTGCTCC
* * * * * * *
79079 TGCTTCTCCGGTTTCAGGGAGACCTGCTCCTGCTTCTCCGGTTTCTGGAGACCTGTTCCTGCTTC
65 TGCTTCTCCGATTTCTGGGAGATCTACTCCTGCTTCTCCAGTTTATGGAGACCTGCTCCTGCTTC
* * * *
79144 TCCGGTTTCTGGGAGACCT
130 TTCGGTTTCTCGGACACCA
* * * *
79163 GCTCCTGCTTCTCCTGTTTCTGGGAGACCTGCTCCTGCTTCTCTGATTTCTGGGAGATCTGCTGC
1 GCTCCTGCTTCTCCAGTTTCTAGGAGACCTGCTCCTGCTTCTC-GATTTCTGGGAGACCTGCTCC
* * * *
79228 TGCTTCTGCAATTACTGGGAGATCTACTCCTGCTTCTCCAGTTTATGGGAGATCTGCTCCTGCTT
65 TGCTTCTCCGATTTCTGGGAGATCTACTCCTGCTTCTCCAGTTTAT-GGAGACCTGCTCCTGCTT
79293 CTTCGGTTTCTCGGACA-CA
129 CTTCGGTTTCTCGGACACCA
* * *
79312 GCTCCTGCTTCT-CAGGTTTCTCGGAGACCTACTCCTGC-TC-CCATTTCTGGGAGACCTGCTCC
1 GCTCCTGCTTCTCCA-GTTTCTAGGAGACCTGCTCCTGCTTCTCGATTTCTGGGAGACCTGCTCC
* * *
79374 TGCTTCTCCGATTTCTTGGAGATC-AGCTCCTGC-TC-CAATTTTATGGAGACCTGCTCCTGCTT
65 TGCTTCTCCGATTTCTGGGAGATCTA-CTCCTGCTTCTCCAGTTTATGGAGACCTGCTCCTGCTT
* *
79436 C-TCTGGTTTCTGGGAGACCA
129 CTTC-GGTTTCTCGGACACCA
79456 ACTAAAAAAA
Statistics
Matches: 250, Mismatches: 37, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
142 2 0.01
143 29 0.12
144 9 0.04
145 3 0.01
146 45 0.18
147 1 0.00
148 4 0.02
149 127 0.51
150 30 0.12
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.34
Consensus pattern (148 bp):
GCTCCTGCTTCTCCAGTTTCTAGGAGACCTGCTCCTGCTTCTCGATTTCTGGGAGACCTGCTCCT
GCTTCTCCGATTTCTGGGAGATCTACTCCTGCTTCTCCAGTTTATGGAGACCTGCTCCTGCTTCT
TCGGTTTCTCGGACACCA
Found at i:81040 original size:39 final size:38
Alignment explanation
Indices: 80985--81081 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 38
80975 ACGAAGAGGA
80985 AAATGGTGAATTAGGGATTGAGATGCGA-AGGAGAAATGAG-
1 AAATGG-GAATTAGGGATTGAGATGCGAGAGG-GAAA--AGT
*
81025 AAATGGGAATTAGGGATTGAGGTGCGAGAGGGAAAAGT
1 AAATGGGAATTAGGGATTGAGATGCGAGAGGGAAAAGT
81063 AAATGGGGAATTAGGGATT
1 AAAT-GGGAATTAGGGATT
81082 CTGGCAATTG
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
37 2 0.04
38 4 0.08
39 38 0.72
40 9 0.17
ACGTcount: A:0.38, C:0.02, G:0.39, T:0.21
Consensus pattern (38 bp):
AAATGGGAATTAGGGATTGAGATGCGAGAGGGAAAAGT
Found at i:86234 original size:39 final size:39
Alignment explanation
Indices: 86168--86264 Score: 119
Period size: 39 Copynumber: 2.5 Consensus size: 39
86158 ACGAAGAGGA
* *
86168 AAATGGTGAATTAGGAATTGAGATGCGA-AGGAGAAATGAG-
1 AAATGGGGAATTAGGGATTGAGATGCGAGAGGA-AAA--AGT
*
86208 AAA-GGGGAATTAGGGATTGAGGTGCGAGAGGAAAAAGT
1 AAATGGGGAATTAGGGATTGAGATGCGAGAGGAAAAAGT
86246 AAATGGGGAATTAGGGATT
1 AAATGGGGAATTAGGGATT
86265 CTGGCAATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
37 2 0.04
38 3 0.06
39 39 0.76
40 7 0.14
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.20
Consensus pattern (39 bp):
AAATGGGGAATTAGGGATTGAGATGCGAGAGGAAAAAGT
Found at i:89461 original size:20 final size:21
Alignment explanation
Indices: 89436--89487 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
89426 TTTTCCCAAT
*
89436 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
89456 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
89477 TCGCAATGCGA
1 TCGCAATGCGA
89488 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:89501 original size:20 final size:19
Alignment explanation
Indices: 89476--89590 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 19
89466 AATTGGGAAA
89476 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACT-ACT
*
89496 ATCGCAATACGATACTTACT
1 ATCGCAATGCGATAC-TACT
* *
89516 ATCGCAATGCGATAATACAAA
1 ATCGCAATGCGATACTAC--T
* *
89537 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACT-ACT
* * *
89557 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATACTAC-T
89577 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
89591 TTTCAAAGCG
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
19 5 0.07
20 44 0.58
21 25 0.33
22 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAATGCGATACTACT
Found at i:89541 original size:41 final size:41
Alignment explanation
Indices: 89496--89590 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
89486 GATACTGACT
* *
89496 ATCGCAATACGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATACGATACTGACTATCGCAACGCGATAATACAAA
* * *
89537 ATCGCAACGA-GATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAA-TACGATACTGACTATCGCAACGCGATAATACAAA
*
89578 ATCGCAATGCGAT
1 ATCGCAATACGAT
89591 TTTCAAAGCG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
41 44 0.98
42 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
ATCGCAATACGATACTGACTATCGCAACGCGATAATACAAA
Found at i:89542 original size:21 final size:20
Alignment explanation
Indices: 89516--89590 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
89506 GATACTTACT
*
89516 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
* * *
89537 ATCGCAACGAGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAA
*
89557 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACA-A
*
89578 ATCGCAATGCGAT
1 ATCGCAACGCGAT
89591 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:89570 original size:61 final size:62
Alignment explanation
Indices: 89473--89590 Score: 159
Period size: 61 Copynumber: 1.9 Consensus size: 62
89463 GCGAATTGGG
* * * *
89473 AAAATCGCAATGCGATACTGACTATCGCAATACGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA-ATACATAATCGCAATGCGATAATAC
* *
89534 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATACATAATCGCAATGCGAT
89591 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
60 3 0.06
61 33 0.67
62 13 0.27
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATACATAATCGCAATGCGATAATAC
Found at i:90109 original size:20 final size:20
Alignment explanation
Indices: 90055--90113 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
90045 GCGATTCTCT
**
90055 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
90075 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
90095 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
90114 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:90304 original size:25 final size:24
Alignment explanation
Indices: 90250--90304 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
90240 TGTTTATTAT
* *
90250 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
90274 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
90300 TGTTT
1 TGTTT
90305 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:91461 original size:18 final size:18
Alignment explanation
Indices: 91434--91477 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
91424 CCACTTCGGA
* *
91434 AGCCATCACCTCGCCTAG
1 AGCCATCACCTCACCCAG
*
91452 AGCTATCACCTCACCCAG
1 AGCCATCACCTCACCCAG
91470 AGCCATCA
1 AGCCATCA
91478 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.27, C:0.43, G:0.14, T:0.16
Consensus pattern (18 bp):
AGCCATCACCTCACCCAG
Found at i:92013 original size:19 final size:20
Alignment explanation
Indices: 91959--92024 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
91949 TAGTTTACTT
* *
91959 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
91979 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
91999 TCGCAATGC-GAAATGA-AA
1 TCGCAACGCGGAAATGACTA
92017 TCGCAACG
1 TCGCAACG
92025 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.21
19 6 0.15
20 25 0.64
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:92049 original size:19 final size:19
Alignment explanation
Indices: 91959--92060 Score: 63
Period size: 20 Copynumber: 5.6 Consensus size: 19
91949 TAGTTTACTT
* **
91959 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
91979 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
91999 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
92017 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
92031 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
92050 TCGCAATGCGA
1 TCGCAACGCGA
92061 TTTGTGTTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.15
16 4 0.06
18 8 0.12
19 20 0.30
20 24 0.36
21 1 0.01
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:92091 original size:14 final size:14
Alignment explanation
Indices: 92072--92129 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
92062 TTGTGTTTCG
92072 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
92086 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
92102 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
92118 CGTTGCGATTTT
1 CGTTGCGATTTT
92130 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:92110 original size:32 final size:33
Alignment explanation
Indices: 92067--92145 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
92057 GCGATTTGTG
*
92067 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
92099 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
92132 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
92146 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:92164 original size:20 final size:19
Alignment explanation
Indices: 92130--92185 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
92120 TTGCGATTTT
*
92130 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
92149 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
92169 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
92186 TTTATGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:94076 original size:14 final size:14
Alignment explanation
Indices: 94057--94092 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
94047 ATTGTTTAAT
94057 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
94071 TGATTTGTAAACGT
1 TGATTTGTAAAAGA
94085 TGATTTGT
1 TGATTTGT
94093 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:94200 original size:20 final size:20
Alignment explanation
Indices: 94175--94213 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
94165 ATGTTGAAGG
94175 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
94195 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
94214 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:94243 original size:19 final size:19
Alignment explanation
Indices: 94219--94264 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
94209 GCAACGAGAG
*
94219 AATCGCAATGTGAAATGAA
1 AATCGCAATGAGAAATGAA
94238 AATCGCAATGAGAAATGAA
1 AATCGCAATGAGAAATGAA
94257 AATCGCAA
1 AATCGCAA
94265 CGACAAGCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.50, C:0.13, G:0.20, T:0.17
Consensus pattern (19 bp):
AATCGCAATGAGAAATGAA
Found at i:94318 original size:20 final size:20
Alignment explanation
Indices: 94279--94348 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
94269 AAGCCATATT
94279 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
94298 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
*
94318 CGTTGCGATAGCCATTTTTG
1 CGTTGCGATAGCCATTTTCG
94338 CGTTGCGATAG
1 CGTTGCGATAG
94349 TCAAATGAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 14 0.29
20 35 0.71
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:94586 original size:20 final size:20
Alignment explanation
Indices: 94561--94611 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
94551 AAATGATTGC
94561 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
94581 CTTTCGCAACGCGATTCTGA
1 CTTTCGCAACGCGATTCTGA
94601 CTTTCGCAACG
1 CTTTCGCAACG
94612 AGATAATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (20 bp):
CTTTCGCAACGCGATTCTGA
Found at i:95383 original size:24 final size:24
Alignment explanation
Indices: 95356--95409 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
95346 GTATTCGAAA
*
95356 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
95380 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
95404 TTTGAT
1 TTTGAT
95410 GATGTGTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:95601 original size:12 final size:12
Alignment explanation
Indices: 95584--95608 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
95574 ATATAATCCT
95584 GAAGAAGAAAAA
1 GAAGAAGAAAAA
95596 GAAGAAGAAAAA
1 GAAGAAGAAAAA
95608 G
1 G
95609 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:97916 original size:19 final size:19
Alignment explanation
Indices: 97894--97952 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
97884 GGAAATTACT
97894 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
97913 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
97927 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
97946 ATCGCAA
1 ATCGCAA
97953 CGCTAATTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:98131 original size:14 final size:14
Alignment explanation
Indices: 98112--98148 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
98102 CATCAATTAA
98112 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
98126 ACAAATCACCTTTT
1 ACAAATCAACTTTT
98140 ACAAATCAA
1 ACAAATCAA
98149 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:99557 original size:21 final size:21
Alignment explanation
Indices: 99528--99641 Score: 52
Period size: 21 Copynumber: 5.4 Consensus size: 21
99518 GGGAGGGACT
*
99528 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGATGACAGTGGCC
* ** * *
99549 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGTGGCC
* * * *
99570 TCTCG-AGGAATGATAGGGGCC
1 TCTTGAACG-ATGACAGTGGCC
* * * *
99591 TCTTCAATGAT-AGGAGTGGAC
1 TCTTGAACGATGA-CAGTGGCC
**
99612 TCTTGAGGGATGACAGTGGCC
1 TCTTGAACGATGACAGTGGCC
99633 TCTTGAACG
1 TCTTGAACG
99642 GTGGGAGGGG
Statistics
Matches: 64, Mismatches: 25, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
20 3 0.05
21 58 0.91
22 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (21 bp):
TCTTGAACGATGACAGTGGCC
Found at i:99565 original size:42 final size:41
Alignment explanation
Indices: 99506--99708 Score: 158
Period size: 42 Copynumber: 4.8 Consensus size: 41
99496 GTGAATCGGG
* *
99506 CTCTTGAATGGTGGGAGGGACTTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGAC-TCTTCAAGGATGACAGTGGC
* * *
99548 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
99590 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
99632 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
99674 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGA
99709 TAGGCGAGTC
Statistics
Matches: 124, Mismatches: 29, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 103 0.83
43 12 0.10
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:99647 original size:84 final size:84
Alignment explanation
Indices: 99536--99708 Score: 337
Period size: 84 Copynumber: 2.1 Consensus size: 84
99526 CTTCTTCAAC
*
99536 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
99601 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
99620 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
99685 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
99704 GATGA
1 GATGA
99709 TAGGCGAGTC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:99709 original size:42 final size:42
Alignment explanation
Indices: 99536--99712 Score: 201
Period size: 42 Copynumber: 4.2 Consensus size: 42
99526 CTTCTTCAAC
* * * * *
99536 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * *
99578 AATGATAGGGGCCTCTTCAATGATAGGAGTGGACTCTTGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * * * *
99620 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
* * *
99662 AATGATAGGGGCCTCTTCAACGATAGGAGTGGACTCTTGAGG
1 GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
99704 GATGATAGG
1 GATGATAGG
99713 CGAGTCGGGC
Statistics
Matches: 108, Mismatches: 27, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 108 1.00
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGG
Found at i:100046 original size:93 final size:89
Alignment explanation
Indices: 99928--100112 Score: 291
Period size: 89 Copynumber: 2.0 Consensus size: 89
99918 ATATTTCAAA
* *
99928 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTA
99993 GCAGAATTGGCAGCAACCGAATAAATTT
62 GCAGAATTGGCAGCAACCGAATAAATTT
100021 ACTTCAACC-AAAGACAAACAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCA
1 ACTTCAACCAAAAGACAAA-AAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCA
*
100085 GTATTGGCAGCAACCGAATAAATTT
65 GAATTGGCAGCAACCGAATAAATTT
100110 ACT
1 ACT
100113 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
89 42 0.48
92 9 0.10
93 37 0.42
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (89 bp):
ACTTCAACCAAAAGACAAAAAAAAGACAAATACTAACTTCACAGTGTTAATAAACAGTTTAGCAG
AATTGGCAGCAACCGAATAAATTT
Found at i:100351 original size:63 final size:63
Alignment explanation
Indices: 100279--100472 Score: 370
Period size: 63 Copynumber: 3.1 Consensus size: 63
100269 TAAAGTAGAT
100279 ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
100342 ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
* *
100405 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCAATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
100468 ACCTC
1 ACCTC
100473 ATCACGTAAC
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 129 1.00
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.22
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACTATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:101971 original size:19 final size:19
Alignment explanation
Indices: 101918--102100 Score: 206
Period size: 19 Copynumber: 10.1 Consensus size: 19
101908 TCTTTTGGTT
*
101918 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
101937 GATAAAGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
101957 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
101974 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
101990 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
102009 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
102028 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
102047 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
102064 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
102080 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
102099 GA
1 GA
102101 TTTTGGTTTC
Statistics
Matches: 139, Mismatches: 14, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
14 18 0.13
15 2 0.01
16 4 0.03
17 4 0.03
18 2 0.01
19 93 0.67
20 16 0.12
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:102048 original size:90 final size:91
Alignment explanation
Indices: 101918--102100 Score: 296
Period size: 90 Copynumber: 2.0 Consensus size: 91
101908 TCTTTTGGTT
* **
101918 GAAATGAAAATCGCAACGAGATAAAGAGAATCGCAACGCGAAATGACTATCGCAACGAGAGAATC
1 GAAATGAAAATCGCAACGAGATAAAGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
101983 GCAACGCGAAATGAAAATCGCAACGC
66 GCAACGCGAAATGAAAATCGCAACGC
* *
102009 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
1 GAAATGAAAATCGCAACGAGATAAAGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
* *
102073 GTAACGCGAAATGAAAATCGCAATGC
66 GCAACGCGAAATGAAAATCGCAACGC
102099 GA
1 GA
102101 TTTTGGTTTC
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 65 0.76
91 20 0.24
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (91 bp):
GAAATGAAAATCGCAACGAGATAAAGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATC
GCAACGCGAAATGAAAATCGCAACGC
Found at i:102079 original size:33 final size:36
Alignment explanation
Indices: 101920--102095 Score: 161
Period size: 33 Copynumber: 4.9 Consensus size: 36
101910 TTTTGGTTGA
* * *
101920 AATGAAAATCGCAACGAGATAAAGAGAATCGCAACGCG
1 AATGAAAATCGCAACGCGA-AATGAAAATCGCAAC-CG
** *
101958 AAATGACTATCGCAA--CG--A-GAGAATCGCAACGCG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAAC-CG
101991 AAATGAAAATCGCAACGCGAAATGAAAATCGCAACGCG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAAC-CG
102029 AAATGAAAATCGCAACGCGAAATGAAAATCGCAA-CG
1 -AATGAAAATCGCAACGCGAAATGAAAATCGCAACCG
* *
102065 -A-GAGAATCGTAACGCGAAATGAAAATCGCAA
1 AATGAAAATCGCAACGCGAAATGAAAATCGCAA
102096 TGCGATTTTG
Statistics
Matches: 124, Mismatches: 8, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
33 56 0.45
34 2 0.02
35 2 0.02
36 2 0.02
37 2 0.02
38 48 0.39
39 12 0.10
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.11
Consensus pattern (36 bp):
AATGAAAATCGCAACGCGAAATGAAAATCGCAACCG
Found at i:102722 original size:20 final size:20
Alignment explanation
Indices: 102673--102711 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
102663 ACGCTATGTA
102673 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
102693 AATCGCGTTGCGAAAGTCA
1 AATCGCGTTGCGAAAGTCA
102712 ATATCTCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:102878 original size:21 final size:21
Alignment explanation
Indices: 102838--102878 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
102828 ACTGTAGACC
**
102838 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
102859 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
102879 GTGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:107177 original size:30 final size:30
Alignment explanation
Indices: 107141--107330 Score: 326
Period size: 30 Copynumber: 6.3 Consensus size: 30
107131 ATGCTTAAAA
*
107141 CTGGGAGATCTGCTCCTGCTTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
* *
107171 CTGGGAGATCTGCTCCTGCTCCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
*
107201 CTGGGAGACCTGCTCCTGCATCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
*
107231 CTGGGAGACCTGCTCCTGCATCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
107261 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
*
107291 CTGGGAGACTTGCTCCTGCTTCTCCGATTT
1 CTGGGAGACCTGCTCCTGCTTCTCCGATTT
107321 CTGGGAGACC
1 CTGGGAGACC
107331 AACTAAAACG
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 153 1.00
ACGTcount: A:0.12, C:0.32, G:0.24, T:0.32
Consensus pattern (30 bp):
CTGGGAGACCTGCTCCTGCTTCTCCGATTT
Found at i:110889 original size:9 final size:9
Alignment explanation
Indices: 110875--110999 Score: 58
Period size: 9 Copynumber: 14.6 Consensus size: 9
110865 GACCCGATTA
110875 TATATATTT
1 TATATATTT
110884 TATATATTT
1 TATATATTT
*
110893 TATAT-TAAT
1 TATATAT-TT
*
110902 TATATA-TA
1 TATATATTT
110910 TA-ATATTT
1 TATATATTT
110918 TATAT-TTT
1 TATATATTT
110926 T-T-TATTAAT
1 TATATATT--T
* *
110935 TATACA-TA
1 TATATATTT
110943 TATA-ATGTT
1 TATATAT-TT
110952 T-TATATTT
1 TATATATTT
*
110960 TTTATATTACT
1 TATATATT--T
*
110971 TATATA-TA
1 TATATATTT
110979 TA-ATATTT
1 TATATATTT
110987 TATAT-TTT
1 TATATATTT
110995 TATAT
1 TATAT
111000 TAATTATATA
Statistics
Matches: 89, Mismatches: 10, Indels: 35
0.66 0.07 0.26
Matches are distributed among these distances:
6 1 0.01
7 10 0.11
8 32 0.36
9 36 0.40
10 3 0.03
11 7 0.08
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.62
Consensus pattern (9 bp):
TATATATTT
Found at i:110932 original size:33 final size:33
Alignment explanation
Indices: 110873--111009 Score: 204
Period size: 33 Copynumber: 4.1 Consensus size: 33
110863 CCGACCCGAT
110873 TATAT-ATATTTTATATATTTTATATTAATTATA
1 TATATAATATTTTATAT-TTTTATATTAATTATA
*
110906 TATATAATATTTTATATTTTTTTATTAATTATACA
1 TATATAATATTTTATATTTTTATATTAATTAT--A
* *
110941 TATATAATGTTTTATATTTTTTATATTACTTATA
1 TATATAATATTTTATA-TTTTTATATTAATTATA
110975 TATATAATATTTTATATTTTTATATTAATTATA
1 TATATAATATTTTATATTTTTATATTAATTATA
111008 TA
1 TA
111010 ATACAAACCC
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
33 37 0.39
34 27 0.29
35 16 0.17
36 14 0.15
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
TATATAATATTTTATATTTTTATATTAATTATA
Found at i:110992 original size:25 final size:24
Alignment explanation
Indices: 110887--111003 Score: 74
Period size: 25 Copynumber: 5.1 Consensus size: 24
110877 TATATTTTAT
110887 ATATTTTATATTAATTATATATATA
1 ATATTTTATATTAATT-TATATATA
*
110912 ATATTTTATATT--TTTTTAT-TA
1 ATATTTTATATTAATTTATATATA
**
110933 AT-TATACATATATAATGTT-T-TAT-
1 ATAT-TTTATAT-TAAT-TTATATATA
* *
110956 ATTTTTTATATTACTTATATATATA
1 ATATTTTATATTAATT-TATATATA
110981 ATATTTTATATT--TTTATAT-TA
1 ATATTTTATATTAATTTATATATA
111002 AT
1 AT
111004 TATATAATAC
Statistics
Matches: 74, Mismatches: 7, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
20 1 0.01
21 14 0.19
22 14 0.19
23 13 0.18
24 7 0.09
25 25 0.34
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (24 bp):
ATATTTTATATTAATTTATATATA
Found at i:110992 original size:69 final size:68
Alignment explanation
Indices: 110873--111007 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 68
110863 CCGACCCGAT
*
110873 TATATATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTTTATTAATTAT
1 TATATATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTATATTAATTAT
110938 ACA
66 ACA
* * *
110941 TATATAATGTTTTATATTTTTTATATTACTTATATATATAATATTTTATATTTTTATATTAATTA
1 TATAT-ATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTATATTAATTA
111006 TA
65 TA
111008 TAATACAAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
68 5 0.08
69 57 0.92
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (68 bp):
TATATATATTTTATATATTTTATATTAATTATATATATAATATTTTATATTTTTATATTAATTAT
ACA
Found at i:118794 original size:4 final size:4
Alignment explanation
Indices: 118680--118774 Score: 172
Period size: 4 Copynumber: 23.8 Consensus size: 4
118670 TATTTCTAAT
*
118680 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
118728 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
118775 TATATATATA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 87 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:118801 original size:12 final size:12
Alignment explanation
Indices: 118680--118798 Score: 148
Period size: 12 Copynumber: 9.9 Consensus size: 12
118670 TATTTCTAAT
*
118680 ATACATACATAC
1 ATACATATATAC
*
118692 ATACATACATAC
1 ATACATATATAC
*
118704 ATACATACATAC
1 ATACATATATAC
118716 ATACATATATAC
1 ATACATATATAC
*
118728 ATACATACATAC
1 ATACATATATAC
118740 ATACATATATAC
1 ATACATATATAC
*
118752 ATACATACATAC
1 ATACATATATAC
* *
118764 ATACATACATAT
1 ATACATATATAC
* *
118776 ATATATATATAT
1 ATACATATATAC
*
118788 ATATATATATA
1 ATACATATATA
118799 TATTATCTTC
Statistics
Matches: 100, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 100 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (12 bp):
ATACATATATAC
Found at i:118928 original size:27 final size:25
Alignment explanation
Indices: 118848--118935 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 25
118838 TTTTATTCCT
* *
118848 TTTTTATTGATTTAT-TTT-TTATA
1 TTTTTATTTATTTATCTTTGTTTTA
118871 -TTTTATTTATTTATCTTTGTTTCT-
1 TTTTTATTTATTTATCTTTGTTT-TA
118895 TTGTTTATCTTATTCTAT-TTTGTCTTTA
1 TT-TTTAT-TTATT-TATCTTTGT-TTTA
*
118923 TTTTTATTCATTT
1 TTTTTATTTATTT
118936 CTGTTTCACT
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
22 13 0.25
23 3 0.06
24 2 0.04
25 3 0.06
26 9 0.17
27 16 0.30
28 7 0.13
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.73
Consensus pattern (25 bp):
TTTTTATTTATTTATCTTTGTTTTA
Found at i:128429 original size:20 final size:19
Alignment explanation
Indices: 128403--128472 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
128393 CCGTTATACA
128403 GGGGGAATCGGTACCCCCTG
1 GGGGGAATC-GTACCCCCTG
* *
128423 AGGGGAAATCTGTTCCCCCTG
1 -GGGGGAATC-GTACCCCCTG
128444 GGGGGAATCGTACCCCCTGG
1 GGGGGAATCGTACCCCCT-G
128464 GGGGGAATC
1 GGGGGAATC
128473 TGTTCCCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 8 0.19
20 18 0.42
21 17 0.40
ACGTcount: A:0.17, C:0.27, G:0.39, T:0.17
Consensus pattern (19 bp):
GGGGGAATCGTACCCCCTG
Found at i:128432 original size:21 final size:20
Alignment explanation
Indices: 128402--128472 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 20
128392 ACCGTTATAC
128402 AGGGGGAATCGGTACCCCCTG
1 AGGGGGAATC-GTACCCCCTG
* *
128423 AGGGGAAATCTGTTCCCCCTG
1 AGGGGGAATC-GTACCCCCTG
128444 -GGGGGAATCGTACCCCCTG
1 AGGGGGAATCGTACCCCCTG
*
128463 GGGGGGAATC
1 AGGGGGAATC
128473 TGTTCCCTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
19 9 0.20
20 17 0.39
21 18 0.41
ACGTcount: A:0.18, C:0.27, G:0.38, T:0.17
Consensus pattern (20 bp):
AGGGGGAATCGTACCCCCTG
Found at i:128458 original size:40 final size:41
Alignment explanation
Indices: 128403--128479 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
128393 CCGTTATACA
128403 GGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
1 GGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
* *
128444 GGGGGAATC-GTACCCCCTGGGGGGGAATCTGTTCCC
1 GGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCC
128480 TTCCCCCTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 25 0.74
41 9 0.26
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.19
Consensus pattern (41 bp):
GGGGGAATCGGTACCCCCTGAGGGGAAATCTGTTCCCCCTG
Found at i:128508 original size:21 final size:21
Alignment explanation
Indices: 128413--128509 Score: 63
Period size: 21 Copynumber: 4.5 Consensus size: 21
128403 GGGGGAATCG
*
128413 GTACCCCCTGAGGGGAAATCT
1 GTACCCCCTGAGGGGAAATTT
* * *
128434 GTTCCCCCTG-GGGGGAA-TC
1 GTACCCCCTGAGGGGAAATTT
* *
128453 GTACCCCCTGGGGGGGAATCTGTT
1 GTACCCCCT-GAGGGGAA-AT-TT
* *
128477 CCCTTCCCCCTGAGGGGAAATTT
1 --GTACCCCCTGAGGGGAAATTT
128500 GTACCCCCTG
1 GTACCCCCTG
128510 GACAATCTGA
Statistics
Matches: 55, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
19 8 0.15
20 7 0.13
21 22 0.40
23 2 0.04
24 2 0.04
25 7 0.13
26 7 0.13
ACGTcount: A:0.15, C:0.32, G:0.30, T:0.23
Consensus pattern (21 bp):
GTACCCCCTGAGGGGAAATTT
Found at i:130450 original size:3 final size:3
Alignment explanation
Indices: 130442--130479 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
130432 TACATCCTCA
* *
130442 TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
130480 CCTTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:131915 original size:21 final size:20
Alignment explanation
Indices: 131890--131971 Score: 119
Period size: 21 Copynumber: 4.0 Consensus size: 20
131880 CATTAGACAA
131890 GGGGAATCGGTACCCCCTAGG
1 GGGGAATCGGTACCCCCT-GG
* *
131911 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCGGTACCCCCTGG
131931 GGGGAATCGGTACCCCCTGGG
1 GGGGAATCGGTACCCCCT-GG
*
131952 GGGGAATCTGTACCCCCTGG
1 GGGGAATCGGTACCCCCTGG
131972 ACAATCTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 20 0.36
21 35 0.64
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (20 bp):
GGGGAATCGGTACCCCCTGG
Found at i:131947 original size:41 final size:41
Alignment explanation
Indices: 131890--131971 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
131880 CATTAGACAA
*
131890 GGGGAATCGGTACCCCCTAGGGGGGAATCTGTTCCCCCTGG
1 GGGGAATCGGTACCCCCTAGGGGGGAATCTGTACCCCCTGG
*
131931 GGGGAATCGGTACCCCCTGGGGGGGAATCTGTACCCCCTGG
1 GGGGAATCGGTACCCCCTAGGGGGGAATCTGTACCCCCTGG
131972 ACAATCTGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.15, C:0.29, G:0.38, T:0.18
Consensus pattern (41 bp):
GGGGAATCGGTACCCCCTAGGGGGGAATCTGTACCCCCTGG
Found at i:133608 original size:7 final size:7
Alignment explanation
Indices: 133596--133640 Score: 63
Period size: 7 Copynumber: 6.1 Consensus size: 7
133586 TAAATTGAAA
133596 AAAAAAG
1 AAAAAAG
133603 AAAAAAG
1 AAAAAAG
*
133610 AGAAAATG
1 A-AAAAAG
133618 AAAAAAG
1 AAAAAAG
133625 AACAAAAG
1 AA-AAAAG
133633 AAAAAAG
1 AAAAAAG
133640 A
1 A
133641 GGAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 21 0.62
8 13 0.38
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:133620 original size:15 final size:15
Alignment explanation
Indices: 133597--133647 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
133587 AAATTGAAAA
133597 AAAAAGAAAAAAGAG
1 AAAAAGAAAAAAGAG
*
133612 AAAATGAAAAAAGA-
1 AAAAAGAAAAAAGAG
133626 ACAAAAGAAAAAAGAGG
1 A-AAAAGAAAAAAGA-G
133643 AAAAA
1 AAAAA
133648 ATAAGGTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 1 0.03
15 25 0.81
16 4 0.13
17 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAAAAGAG
Found at i:134978 original size:110 final size:110
Alignment explanation
Indices: 134765--134978 Score: 295
Period size: 110 Copynumber: 1.9 Consensus size: 110
134755 TCCCAATTTT
* *
134765 AGAGCCAATTTCAACTTCACAGTGAATGATATTGGACTCAAGACAACACAAGCTCAACTTTACAA
1 AGAGCCAATTTCAACTTCACAGTGAATGATATTAGACTCAAGACAACACAAGCTCAACTTCACAA
* ** * *
134830 TGAAGGGGTGGCTGATTGTCAACAAACAACTTTTCAGTTTTATTC
66 CGAAGGGGCAGCTGACTGTCAACAAACAACTTTCCAGTTTTATTC
* * * *
134875 AGAGTCAATTTCAACTTCACAGTGAATGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGTGAATGATATTAGACTCAAGACAACACAAGCTCAACTTCACAA
* *
134940 CGAAGGGGCAGCTGACTGTCAATAAATAA-TTTCCCAGTT
66 CGAAGGGGCAGCTGACTGTCAACAAACAACTTT-CCAGTT
134979 CCAGAACCAA
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 3 0.03
110 87 0.97
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (110 bp):
AGAGCCAATTTCAACTTCACAGTGAATGATATTAGACTCAAGACAACACAAGCTCAACTTCACAA
CGAAGGGGCAGCTGACTGTCAACAAACAACTTTCCAGTTTTATTC
Found at i:136499 original size:30 final size:30
Alignment explanation
Indices: 136465--136531 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
136455 TTTGTTTTTT
* * * *
136465 TTAAAAACGTTTTTG-GTTTTTGAAAAATGA
1 TTAAAAACGCTTTCGAGATTTTGAAAAA-AA
136495 TTAAAAACGCTTTCGAGATTTTGAAAAAAA
1 TTAAAAACGCTTTCGAGATTTTGAAAAAAA
136525 TTAAAAA
1 TTAAAAA
136532 TATTATTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (30 bp):
TTAAAAACGCTTTCGAGATTTTGAAAAAAA
Found at i:136948 original size:2 final size:2
Alignment explanation
Indices: 136943--136993 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
136933 TTTCCTTTTT
*
136943 TA TA TA T- TA CA T- TA TA -A 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
136982 TA -A TA TA TA TA T
1 TA TA TA TA TA TA T
136994 TATGATTACT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:136960 original size:28 final size:28
Alignment explanation
Indices: 136907--136960 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
136897 TACAAATTGG
* *
136907 TCCTTTTTCTAAATCTTAATTTTAATTT
1 TCCTTTTTCTAAATATTAATTATAATTT
*
136935 TCCTTTTT-TATATATTACATTATAAT
1 TCCTTTTTCTAAATATTA-ATTATAAT
136961 ATATATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (28 bp):
TCCTTTTTCTAAATATTAATTATAATTT
Found at i:136974 original size:25 final size:26
Alignment explanation
Indices: 136943--137002 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 26
136933 TTTCCTTTTT
136943 TATATATTACAT-TATAATATATATA
1 TATATATTACATATATAATATATATA
*
136968 TATATA-TATATATATAATATATATA
1 TATATATTACATATATAATATATATA
136993 T-TATGATTAC
1 TATAT-ATTAC
137003 TTTTTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.23
25 21 0.70
26 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (26 bp):
TATATATTACATATATAATATATATA
Found at i:137139 original size:2 final size:2
Alignment explanation
Indices: 137132--137162 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
137122 CCACAAGCTA
137132 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
137163 CTTCTTTTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:137234 original size:15 final size:14
Alignment explanation
Indices: 137216--137286 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 14
137206 ATTTTATTGA
*
137216 TTTATTTTTTTATAT
1 TTTATTTTTTTAT-C
*
137231 TTTATTTATTTATC
1 TTTATTTTTTTATC
*
137245 TTTATTTCTTTTTTC
1 TTTATTT-TTTTATC
*
137260 ATCTTATTCTATTTTGTC
1 -T-TTATT-T-TTTTATC
137278 TTTATTTTT
1 TTTATTTTT
137287 ATTCATTTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.20
15 18 0.39
16 6 0.13
17 6 0.13
18 7 0.15
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.75
Consensus pattern (14 bp):
TTTATTTTTTTATC
Found at i:137256 original size:23 final size:23
Alignment explanation
Indices: 137194--137250 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
137184 TCATTTATCC
*
137194 TATTTTATTCCTATTTTATTGATT
1 TATTTTATT-ATATTTTATTGATT
* *
137218 TATTTTTTTATATTTTATTTATT
1 TATTTTATTATATTTTATTGATT
137241 TATCTTTATT
1 TAT-TTTATT
137251 TCTTTTTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (23 bp):
TATTTTATTATATTTTATTGATT
Found at i:139530 original size:16 final size:16
Alignment explanation
Indices: 139495--139538 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
139485 TCAAACGTAT
* **
139495 TTTTAATAATTTTATT
1 TTTTAATAATTTAAAA
139511 TTTTAATAATTTAAAA
1 TTTTAATAATTTAAAA
*
139527 TTTTCATAATTT
1 TTTTAATAATTT
139539 TTTTCTGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATAATTTAAAA
Found at i:141509 original size:385 final size:385
Alignment explanation
Indices: 140799--141574 Score: 1498
Period size: 385 Copynumber: 2.0 Consensus size: 385
140789 ATAGGATGCG
*
140799 TAAATATAGTTTGGTATTTGAATTTTTACCTTTGCATTATCTTAATCCAAAAAAAGAAGATCAAA
1 TAAATATAGTTTGGTATTTGAATTTTTACCTTTGCATTATCCTAATCCAAAAAAAGAAGATCAAA
140864 ACAAAATTAAGAGGATTAGATCTGAAAACTGGAGTATTCACCTCACGACAAATTAAAACGGCCAC
66 ACAAAATTAAGAGGATTAGATCTGAAAACTGGAGTATTCACCTCACGACAAATTAAAACGGCCAC
*
140929 AAATAATTTTGATGCAGCAAACAAGATTGGGGAAGGTGGTTTGGATCTGTGTATAAGGTGACATA
131 AAATAATTTCGATGCAGCAAACAAGATTGGGGAAGGTGGTTTGGATCTGTGTATAAGGTGACATA
140994 CAACTCTACTACACGCAGAGGAAACCAGAGTAAAGACTAAAGAAGACGAAAAAGGCGTACCTGAA
196 CAACTCTACTACACGCAGAGGAAACCAGAGTAAAGACTAAAGAAGACGAAAAAGGCGTACCTGAA
*
141059 TAAGATGGAGACCAAAGTTTGAAACTTAGAGAAAAAGAACTATCAGAATATCGATGCAATAACAA
261 TAAGATGGAGACCAAAGTTTGAAACTTAGAGAAAAAGAACTATCAGAAAATCGATGCAATAACAA
141124 GCAAAGCACAAGAGGTTTGAAAGAAAAAAATTATTCATAAACTTATCCCTAATATTTGGT
326 GCAAAGCACAAGAGGTTTGAAAGAAAAAAATTATTCATAAACTTATCCCTAATATTTGGT
141184 TAAATATAGTTTGGTATTTGAATTTTTACCTTTGCATTATCCTAATCCAAAAAAAGAAGATCAAA
1 TAAATATAGTTTGGTATTTGAATTTTTACCTTTGCATTATCCTAATCCAAAAAAAGAAGATCAAA
*
141249 ACAAAATTAAGAGGATTAGATCTGAAAATTGGAGTATTCACCTCACGACAAATTAAAACGGCCAC
66 ACAAAATTAAGAGGATTAGATCTGAAAACTGGAGTATTCACCTCACGACAAATTAAAACGGCCAC
141314 AAATAATTTCGATGCAGCAAACAAGATTGGGGAAGGTGGTTTGGATCTGTGTATAAGGTGACATA
131 AAATAATTTCGATGCAGCAAACAAGATTGGGGAAGGTGGTTTGGATCTGTGTATAAGGTGACATA
*
141379 CAACTCTACTACACGCAGAGGAAACCAGAGTAAATACTAAAGAAGACGAAAAAGGCGTACCTGAA
196 CAACTCTACTACACGCAGAGGAAACCAGAGTAAAGACTAAAGAAGACGAAAAAGGCGTACCTGAA
141444 TAAGATGGAGACCAAAGTTTGAAACTTAGAGAAAAAGAACTATCAGAAAATCGATGCAATAACAA
261 TAAGATGGAGACCAAAGTTTGAAACTTAGAGAAAAAGAACTATCAGAAAATCGATGCAATAACAA
*
141509 GCAAAGCATAAGAGGTTTGAAAGAAAAAAATTATTCATAAACTTATCCCTAATATTTGGT
326 GCAAAGCACAAGAGGTTTGAAAGAAAAAAATTATTCATAAACTTATCCCTAATATTTGGT
141569 TAAATA
1 TAAATA
141575 ATAAGTTATA
Statistics
Matches: 385, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
385 385 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.24
Consensus pattern (385 bp):
TAAATATAGTTTGGTATTTGAATTTTTACCTTTGCATTATCCTAATCCAAAAAAAGAAGATCAAA
ACAAAATTAAGAGGATTAGATCTGAAAACTGGAGTATTCACCTCACGACAAATTAAAACGGCCAC
AAATAATTTCGATGCAGCAAACAAGATTGGGGAAGGTGGTTTGGATCTGTGTATAAGGTGACATA
CAACTCTACTACACGCAGAGGAAACCAGAGTAAAGACTAAAGAAGACGAAAAAGGCGTACCTGAA
TAAGATGGAGACCAAAGTTTGAAACTTAGAGAAAAAGAACTATCAGAAAATCGATGCAATAACAA
GCAAAGCACAAGAGGTTTGAAAGAAAAAAATTATTCATAAACTTATCCCTAATATTTGGT
Found at i:144388 original size:25 final size:25
Alignment explanation
Indices: 144358--144428 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
144348 CCTACGAAGT
*
144358 CAAATCAGATCAGCTAGCCATATTG
1 CAAATCAGATCAACTAGCCATATTG
* * *
144383 TAAATCATATCAACTAGCTATATTG
1 CAAATCAGATCAACTAGCCATATTG
* *
144408 CAAATCAGATAAAATAGCCAT
1 CAAATCAGATCAACTAGCCAT
144429 GTACACATGA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (25 bp):
CAAATCAGATCAACTAGCCATATTG
Found at i:144467 original size:2 final size:2
Alignment explanation
Indices: 144456--144531 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
144446 TACATGTATT
144456 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
144497 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
144532 TGCACACAAG
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 72 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:146544 original size:20 final size:20
Alignment explanation
Indices: 146506--146545 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
146496 CCTAGAACCG
* *
146506 GTTCGAGTTAACTTAAATCA
1 GTTCGAGTCAACTCAAATCA
*
146526 GTTCGAGTCAACTCGAATCA
1 GTTCGAGTCAACTCAAATCA
146546 ACCTGAACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (20 bp):
GTTCGAGTCAACTCAAATCA
Found at i:148937 original size:27 final size:27
Alignment explanation
Indices: 148882--148941 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
148872 TGCTCGGTGT
* *
148882 TCACTGTTGCGACAGTTGGAGAGGCTG
1 TCACTGTTGCGACAGTTGGAAAAGCTG
* * *
148909 TCACTGTTGCGGCGGTTGGAAAAGTTG
1 TCACTGTTGCGACAGTTGGAAAAGCTG
148936 TCACTG
1 TCACTG
148942 GCGTTGGAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.28
Consensus pattern (27 bp):
TCACTGTTGCGACAGTTGGAAAAGCTG
Found at i:151373 original size:2 final size:2
Alignment explanation
Indices: 151366--151403 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
151356 GATTATACAT
151366 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
151404 GAGATTCCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152853 original size:2 final size:2
Alignment explanation
Indices: 152841--152899 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
152831 TGTAGCCATA
152841 AT AT CAT 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
152884 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
152900 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:152904 original size:2 final size:2
Alignment explanation
Indices: 152899--152923 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
152889 TATATATATA
152899 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
152924 AAACCCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:153303 original size:37 final size:37
Alignment explanation
Indices: 153253--153398 Score: 238
Period size: 37 Copynumber: 3.9 Consensus size: 37
153243 AGACTCGATC
* *
153253 TTGATTTGCTTCACTACTCTTCCGTGAATGCTTAATA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
*
153290 TTGATTTGCTTCACTACTCTTCCTTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
*
153327 TTGATTTGTTTCACTACTCTTCCGTGAAGGCTTAAGA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
* *
153364 TTAATTTGGTTCACTACTCTTCCGTGAAGGCTTAA
1 TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAA
153399 AATAGCTCAG
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 102 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (37 bp):
TTGATTTGCTTCACTACTCTTCCGTGAAGGCTTAAGA
Found at i:153465 original size:42 final size:42
Alignment explanation
Indices: 153416--153522 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
153406 CAGAGAACTT
*
153416 ATCATCTTGCTCGAAAGGCTTACAGATAACCCGAAGGATTTA
1 ATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTA
* ** * *
153458 ATCATCTTGCTCGAAAGACTGATTGATGACCCGAATGATTTA
1 ATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTA
* * *
153500 ATAATCATGCTCAAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTAC
153523 TGATGGCCCG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (42 bp):
ATCATCTTGCTCGAAAGACTTACAGATAACCCGAAGGATTTA
Found at i:153923 original size:235 final size:233
Alignment explanation
Indices: 153458--154095 Score: 893
Period size: 235 Copynumber: 2.7 Consensus size: 233
153448 GAAGGATTTA
* ** * * *
153458 ATCATCTTGCTCGAAAGACTGATTGATGACCCGAATGATTTAATAATCATGCTCAAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTAC
* *
153523 TGATGGCCCGACGGTCTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTC
66 TGATGG-CCGAAGGTCTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTT
* * *
153588 CATTTTCAAAAGTCATTAAATGAGAAACTTTGAAAATCGCTCTCATTTTCCAAACTCATGTGAAC
130 CATTTTCAAAAATCATTAAATGAGAAACTTTGAAAATCGCTCTAATTTTCCAAACTCATGTGAAA
* *
153653 ACATCTTGCCCGAAGGTCCTATGGATGGCCCAAAAGACTT
195 ACATCTT-CCCAAAGGTCCTATAGATGGCCCAAAAGACTT
* *
153693 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAATACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTAC
* *
153758 TGATGGCTCGAAGGTCTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTGCTTTTCAAATATTT
66 TGATGGC-CGAAGGTCTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTT
* * *
153823 CATTTTCAAAAAACATTAAATGAGAAACTTTGAAAATCGATTTCTAATTTT-CAAATTCATGTGA
130 CATTTTCAAAAATCATTAAATGAGAAACTTTGAAAATCG--CTCTAATTTTCCAAACTCATGTGA
* *
153887 AAACATCCTT-CCAAAGGTCTTATAGATGGTCCAAAAGACTT
193 AAACAT-CTTCCCAAAGGTCCTATAGATGGCCCAAAAGACTT
* *
153928 ATCATCTTGCTTGAAAGACCTACAGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTAC
1 ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTAC
* * * * ***
153993 TGATGGCCTGAATGACTTACTAAGTAAGAAAATTTGAAAATTGCTTTCTTACTTTTCAAAAATTT
66 TGATGGCC-GAAGGTCTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTT
* *
154058 CATTTTCAAAAATGATTTAAATGAGAAACTTTGGAAAT
130 CATTTTCAAAAATCA-TTAAATGAGAAACTTTGAAAAT
154096 TACTTTCTCA
Statistics
Matches: 360, Mismatches: 37, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
234 2 0.01
235 309 0.86
236 38 0.11
237 11 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (233 bp):
ATCATCTTGCTCGAAAGACTTACAGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTAC
TGATGGCCGAAGGTCTTACTAAGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTC
ATTTTCAAAAATCATTAAATGAGAAACTTTGAAAATCGCTCTAATTTTCCAAACTCATGTGAAAA
CATCTTCCCAAAGGTCCTATAGATGGCCCAAAAGACTT
Found at i:163471 original size:20 final size:21
Alignment explanation
Indices: 163446--163487 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
163436 GACCTTGAGG
163446 ATTAAAA-AAAAATAAGAGAA
1 ATTAAAATAAAAATAAGAGAA
163466 ATTAAAATAAAAATAAGAGAA
1 ATTAAAATAAAAATAAGAGAA
163487 A
1 A
163488 AAGGTTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
ATTAAAATAAAAATAAGAGAA
Found at i:164022 original size:20 final size:20
Alignment explanation
Indices: 163997--164067 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
163987 CTACAGTTGT
163997 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
** *
164017 CGTTGCGATAGTCTATAGTT-G
1 CGTTGCGATTTTCCAT--TTCG
164038 TCGTTGCGATTTTCCATTTCG
1 -CGTTGCGATTTTCCATTTCG
164059 CGTTGCGAT
1 CGTTGCGAT
164068 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 24 0.59
21 2 0.05
22 15 0.37
ACGTcount: A:0.13, C:0.21, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:164030 original size:42 final size:42
Alignment explanation
Indices: 163971--164089 Score: 220
Period size: 42 Copynumber: 2.8 Consensus size: 42
163961 CTATCGCAAA
*
163971 TTCGCGTTGCAATAGTCTACAGTTGTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAT
*
164013 TTCGCGTTGCGATAGTCTATAGTTGTCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAT
164055 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT
1 TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGAT
164090 AGTTAAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.40
Consensus pattern (42 bp):
TTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAT
Found at i:164045 original size:22 final size:22
Alignment explanation
Indices: 163975--164092 Score: 95
Period size: 22 Copynumber: 5.5 Consensus size: 22
163965 CGCAAATTCG
* *
163975 CGTTGCAATAGTCTACAGTTGT
1 CGTTGCGATAGTCTATAGTTGT
** *
163997 CGTTGCGATTTTCCAT--TTCG-
1 CGTTGCGATAGTCTATAGTT-GT
164017 CGTTGCGATAGTCTATAGTTGT
1 CGTTGCGATAGTCTATAGTTGT
** *
164039 CGTTGCGATTTTCCAT--TTCG-
1 CGTTGCGATAGTCTATAGTT-GT
*
164059 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTATAGTTGT
164081 CGTTGCGATAGT
1 CGTTGCGATAGT
164093 TAAAAAAAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
20 29 0.40
21 4 0.05
22 40 0.55
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.40
Consensus pattern (22 bp):
CGTTGCGATAGTCTATAGTTGT
Found at i:164202 original size:43 final size:43
Alignment explanation
Indices: 164141--164227 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
164131 AAGATAGTAT
* *
164141 CCGCGCGGATGTGTCGAAGACACGTATTACCACGACCACGACC
1 CCGCGCGGACGTGTCGAAGACACGTATTACCACGACCACAACC
164184 CCGCGCGGACGTGTCGAAGACACGTATTACCACGACCACAACC
1 CCGCGCGGACGTGTCGAAGACACGTATTACCACGACCACAACC
164227 C
1 C
164228 GAGACGAGAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.37, G:0.24, T:0.13
Consensus pattern (43 bp):
CCGCGCGGACGTGTCGAAGACACGTATTACCACGACCACAACC
Found at i:164735 original size:6 final size:6
Alignment explanation
Indices: 164724--164765 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
164714 TCTCGTCTCG
164724 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
164766 ACATGTCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:170196 original size:2 final size:2
Alignment explanation
Indices: 170189--170213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
170179 ACTCATACTA
170189 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
170214 GGGCCAGTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:170736 original size:21 final size:22
Alignment explanation
Indices: 170706--170747 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
170696 AATATTTTTC
**
170706 TTTTATTATATTGTTAAATATT
1 TTTTATTATATTCATAAATATT
170728 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
170748 ATATATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATTATATTCATAAATATT
Found at i:171252 original size:10 final size:10
Alignment explanation
Indices: 171237--171292 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
171227 TTAATAAATT
171237 AACGAACATA
1 AACGAACATA
*
171247 AACGAACATG
1 AACGAACATA
*
171257 AAC-ATAAATGA
1 AACGA-ACAT-A
*
171268 ACACAAACATA
1 A-ACGAACATA
171279 AACGAACATA
1 AACGAACATA
171289 AACG
1 AACG
171293 TTGGAGACCC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 1 0.03
10 27 0.73
11 3 0.08
12 5 0.14
13 1 0.03
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:171291 original size:16 final size:16
Alignment explanation
Indices: 171241--171291 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
171231 TAAATTAACG
*
171241 AACATAAACGAACATG
1 AACATAAACGAACATA
* *
171257 AACATAAATGAACACA
1 AACATAAACGAACATA
171273 AACATAAACGAACATA
1 AACATAAACGAACATA
171289 AAC
1 AAC
171292 GTTGGAGACC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.61, C:0.20, G:0.08, T:0.12
Consensus pattern (16 bp):
AACATAAACGAACATA
Found at i:171530 original size:36 final size:35
Alignment explanation
Indices: 171490--171566 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 35
171480 AAAAAATTAA
171490 GAGCTCGATTAAAACTCGAGACTCAAGCTCGATTCT
1 GAGCTCGATTAAAACTCGAGACTCAA-CTCGATTCT
* * ** *
171526 GAGCTCGATTCAAGCTCGATTCTGAACTCGATTCT
1 GAGCTCGATTAAAACTCGAGACTCAACTCGATTCT
171561 GAGCTC
1 GAGCTC
171567 AATTCAAGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
35 15 0.42
36 21 0.58
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (35 bp):
GAGCTCGATTAAAACTCGAGACTCAACTCGATTCT
Found at i:171532 original size:12 final size:12
Alignment explanation
Indices: 171515--171584 Score: 90
Period size: 12 Copynumber: 6.0 Consensus size: 12
171505 TCGAGACTCA
171515 AGCTCGATTCTG
1 AGCTCGATTCTG
*
171527 AGCTCGATTC-A
1 AGCTCGATTCTG
171538 AGCTCGATTCTG
1 AGCTCGATTCTG
*
171550 AACTCGATTCTG
1 AGCTCGATTCTG
* *
171562 AGCTCAATTC-A
1 AGCTCGATTCTG
171573 AGCTCGATTCTG
1 AGCTCGATTCTG
171585 TAACATCCTC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 19 0.40
12 29 0.60
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (12 bp):
AGCTCGATTCTG
Found at i:171542 original size:23 final size:23
Alignment explanation
Indices: 171512--171582 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
171502 AACTCGAGAC
171512 TCAAGCTCGATTCTGAGCTCGAT
1 TCAAGCTCGATTCTGAGCTCGAT
*
171535 TCAAGCTCGATTCTGAACTCGAT
1 TCAAGCTCGATTCTGAGCTCGAT
* * *
171558 TCTGAGCTCAATTC-AAGCTCGAT
1 TC-AAGCTCGATTCTGAGCTCGAT
171581 TC
1 TC
171583 TGTAACATCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 33 0.79
24 9 0.21
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (23 bp):
TCAAGCTCGATTCTGAGCTCGAT
Found at i:172493 original size:64 final size:63
Alignment explanation
Indices: 172395--172515 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 63
172385 ACTTTTTTAA
* *
172395 AATAAAAAAGATCGAATGCAATTAGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCATT
1 AATAAAAAAGATCGAATGCAATTAGTGCACCGATGCACAA-GCAGTGCATCGATGCATCCCATT
* * * *
172458 AATAATAAAATATCGAATGTATTTTA-TGCACCGATGCACAAGTAGTGCATCGATGCAT
1 AATAA-AAAAGATCGAATGCA-ATTAGTGCACCGATGCACAAGCAGTGCATCGATGCAT
172516 ACCTTCATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
63 7 0.14
64 39 0.80
65 3 0.06
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (63 bp):
AATAAAAAAGATCGAATGCAATTAGTGCACCGATGCACAAGCAGTGCATCGATGCATCCCATT
Done.