Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007864.1 Hibiscus syriacus cultivar Beakdansim tig00110236_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: 1537186
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:12708 original size:22 final size:21
Alignment explanation
Indices: 12666--12705 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12656 GAGCTTATTT
*
12666 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
12687 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
12706 ACAATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:15292 original size:23 final size:23
Alignment explanation
Indices: 15241--15310 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
15231 GTCAATTAGA
* ** *
15241 ATATATATGTGGTCCTTAAGGAG
1 ATATCTATGTGGTCCTTCGGGAC
*
15264 AAATCTATGTGGTCCTTCGGGAC
1 ATATCTATGTGGTCCTTCGGGAC
* *
15287 ATATCTACGCGGTCCTTCGGGAC
1 ATATCTATGTGGTCCTTCGGGAC
15310 A
1 A
15311 ATTTTATATG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
ATATCTATGTGGTCCTTCGGGAC
Found at i:19701 original size:23 final size:23
Alignment explanation
Indices: 19650--19702 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
19640 GTCAATTGGA
* *
19650 ATATATATGTGGTCCTTAAGGAG
1 ATATCTATGTGGTCCTTAAGGAC
* **
19673 AAATCTATGTGGTCCTTCGGGAC
1 ATATCTATGTGGTCCTTAAGGAC
19696 ATATCTA
1 ATATCTA
19703 CACGGTCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (23 bp):
ATATCTATGTGGTCCTTAAGGAC
Found at i:30242 original size:15 final size:16
Alignment explanation
Indices: 30222--30254 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
30212 TGCTTAACTG
30222 AAAATATTTTTT-TGA
1 AAAATATTTTTTGTGA
30237 AAAATATTTTTTGTGA
1 AAAATATTTTTTGTGA
30253 AA
1 AA
30255 TAAATTACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
AAAATATTTTTTGTGA
Found at i:30607 original size:24 final size:25
Alignment explanation
Indices: 30580--30631 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
30570 AATATTATAT
30580 TATATTTTAA-AATTATTAATAAAA
1 TATATTTTAATAATTATTAATAAAA
* * *
30604 TATATTTTAATTATTTTTATTAAAA
1 TATATTTTAATAATTATTAATAAAA
30629 TAT
1 TAT
30632 TATTAGGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATATTTTAATAATTATTAATAAAA
Found at i:30780 original size:23 final size:23
Alignment explanation
Indices: 30754--30819 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
30744 TTAAAAAGTT
*
30754 ATAATATCATATATTATTATAGC
1 ATAATAACATATATTATTATAGC
* *
30777 ATAATAAGATATATTATTATAGT
1 ATAATAACATATATTATTATAGC
*
30800 ATTAA-AA-ATATAATATTATA
1 A-TAATAACATATATTATTATA
30820 TTATTAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 12 0.32
23 23 0.61
24 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (23 bp):
ATAATAACATATATTATTATAGC
Found at i:30816 original size:22 final size:22
Alignment explanation
Indices: 30762--30832 Score: 90
Period size: 22 Copynumber: 3.2 Consensus size: 22
30752 TTATAATATC
*
30762 ATATATTATTATAGCA-TAATAA
1 ATATATTATTATAGTATTAA-AA
30784 GATATATTATTATAGTATTAAAA
1 -ATATATTATTATAGTATTAAAA
* *
30807 ATATAATATTATATTATTAAAA
1 ATATATTATTATAGTATTAAAA
30829 ATAT
1 ATAT
30833 TAATGAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
22 24 0.55
23 17 0.39
24 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (22 bp):
ATATATTATTATAGTATTAAAA
Found at i:31989 original size:32 final size:31
Alignment explanation
Indices: 31953--32016 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
31943 AATTTACGTT
31953 ATTAGCATGAACTAAATGACTTCAATGGATAA
1 ATTAGCATGAACTAAATGACTTCAAT-GATAA
31985 ATTAGCATGAACTAAATGACTTCAATGATAA
1 ATTAGCATGAACTAAATGACTTCAATGATAA
32016 A
1 A
32017 GAGATGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 6 0.19
32 26 0.81
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (31 bp):
ATTAGCATGAACTAAATGACTTCAATGATAA
Found at i:37111 original size:2 final size:2
Alignment explanation
Indices: 37104--37128 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
37094 GGTTCATACA
37104 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
37129 AACCGTATAA
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:38320 original size:3 final size:3
Alignment explanation
Indices: 38312--38367 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
38302 GTACTGCAAA
38312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38360 AAT AAT AA
1 AAT AAT AA
38368 AAGCTAGACA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:38466 original size:16 final size:18
Alignment explanation
Indices: 38434--38466 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
38424 TCTTAAATAA
38434 TTAAATAAATCCAATTTT
1 TTAAATAAATCCAATTTT
38452 TTAAA-AAAT-CAATTT
1 TTAAATAAATCCAATTT
38467 GACTCTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAAATAAATCCAATTTT
Found at i:38890 original size:18 final size:19
Alignment explanation
Indices: 38855--38891 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
38845 CACGGAATGT
38855 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
38875 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
38892 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:39229 original size:15 final size:15
Alignment explanation
Indices: 39209--39238 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39199 TAAAAGGGTA
39209 AAATTTTATTTTAAC
1 AAATTTTATTTTAAC
39224 AAATTTTATTTTAAC
1 AAATTTTATTTTAAC
39239 CCCTGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
AAATTTTATTTTAAC
Found at i:39643 original size:3 final size:3
Alignment explanation
Indices: 39635--39695 Score: 97
Period size: 3 Copynumber: 20.3 Consensus size: 3
39625 TTTATCTGAG
*
39635 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T
39684 TAT TAT T-T TAT T
1 TAT TAT TAT TAT T
39696 GTATTATCAC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41417 original size:34 final size:34
Alignment explanation
Indices: 41374--41483 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 34
41364 TGTAAGAAAT
* * *
41374 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
41407 TTATATTTTATATTAATATATTTATGTAAATATTA
1 TTAT-TTTTATATTAATATATTTATGTAAATATTA
* *
41442 TT-TTTTT-TATTAAAATAATATTTATATAATTATTA
1 TTATTTTTATATT--AAT-ATATTTATGTAAATATTA
41477 TTTATTT
1 -TTATTT
41484 AGAATTATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
32 4 0.06
33 8 0.12
34 16 0.25
35 24 0.38
36 9 0.14
37 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:41443 original size:35 final size:35
Alignment explanation
Indices: 41397--41483 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
41387 AGTATTTTTT
*
41397 TAAATAGTTATTATATTTTATATT-AAT-ATATTTATG
1 TAAATA-TTATT-TATTTT-TATTAAATAATATTTATA
41433 TAAATATTATTT-TTTTTATTAAAATAATATTTATA
1 TAAATATTATTTATTTTTATT-AAATAATATTTATA
*
41468 TAATTATTATTTATTT
1 TAAATATTATTTATTT
41484 AGAATTATTA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 4 0.09
33 4 0.09
34 4 0.09
35 24 0.53
36 9 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (35 bp):
TAAATATTATTTATTTTTATTAAATAATATTTATA
Found at i:42088 original size:27 final size:27
Alignment explanation
Indices: 42058--42126 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
42048 TTATCTTGGT
42058 ACACCTAAATAATTTGTCAATGTATGC
1 ACACCTAAATAATTTGTCAATGTATGC
*
42085 ACACCTAAATAATTTGTCAATGTATGT
1 ACACCTAAATAATTTGTCAATGTATGC
42112 ACACCTAAATAATTT
1 ACACCTAAATAATTT
42127 TTTTAACTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (27 bp):
ACACCTAAATAATTTGTCAATGTATGC
Found at i:43098 original size:2 final size:2
Alignment explanation
Indices: 43091--43138 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
43081 GTATTTGGGC
43091 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
43133 AT AT AT
1 AT AT AT
43139 GTGTGTGTGT
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:51162 original size:21 final size:19
Alignment explanation
Indices: 51115--51172 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
51105 ATTATACAAT
*
51115 AAATAATATTATTTATTAA
1 AAATTATATTATTTATTAA
*
51134 AAATTATATTAGTTTTTTAA
1 AAATTATATTA-TTTATTAA
*
51154 AATATTATAATAATTTATT
1 AA-ATTAT-ATTATTTATT
51173 TAATATGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 10 0.31
20 9 0.28
21 10 0.31
22 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
AAATTATATTATTTATTAA
Found at i:51297 original size:37 final size:36
Alignment explanation
Indices: 51245--51389 Score: 112
Period size: 42 Copynumber: 3.7 Consensus size: 36
51235 AAGATTATTA
51245 TATTATATTAAAATAAAAATATTATACATTATATTAAT
1 TATT-TATTAAAATAAAAATATTATA-ATTATATTAAT
* *
51283 TATTTGTTAAAATAAGAATAATATATTATTAATTATTTTAAT
1 TATTTATTAAAAT---AA-AA-ATATTA-TAATTATATTAAT
* * *
51325 TATTAATTAAAATAATAATATTAATAA-AATATTAAAAAT
1 TATTTATTAAAATAAAAATATT-ATAATTATATT---AAT
*
51364 TATATTATTAAAATAAGAATATTATA
1 TAT-TTATTAAAATAAAAATATTATA
51390 TTGAATTATA
Statistics
Matches: 87, Mismatches: 9, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
36 4 0.05
37 16 0.18
38 6 0.07
39 11 0.13
40 19 0.22
41 2 0.02
42 27 0.31
43 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (36 bp):
TATTTATTAAAATAAAAATATTATAATTATATTAAT
Found at i:51318 original size:42 final size:42
Alignment explanation
Indices: 51263--51391 Score: 113
Period size: 42 Copynumber: 3.1 Consensus size: 42
51253 TAAAATAAAA
**
51263 ATATTATACATTATATTAATTATTTGTTAAAATAAGAATAAT
1 ATATTATACATTATATTAATTATTAATTAAAATAAGAATAAT
* * *
51305 ATATTATTA-ATTATTTTAATTATTAATTAAAATAATAATATT
1 ATATTA-TACATTATATTAATTATTAATTAAAATAAGAATAAT
* * * * * *
51347 A-ATAAAATATTA-A-AAATTATATTATTAAAATAAGAATATT
1 ATATTATACATTATATTAATTAT-TAATTAAAATAAGAATAAT
51387 ATATT
1 ATATT
51392 GAATTATATT
Statistics
Matches: 71, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
39 6 0.08
40 19 0.27
41 9 0.13
42 35 0.49
43 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (42 bp):
ATATTATACATTATATTAATTATTAATTAAAATAAGAATAAT
Found at i:51386 original size:14 final size:14
Alignment explanation
Indices: 51330--51387 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
51320 TTAATTATTA
51330 ATTAAAATAATAAT
1 ATTAAAATAATAAT
51344 ATT--AATAA-AAT
1 ATTAAAATAATAAT
* *
51355 ATTAAAAATTATATT
1 ATT-AAAATAATAAT
*
51370 ATTAAAATAAGAAT
1 ATTAAAATAATAAT
51384 ATTA
1 ATTA
51388 TATTGAATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
11 6 0.17
12 5 0.14
14 19 0.54
15 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
ATTAAAATAATAAT
Found at i:51610 original size:27 final size:27
Alignment explanation
Indices: 51589--51643 Score: 83
Period size: 27 Copynumber: 1.9 Consensus size: 27
51579 TTAATATTTT
51589 TATTAAATTATACTAAAATAATATATTAA
1 TATTAAA-TATA-TAAAATAATATATTAA
51618 TATTAAATATATAAAATAATAATATT
1 TATTAAATATATAAAATAAT-ATATT
51644 TTGAGTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
27 9 0.36
28 9 0.36
29 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TATTAAATATATAAAATAATATATTAA
Found at i:58328 original size:30 final size:30
Alignment explanation
Indices: 58294--58352 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
58284 TATACTGTCT
58294 TCGGTTTTAAATATCAATAAAAAAGAATAA
1 TCGGTTTTAAATATCAATAAAAAAGAATAA
*
58324 TCGGTTTTAAATATCAGTAAAAAAGAATA
1 TCGGTTTTAAATATCAATAAAAAAGAATA
58353 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.31
Consensus pattern (30 bp):
TCGGTTTTAAATATCAATAAAAAAGAATAA
Found at i:59092 original size:51 final size:51
Alignment explanation
Indices: 59037--59146 Score: 134
Period size: 51 Copynumber: 2.2 Consensus size: 51
59027 TTTATTTTAA
**
59037 TTTTGTCACT-GTTAGTTTCTCATTTAGTTACTGTTATTTTA-ATTTTTGCAT
1 TTTTGTCACTCGTTA-TTTCTCATTTAGTTACT-AAATTTTATATTTTTGCAT
* * *
59088 TTTTGTCACTCTTTATTTCTGATTTAGTTACTAAATTTTATTTTTTTGCAT
1 TTTTGTCACTCGTTATTTCTCATTTAGTTACTAAATTTTATATTTTTGCAT
*
59139 TTTAGTCA
1 TTTTGTCA
59147 TTTTATTTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
50 6 0.12
51 42 0.82
52 3 0.06
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.59
Consensus pattern (51 bp):
TTTTGTCACTCGTTATTTCTCATTTAGTTACTAAATTTTATATTTTTGCAT
Found at i:59300 original size:36 final size:31
Alignment explanation
Indices: 59247--59322 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 31
59237 AGCTTGGTAA
59247 TTTTATATTTATGTAATTAGGTTATCATATTTTTAT
1 TTTTAT-TTTATGTAATT--GTTA-C-TATTTTTAT
*
59283 TTTTATTTTATGTTAATTTTTACTATTTTTAT
1 TTTTATTTTATG-TAATTGTTACTATTTTTAT
59315 TTTT-TTTT
1 TTTTATTTT
59323 GTTTTTATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 4 0.11
32 13 0.34
33 1 0.03
34 3 0.08
35 6 0.16
36 11 0.29
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (31 bp):
TTTTATTTTATGTAATTGTTACTATTTTTAT
Found at i:63181 original size:7 final size:7
Alignment explanation
Indices: 63142--63210 Score: 59
Period size: 7 Copynumber: 9.6 Consensus size: 7
63132 GAAAGAAATA
63142 AAAAGAG
1 AAAAGAG
*
63149 -AAAGAA
1 AAAAGAG
*
63155 AGAAAGAA
1 A-AAAGAG
*
63163 AGAAAGAA
1 A-AAAGAG
63171 AAAAGAG
1 AAAAGAG
*
63178 AAAAAGAA
1 -AAAAGAG
63186 AAAAGAG
1 AAAAGAG
*
63193 AAAAAAG
1 AAAAGAG
63200 AAAAGAG
1 AAAAGAG
63207 AAAA
1 AAAA
63211 AAGGGAGAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
6 5 0.09
7 27 0.51
8 21 0.40
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (7 bp):
AAAAGAG
Found at i:63212 original size:15 final size:14
Alignment explanation
Indices: 63111--63212 Score: 93
Period size: 15 Copynumber: 7.1 Consensus size: 14
63101 AAAGATATAG
63111 AAAAAAG-GAAAAA
1 AAAAAAGAGAAAAA
63124 ATATAAAAGA-AAGAAA
1 A-A-AAAAGAGAA-AAA
* *
63140 TAAAAAGAGAAAGA
1 AAAAAAGAGAAAAA
*
63154 AAGAAAGA-AAGAAA
1 AAAAAAGAGAA-AAA
63168 GAAAAAAGAGAAAAA
1 -AAAAAAGAGAAAAA
63183 GAAAAAAGAGAAAAA
1 -AAAAAAGAGAAAAA
*
63198 AGAAAAGAGAAAAA
1 AAAAAAGAGAAAAA
63212 A
1 A
63213 GGGAGAGAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
13 3 0.04
14 31 0.42
15 35 0.47
16 5 0.07
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAAAAGAGAAAAA
Found at i:63219 original size:13 final size:14
Alignment explanation
Indices: 63087--63237 Score: 98
Period size: 14 Copynumber: 10.7 Consensus size: 14
63077 TTGATAACAC
*
63087 AAAGAGAAATAAGA
1 AAAGAGAAAAAAGA
* * *
63101 AAAGATATAGAA-A
1 AAAGAGAAAAAAGA
*
63114 AAAG-GAAAAAATA
1 AAAGAGAAAAAAGA
*
63127 TAAA-AGAAAGAAATAA
1 -AAAGAGAAA-AAA-GA
63143 AAAGAGAAAGAAAGA
1 AAAGAGAAA-AAAGA
* *
63158 AAGAAAGAAAGAA-A
1 AA-AGAGAAAAAAGA
*
63172 AAAGAGAAAAAGAAA
1 AAAGAGAAAAA-AGA
63187 AAAGAGAAAAAAGA
1 AAAGAGAAAAAAGA
63201 AAAGAGAAAAAAG-
1 AAAGAGAAAAAAGA
**
63214 GGAGAGAAAAAAGA
1 AAAGAGAAAAAAGA
63228 AGAA-AGAAAA
1 A-AAGAGAAAA
63238 CTGATCAAAT
Statistics
Matches: 109, Mismatches: 17, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
12 4 0.04
13 24 0.22
14 41 0.38
15 24 0.22
16 16 0.15
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAAAAGA
Found at i:65476 original size:20 final size:20
Alignment explanation
Indices: 65451--65511 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
65441 TTTCTTGATG
65451 AGTAAGTCCTTCGGGCCATC
1 AGTAAGTCCTTCGGGCCATC
* * *
65471 AGTAAGTCTTTCGAG-CATG
1 AGTAAGTCCTTCGGGCCATC
65490 ATGCTTAAGTCCTTCGGGCCAT
1 A-G--TAAGTCCTTCGGGCCAT
65512 TTATAAGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.12
20 14 0.44
22 11 0.34
23 3 0.09
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (20 bp):
AGTAAGTCCTTCGGGCCATC
Found at i:65559 original size:41 final size:40
Alignment explanation
Indices: 65458--65559 Score: 107
Period size: 42 Copynumber: 2.5 Consensus size: 40
65448 ATGAGTAAGT
* **
65458 CCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAGT
1 CCTTCGGGCCATCA-TAAGTCTTTCGAGCAAGAT-CTTAAAA
* *
65500 CCTTCGGGCCATTTATAAGTGTTTCGAGCAAGAT-TATAAAA
1 CCTTCGGGCCA-TCATAAGTCTTTCGAGCAAGATCT-TAAAA
65541 CCTTCGGGCCATCCATAAG
1 CCTTCGGGCCAT-CATAAG
65560 ACCTTAAGGC
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
40 2 0.04
41 19 0.37
42 28 0.55
43 2 0.04
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (40 bp):
CCTTCGGGCCATCATAAGTCTTTCGAGCAAGATCTTAAAA
Found at i:65814 original size:260 final size:261
Alignment explanation
Indices: 65106--65881 Score: 1197
Period size: 261 Copynumber: 3.0 Consensus size: 261
65096 TACTTTGACA
65106 TGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAGCTTGAT
1 TGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAGCTTGAT
* *
65171 TTTCAAGGTTTTATTGATCAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
66 TTTCAAGGTTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
* * *
65236 AGTCATTCGAGTA--ATTTATAAGTCTTTCGAGCAAGATGATAAAACCTTCAGGCCATCTATAAG
131 AGTCCTTCG-G-ACCATTTATAAGTCTTTCGAGCAAGATGATAAAACCTTCGGGCCATCCATAAG
* * *
65299 ACCTTCGAGC-TGGAAGTTTTCAACATTTCCAGTACTCGATTCATCACATATAGAGTTGAATCTT
194 ACCTTCGAGCAT-GATGTTTTCAACATTTCTAGTACTCGATTCATCACATATGGAGTTGAATCTT
65363 GATG
258 GATG
*
65367 TGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGGAACTAAGCTTGAT
1 TGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAGCTTGAT
*
65432 TTTTAAGGTTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
66 TTTCAAGGTTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
* * *
65497 AGTCCTTCGGGCCATTTATAAGTGTTTCGAGCAAGATTATAAAACCTTCGGGCCATCCATAAGAC
131 AGTCCTTCGGACCATTTATAAGTCTTTCGAGCAAGATGATAAAACCTTCGGGCCATCCATAAGAC
* * *
65562 CTT-AAGGCATGATGTTTTCAACATTTCTGGTACTCGATTCATCACATATGGAATTGAATCTTGA
196 CTTCGA-GCATGATGTTTTCAACATTTCTAGTACTCGATTCATCACATATGGAGTTGAATCTTGA
65626 TG
260 TG
* *
65628 TGGGGGAATGTTACCCAAACAACATGATATTTTCAAAAGAATTTTT-TAAGAAACTAAGCTTGAT
1 TGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAGCTTGAT
* * *
65692 TTTCAAGATTTTCTTGATGAGTAAGTTCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTTA
66 TTTCAAGGTTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
* * * *
65757 ACTCCTTCGGACCATTTATAAGTC-TTCTAAACAAGATGATAAGACCTTCGGGCCATCCATAAGA
131 AGTCCTTCGGACCATTTATAAGTCTTTC-GAGCAAGATGATAAAACCTTCGGGCCATCCATAAGA
* * *
65821 CCTTCGAGCATGATGTTTTCAATATTTTTTA-TACTCGATTCATAACATATGGAGTTGAATC
195 CCTTCGAGCATGATGTTTTCAACA-TTTCTAGTACTCGATTCATCACATATGGAGTTGAATC
65882 AACAATGTAT
Statistics
Matches: 472, Mismatches: 36, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
259 3 0.01
260 181 0.38
261 287 0.61
262 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.34
Consensus pattern (261 bp):
TGGGGGCACGTTACCCAAACAACATGATATTTTCAAAAGAATTTTTATAAGAAACTAAGCTTGAT
TTTCAAGGTTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTA
AGTCCTTCGGACCATTTATAAGTCTTTCGAGCAAGATGATAAAACCTTCGGGCCATCCATAAGAC
CTTCGAGCATGATGTTTTCAACATTTCTAGTACTCGATTCATCACATATGGAGTTGAATCTTGAT
G
Found at i:68100 original size:25 final size:24
Alignment explanation
Indices: 68072--68126 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
68062 TAATACAACT
*
68072 ATTTTAAATA-ATTGTTTGAACTCTG
1 ATTTTAAATATAATGTTTGAA-T-TG
*
68097 ATTTGAAATATAATGTTTGAATTG
1 ATTTTAAATATAATGTTTGAATTG
68121 ATTTTA
1 ATTTTA
68127 CAACTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 7 0.27
25 10 0.38
26 9 0.35
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (24 bp):
ATTTTAAATATAATGTTTGAATTG
Found at i:70013 original size:6 final size:6
Alignment explanation
Indices: 70002--70055 Score: 54
Period size: 6 Copynumber: 8.2 Consensus size: 6
69992 GGTCCTCATA
*
70002 TTTTAT TTTTAT TTTATGT TTTTACT GTTTTATT TTTTAT TTGTTAT TTTTAT
1 TTTTAT TTTTAT TTT-TAT TTTTA-T -TTTTA-T TTTTAT TT-TTAT TTTTAT
70055 T
1 T
70056 ATTTTAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
6 18 0.44
7 17 0.41
8 6 0.15
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:70060 original size:28 final size:27
Alignment explanation
Indices: 70000--70061 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
69990 TAGGTCCTCA
*
70000 TATTTTATTTTTATTTTATGTTTTTAC
1 TATTTTATTTTTATTTTATATTTTTAC
* *
70027 TGTTTTATTTTTTATTTGT-TATTTTTAT
1 TATTTTA-TTTTTATTT-TATATTTTTAC
70055 TATTTTA
1 TATTTTA
70062 ATTATGTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 6 0.21
28 22 0.76
29 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.76
Consensus pattern (27 bp):
TATTTTATTTTTATTTTATATTTTTAC
Found at i:70069 original size:23 final size:20
Alignment explanation
Indices: 70004--70061 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
69994 TCCTCATATT
* *
70004 TTATTTTTATTTTATGTTT-
1 TTATTTTTATTTTTTATTTG
70023 TTACTGTTTTATTTTTTATTTG
1 TTA-T-TTTTATTTTTTATTTG
70045 TTATTTTTATTATTTTA
1 TTATTTTTATT-TTTTA
70062 ATTATGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 3 0.09
20 8 0.24
21 19 0.58
22 3 0.09
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (20 bp):
TTATTTTTATTTTTTATTTG
Found at i:73417 original size:19 final size:19
Alignment explanation
Indices: 73393--73456 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
73383 TGCATTGGGA
*
73393 TATGAATTTGAAAATAAGC
1 TATGAATATGAAAATAAGC
* * *
73412 TATGAATCTGACAGTAAGC
1 TATGAATATGAAAATAAGC
* *
73431 TATGAGTATGAAAATAAGT
1 TATGAATATGAAAATAAGC
73450 TATGAAT
1 TATGAAT
73457 CTAGAAATAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (19 bp):
TATGAATATGAAAATAAGC
Found at i:73464 original size:19 final size:19
Alignment explanation
Indices: 73402--73493 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
73392 ATATGAATTT
* *
73402 GAAAATAAGCTATGAATCT
1 GAAAATAAGTTATGAATCA
* * * *
73421 GACAGTAAGCTATGAGT-A
1 GAAAATAAGTTATGAATCA
73439 TGAAAATAAGTTATGAATCTA
1 -GAAAATAAGTTATGAATC-A
* *
73460 G-AAATAAGTTCTGATTCA
1 GAAAATAAGTTATGAATCA
*
73478 GAAAATAAATTATGAA
1 GAAAATAAGTTATGAA
73494 ATGTGAAAGT
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
18 2 0.04
19 52 0.93
20 1 0.02
21 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (19 bp):
GAAAATAAGTTATGAATCA
Found at i:73537 original size:12 final size:12
Alignment explanation
Indices: 73520--73553 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
73510 TATAAACATG
73520 GAATATGAAAAT
1 GAATATGAAAAT
*
73532 GAATATGTAAAT
1 GAATATGAAAAT
73544 GAATATGAAA
1 GAATATGAAA
73554 GTGGAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.26
Consensus pattern (12 bp):
GAATATGAAAAT
Found at i:74247 original size:23 final size:23
Alignment explanation
Indices: 74220--74276 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
74210 TTTACATGAT
*
74220 TAATGGAATAATTGTAAAGTTAA
1 TAATGGAACAATTGTAAAGTTAA
74243 TAATGGAACAATTGTAAAGTTAA
1 TAATGGAACAATTGTAAAGTTAA
74266 TAATGGAACAA
1 TAATGGAACAA
74277 ATTTTAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.49, C:0.04, G:0.18, T:0.30
Consensus pattern (23 bp):
TAATGGAACAATTGTAAAGTTAA
Found at i:79309 original size:2 final size:2
Alignment explanation
Indices: 79304--79336 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
79294 ATATTTTAGT
79304 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 T
79337 CTATTAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90060 original size:16 final size:15
Alignment explanation
Indices: 90035--90065 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
90025 TCTCCCAAAA
90035 TTCTCTCAAATTCAT
1 TTCTCTCAAATTCAT
90050 TTCTGCTCAAATTCAT
1 TTCT-CTCAAATTCAT
90066 CATCCTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.26, G:0.03, T:0.45
Consensus pattern (15 bp):
TTCTCTCAAATTCAT
Found at i:92700 original size:29 final size:29
Alignment explanation
Indices: 92658--92732 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
92648 AACCCAACCA
**
92658 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
92687 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
92716 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
92733 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:92738 original size:29 final size:29
Alignment explanation
Indices: 92659--92746 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
92649 ACCCAACCAT
* * ****
92659 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
92688 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
92717 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
92746 A
1 A
92747 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:92976 original size:10 final size:10
Alignment explanation
Indices: 92963--93020 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
92953 CAGGGCATGG
92963 ATGGGCGTGC
1 ATGGGCGTGC
92973 ATGGGCGTGCTCC
1 ATGGGCGTG---C
* * *
92986 TTTGGCGAG-
1 ATGGGCGTGC
92995 ATGGGCGTGC
1 ATGGGCGTGC
93005 ATGGGCGTGC
1 ATGGGCGTGC
93015 ATGGGC
1 ATGGGC
93021 ATGGAGGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 6 0.16
10 25 0.66
13 7 0.18
ACGTcount: A:0.10, C:0.21, G:0.47, T:0.22
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:93087 original size:28 final size:29
Alignment explanation
Indices: 93040--93125 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
93030 GTTGGCTGGT
* *
93040 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCCGGGCGTGCATGGCGACCTACC
* ***
93069 AGGTCG-CTGGCGTGCATGGCGACCTGGT
1 AGGTCGCCGGGCGTGCATGGCGACCTACC
93097 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCCGGGCGTGCATGGCGACCTACC
93126 CCCGGTACTG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
28 22 0.48
29 24 0.52
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.16
Consensus pattern (29 bp):
AGGTCGCCGGGCGTGCATGGCGACCTACC
Found at i:93960 original size:34 final size:34
Alignment explanation
Indices: 93900--93967 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
93890 TTTCTTGAGA
*
93900 ATTGTTTTCTTCTTTTTATCAAGAGAGAA-TTGTT
1 ATTGTTTTCTTCTTTTGATC-AGAGAGAAGTTGTT
93934 ATTGTTTTCTTCTTGTTAGATC-GAGAGAAGTTGT
1 ATTGTTTTCTTCTT-TT-GATCAGAGAGAAGTTGT
93968 AATTCCTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 21 0.70
35 6 0.20
36 3 0.10
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.50
Consensus pattern (34 bp):
ATTGTTTTCTTCTTTTGATCAGAGAGAAGTTGTT
Found at i:100372 original size:23 final size:25
Alignment explanation
Indices: 100327--100386 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
100317 CTAATCTATT
**
100327 TTTATCATCCTAGAAATTTTATAAA
1 TTTATCATCCTAGAAATACTATAAA
100352 TTTATC-TCCTA-AAATACTATAAA
1 TTTATCATCCTAGAAATACTATAAA
*
100375 TTTATTATCCTA
1 TTTATCATCCTA
100387 TCATAAAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 15 0.48
24 10 0.32
25 6 0.19
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (25 bp):
TTTATCATCCTAGAAATACTATAAA
Found at i:102112 original size:25 final size:26
Alignment explanation
Indices: 102060--102117 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
102050 AAATATAGTG
102060 ATAAT-AAATATATAAAATTAAAACA
1 ATAATAAAATATATAAAATTAAAACA
*
102085 ATAACTAAAATATATGAAATT-AAA-A
1 ATAA-TAAAATATATAAAATTAAAACA
102110 ATAATAAA
1 ATAATAAA
102118 CTAACAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.13
25 9 0.30
26 4 0.13
27 13 0.43
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAATAAAATATATAAAATTAAAACA
Found at i:102376 original size:17 final size:17
Alignment explanation
Indices: 102354--102388 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
102344 TTTGGGAGTC
*
102354 GCCATTGACCTTTTTGA
1 GCCATTGACCATTTTGA
102371 GCCATTGACCATTTTGA
1 GCCATTGACCATTTTGA
102388 G
1 G
102389 TTAGGTAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (17 bp):
GCCATTGACCATTTTGA
Found at i:104364 original size:3 final size:3
Alignment explanation
Indices: 104358--104390 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
104348 ATTTATTATT
104358 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TA
104391 TAAGTAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:107762 original size:66 final size:66
Alignment explanation
Indices: 107646--107778 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 66
107636 GACAAGCGTG
* * * *
107646 CGCCATAGACCCATAACGCCTTGTCTTGGGAGCAAACACCGAGCGTCCCATGTTTATAAAATTGC
1 CGCCATAGACCCATAACGCATTGTCTTGGGAGCAAACACCGAGCGCCCCATGCTTATAAAAGTGC
107711 C
66 C
* * * *
107712 CGCCATTGTCCCATAACGCATTGTCTTGGGAGCAATA-ACCTAGCGCCCCATGCTTGTAAAAGTG
1 CGCCATAGACCCATAACGCATTGTCTTGGGAGCAA-ACACCGAGCGCCCCATGCTTATAAAAGTG
107776 CC
65 CC
107778 C
1 C
107779 TTTTTCAACA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (66 bp):
CGCCATAGACCCATAACGCATTGTCTTGGGAGCAAACACCGAGCGCCCCATGCTTATAAAAGTGC
C
Found at i:109943 original size:21 final size:19
Alignment explanation
Indices: 109904--109943 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
109894 GAGTTTAAGG
*
109904 GTGTTTTCTGGGCAAAATA
1 GTGTTTTCTGGGAAAAATA
109923 GTGTGTTTCTGGGAAACAATA
1 GTGT-TTTCTGGGAAA-AATA
109944 TCGATACTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.35
Consensus pattern (19 bp):
GTGTTTTCTGGGAAAAATA
Found at i:112252 original size:30 final size:31
Alignment explanation
Indices: 112216--112279 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
112206 AGCCATTTCT
112216 TAGGTAAAACA-CTTAGTGTTCAAGAGAAAC
1 TAGGTAAAACACCTTAGTGTTCAAGAGAAAC
* *
112246 TAGGTAAAAGATCCTTAGTGTTCGAGAGAAAC
1 TAGGTAAAACA-CCTTAGTGTTCAAGAGAAAC
112278 TA
1 TA
112280 AGGGAAGATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 10 0.33
32 20 0.67
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (31 bp):
TAGGTAAAACACCTTAGTGTTCAAGAGAAAC
Found at i:113821 original size:22 final size:22
Alignment explanation
Indices: 113776--113822 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
113766 GTGAATTATA
*
113776 TCCCGAATGACCTATGCATGTG
1 TCCCGAATGACCTATGCATATG
*
113798 TCCCGGATGACCTAT-CTATATG
1 TCCCGAATGACCTATGC-ATATG
113820 TCC
1 TCC
113823 AGAAGAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.30
Consensus pattern (22 bp):
TCCCGAATGACCTATGCATATG
Found at i:113853 original size:31 final size:31
Alignment explanation
Indices: 113815--113902 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
113805 TGACCTATCT
* *
113815 ATATGTCCAGAAGAACATAGGTAACCTGTTC
1 ATATGTCCAGAAGAACATAGGTAACATGTCC
* *
113846 ATATGTCCTGAAGAATATAGGTAATCATGTCC
1 ATATGTCCAGAAGAACATAGGTAA-CATGTCC
* *
113878 ATATGTCCCGAA-AGACATATGTAAC
1 ATATGTCCAGAAGA-ACATAGGTAAC
113903 TCTCTACTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (31 bp):
ATATGTCCAGAAGAACATAGGTAACATGTCC
Found at i:115214 original size:44 final size:44
Alignment explanation
Indices: 115151--115250 Score: 182
Period size: 44 Copynumber: 2.3 Consensus size: 44
115141 ACCATGCCTA
* *
115151 GGTATCGATACCCATTTTGTATTCTGTAATTCTGGTTCAAAAAT
1 GGTATCGATACCCATTTTGTATTCTATAATTCTCGTTCAAAAAT
115195 GGTATCGATACCCATTTTGTATTCTATAATTCTCGTTCAAAAAT
1 GGTATCGATACCCATTTTGTATTCTATAATTCTCGTTCAAAAAT
115239 GGTATCGATACC
1 GGTATCGATACC
115251 TTCCTTAAGG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (44 bp):
GGTATCGATACCCATTTTGTATTCTATAATTCTCGTTCAAAAAT
Found at i:116669 original size:21 final size:21
Alignment explanation
Indices: 116644--116685 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
116634 GAACCAAAAA
116644 ACCTTAA-TGAATAAATGATTG
1 ACCTTAATTGAATAAA-GATTG
*
116665 ACCTTAATTGATTAAAGATTG
1 ACCTTAATTGAATAAAGATTG
116686 TTGTCTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
ACCTTAATTGAATAAAGATTG
Found at i:119380 original size:27 final size:27
Alignment explanation
Indices: 119345--119400 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
119335 CACCGAATGC
*
119345 CATCGATGCATAAGGAGTGCATCGATG
1 CATCAATGCATAAGGAGTGCATCGATG
119372 CATCAATGCATAAGGAGTGCATCGATG
1 CATCAATGCATAAGGAGTGCATCGATG
119399 CA
1 CA
119401 CCCCATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.21
Consensus pattern (27 bp):
CATCAATGCATAAGGAGTGCATCGATG
Found at i:120083 original size:23 final size:23
Alignment explanation
Indices: 120057--120124 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
120047 ATTATTATAT
*
120057 GGCACTACAGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
120080 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
120103 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
120125 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:127008 original size:23 final size:23
Alignment explanation
Indices: 126978--127068 Score: 128
Period size: 23 Copynumber: 4.0 Consensus size: 23
126968 ATTATTATAT
126978 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
127001 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
127024 GGCACTCCGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
** *
127047 GGCACTTTGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
127069 AGCTGTGGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:131125 original size:28 final size:28
Alignment explanation
Indices: 131058--131150 Score: 86
Period size: 28 Copynumber: 3.3 Consensus size: 28
131048 TTAAACAAAT
*
131058 TTTTTATTTAAATCTATT-AAATATGTTTTA
1 TTTTTATTT-AAT-T-TTAAAATATATTTTA
*
131088 TTCTTAATTTAATTTTAAAATATATTTTA
1 TT-TTTATTTAATTTTAAAATATATTTTA
* *
131117 TTTTTATTTTATTCTAAAA-ATA-TTT-
1 TTTTTATTTAATTTTAAAATATATTTTA
131142 TTTTTATTT
1 TTTTTATTT
131151 TTATCTTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
25 9 0.16
26 3 0.05
27 3 0.05
28 16 0.29
29 14 0.25
30 5 0.09
31 6 0.11
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTTATTTAATTTTAAAATATATTTTA
Found at i:144985 original size:87 final size:86
Alignment explanation
Indices: 144861--145021 Score: 286
Period size: 87 Copynumber: 1.9 Consensus size: 86
144851 AAAATAGGCC
*
144861 TAAAATATATCTTAGACTTAAAAAAAAGGTTAACTACACTGATGATCACTTATATTTGTGTTTTG
1 TAAAATATATCTTAGACTTAAAAAAAAGGTTAACTACACGGATGATCACTTATATTTGTGTTTTG
144926 TCCACTTTTGGTCTGATTTTA
66 TCCACTTTTGGTCTGATTTTA
* *
144947 TAAAATATATCTTATACTTTAAAAAAAAGGTTAACTACACGGATGATCACTTATGTTTGTGTTTT
1 TAAAATATATCTTAGAC-TTAAAAAAAAGGTTAACTACACGGATGATCACTTATATTTGTGTTTT
145012 GTCCACTTTT
65 GTCCACTTTT
145022 AGTCACTAAT
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 16 0.23
87 55 0.77
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (86 bp):
TAAAATATATCTTAGACTTAAAAAAAAGGTTAACTACACGGATGATCACTTATATTTGTGTTTTG
TCCACTTTTGGTCTGATTTTA
Found at i:145053 original size:87 final size:87
Alignment explanation
Indices: 144861--145040 Score: 236
Period size: 87 Copynumber: 2.1 Consensus size: 87
144851 AAAATAGGCC
* * * *
144861 TAAAATATATCTTAGAC-TTAAAAAAAAGGTTAACTACACTGATGATCACTTATATTTGTGTTTT
1 TAAAATACATCTAATACTTTAAAAAAAAGGTTAACTACACGGATGATCACTTATATTTGTGTTTT
* * *
144925 GTCCACTTTTGGTCTGATTTTA
66 GTCCACTTTTAGTCTAATTTCA
* * *
144947 TAAAATATATCTTATACTTTAAAAAAAAGGTTAACTACACGGATGATCACTTATGTTTGTGTTTT
1 TAAAATACATCTAATACTTTAAAAAAAAGGTTAACTACACGGATGATCACTTATATTTGTGTTTT
145012 GTCCACTTTTAGTCACTAATTTCA
66 GTCCACTTTTAGT--CTAATTTCA
*
145036 AAAAA
1 TAAAA
145041 CACAAGTCAC
Statistics
Matches: 84, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
86 16 0.19
87 57 0.68
89 11 0.13
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (87 bp):
TAAAATACATCTAATACTTTAAAAAAAAGGTTAACTACACGGATGATCACTTATATTTGTGTTTT
GTCCACTTTTAGTCTAATTTCA
Found at i:145277 original size:21 final size:21
Alignment explanation
Indices: 145229--145279 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
145219 TTTAAATAAA
* *
145229 TTTTAACAT-AAAATATATAT
1 TTTTAAAATAAAAATAAATAT
145249 TTTT-AAATAAAAATAAATAT
1 TTTTAAAATAAAAATAAATAT
145269 TTTTAAAATAA
1 TTTTAAAATAA
145280 GTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 3 0.11
20 18 0.67
21 6 0.22
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTAAAATAAAAATAAATAT
Found at i:150969 original size:3 final size:3
Alignment explanation
Indices: 150961--151007 Score: 60
Period size: 3 Copynumber: 15.3 Consensus size: 3
150951 CACCAAACAC
*
150961 TCT TCT TCT TCT TCT TCT TCT TCT TCAT TC- TCC TCT CTCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT -TCT TCT TCT
151007 T
1 T
151008 TATTGCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:152760 original size:16 final size:16
Alignment explanation
Indices: 152739--152769 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
152729 TATTTTAAAA
152739 CCTATAAGAACTCAAC
1 CCTATAAGAACTCAAC
152755 CCTATAAGAACTCAA
1 CCTATAAGAACTCAA
152770 GAGTCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (16 bp):
CCTATAAGAACTCAAC
Found at i:153544 original size:25 final size:27
Alignment explanation
Indices: 153516--153581 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
153506 ATTTAAACAT
153516 ATATATTTTTATTTCAATCT-ATTA-A
1 ATATATTTTTATTTCAATCTAATTATA
* * *
153541 ATAT-GTTTTATTCTTAATTTAATTATA
1 ATATATTTTTATT-TCAATCTAATTATA
*
153568 AAATATTTTTATTT
1 ATATATTTTTATTT
153582 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 7 0.22
25 9 0.28
26 4 0.12
27 5 0.16
28 7 0.22
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (27 bp):
ATATATTTTTATTTCAATCTAATTATA
Found at i:153598 original size:28 final size:28
Alignment explanation
Indices: 153519--153616 Score: 99
Period size: 28 Copynumber: 3.3 Consensus size: 28
153509 TAAACATATA
* *
153519 TATTTTTATTTCAATCTATTAAATATGTTT
1 TATTTTTATTTTAAT-TATAAAATAT-TTT
* *
153549 TATTCTTAATTTAATTATAAAATATTTT
1 TATTTTTATTTTAATTATAAAATATTTT
153577 TATTTTTATTTTAATTCA-AAAATGTATTTTT
1 TATTTTTATTTTAATT-ATAAAA--TA-TTTT
153608 TATTTTTAT
1 TATTTTTAT
153617 CTTATTTTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
28 21 0.36
29 10 0.17
30 14 0.24
31 13 0.22
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (28 bp):
TATTTTTATTTTAATTATAAAATATTTT
Found at i:154459 original size:20 final size:21
Alignment explanation
Indices: 154434--154485 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
154424 TTTTACCAAT
*
154434 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
154454 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
154475 TCGCAATGCGA
1 TCGCAATGCGA
154486 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:154499 original size:20 final size:20
Alignment explanation
Indices: 154474--154567 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
154464 AATTGGGAAA
*
154474 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
154494 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
154515 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
154535 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
154555 TTCGCAACGCGAT
1 ATCGCAACGCGAT
154568 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:155143 original size:19 final size:19
Alignment explanation
Indices: 155119--155163 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
155109 GCAACGAGAG
*
155119 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
155138 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
155157 AATCGCA
1 AATCGCA
155164 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:155230 original size:20 final size:19
Alignment explanation
Indices: 155159--155238 Score: 97
Period size: 20 Copynumber: 4.1 Consensus size: 19
155149 GAAACCAAAA
*
155159 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
155178 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
155197 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
155217 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
155237 TC
1 TC
155239 AACCAAAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 19 0.37
20 32 0.62
21 1 0.02
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:157405 original size:21 final size:21
Alignment explanation
Indices: 157381--157447 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
157371 TCATTCCTCG
157381 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
157402 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
157423 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
157444 AGAG
1 AGAG
157448 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:157405 original size:42 final size:42
Alignment explanation
Indices: 157329--157447 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
157319 GACTCGCCTG
* * * * * * *
157329 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
157371 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
157413 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
157448 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:158827 original size:14 final size:14
Alignment explanation
Indices: 158808--158843 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
158798 ATTGTTTAAT
158808 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
158822 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
158836 TGATTTGT
1 TGATTTGT
158844 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:158987 original size:14 final size:14
Alignment explanation
Indices: 158968--159024 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
158958 GCGAAATGAA
158968 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
158982 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
159001 AATCGCAACGAGAG
1 AATCGCAACGAGAG
159015 AATCGCAACG
1 AATCGCAACG
159025 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:158995 original size:33 final size:33
Alignment explanation
Indices: 158950--159039 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
158940 AAAAAGTACT
*
158950 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
158983 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
159016 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
159040 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:159009 original size:19 final size:19
Alignment explanation
Indices: 158950--159010 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
158940 AAAAAGTACT
*
158950 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
158969 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
158983 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
159002 ATCGCAACG
1 ATCGCAACG
159011 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:159057 original size:19 final size:19
Alignment explanation
Indices: 159035--159185 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
159025 CGAAATTAAA
159035 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
159054 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
159069 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
159087 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
* *
159101 TTAGTGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
159120 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
159135 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* ** *
159153 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
159172 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
159186 AGACATTAAG
Statistics
Matches: 92, Mismatches: 24, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 5 0.05
17 6 0.07
19 45 0.49
20 9 0.10
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:159081 original size:33 final size:33
Alignment explanation
Indices: 159039--159165 Score: 186
Period size: 33 Copynumber: 3.8 Consensus size: 33
159029 ATTAAATTCG
*
159039 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
159072 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AGT
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCACT
*
159106 -GTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
159138 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
159166 AGTAATTTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
32 1 0.01
33 77 0.91
34 1 0.01
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:159119 original size:66 final size:66
Alignment explanation
Indices: 159040--159164 Score: 232
Period size: 66 Copynumber: 1.9 Consensus size: 66
159030 TTAAATTCGC
159040 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
159105 T
66 T
* *
159106 GTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCGCATTGCGA
1 GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGA
159165 TAGTAATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (66 bp):
GTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGAAATTAG
T
Found at i:161473 original size:12 final size:12
Alignment explanation
Indices: 161456--161480 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
161446 TCTTCAGGGA
161456 CTTTTTCTTCTT
1 CTTTTTCTTCTT
161468 CTTTTTCTTCTT
1 CTTTTTCTTCTT
161480 C
1 C
161481 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:161682 original size:24 final size:24
Alignment explanation
Indices: 161655--161708 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
161645 TTGAAACATC
*
161655 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
*
161679 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAT
161703 ATCAAA
1 ATCAAA
161709 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAT
Found at i:161722 original size:24 final size:24
Alignment explanation
Indices: 161671--161722 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
161661 ATCCGTGTAT
** *
161671 TGACCAATATCAAAGTCCGGGTAT
1 TGACCAATATCAAAGTCCGAATAC
* *
161695 TGACCAATATCAAATTTCGAATAC
1 TGACCAATATCAAAGTCCGAATAC
161719 TGAC
1 TGAC
161723 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAATATCAAAGTCCGAATAC
Found at i:162787 original size:20 final size:20
Alignment explanation
Indices: 162762--162819 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
162752 ATTCATTTGA
*
162762 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
162782 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
162802 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
162820 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:162862 original size:14 final size:16
Alignment explanation
Indices: 162842--162915 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
162832 TGAAAATCGC
162842 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
162857 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
162874 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
162893 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
162909 -TTGCGAT
1 ATTGCGAT
162916 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:162879 original size:19 final size:19
Alignment explanation
Indices: 162838--162905 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
162828 GAAATGAAAA
162838 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
162854 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
162871 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
162890 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
162906 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:164949 original size:20 final size:20
Alignment explanation
Indices: 164926--164977 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
164916 AAAACTTAAA
164926 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
164946 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAAATGACT
*
164966 ATCGCAATGCGA
1 ATCGCAACGCGA
164978 TAGCCATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:165017 original size:20 final size:20
Alignment explanation
Indices: 164968--165006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
164958 AAATGGCTAT
*
164968 CGCAATGCGATAGCCATTTC
1 CGCATTGCGATAGCCATTTC
*
164988 CGCATTGCGATAGTCATTT
1 CGCATTGCGATAGCCATTT
165007 TCGTGTTGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (20 bp):
CGCATTGCGATAGCCATTTC
Found at i:165523 original size:18 final size:18
Alignment explanation
Indices: 165497--165541 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
165487 GTCGATCAGA
*
165497 TGATGGCTCTGGATGAGG
1 TGATGGCTCTGGACGAGG
* *
165515 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGACGAGG
165533 TGATGGCTC
1 TGATGGCTC
165542 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGACGAGG
Found at i:166908 original size:20 final size:20
Alignment explanation
Indices: 166860--166918 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
166850 AATAGTTTCT
** *
166860 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
166880 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
166900 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
166919 AGAGAATCAC
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:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:167208 original size:22 final size:22
Alignment explanation
Indices: 167181--167224 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
167171 GATGGAGATA
167181 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
167203 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
167225 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:167538 original size:20 final size:20
Alignment explanation
Indices: 167412--167566 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
167402 GATTATGTAT
* *
167412 TATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
167432 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
167452 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
167472 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* * * *
167492 TATCTCGTTGCAATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
*
167513 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
167533 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
167553 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
167567 TTTCCCAATT
Statistics
Matches: 118, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.03
20 102 0.86
21 11 0.09
22 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:167564 original size:40 final size:40
Alignment explanation
Indices: 167392--167566 Score: 158
Period size: 40 Copynumber: 4.3 Consensus size: 40
167382 CGCTTTGAAA
* * *
167392 ATCGCATTGCGATTATGT-ATTATCGCGTTACGAAAGTCAGA
1 ATCGCATTGCGA-TA-GTCAGTATCGCGTTGCGAAAGTCAGT
* * *
167433 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
* * * * * *
167473 ATCGCGTTGCGAAAGTAAGTATCTCGTTGC-AATTTTGT-ATT
1 ATCGCATTGCGATAGTCAGTATCGCGTTGCGAA---AGTCAGT
* *
167514 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
167554 ATCGCATTGCGAT
1 ATCGCATTGCGAT
167567 TTTCCCAATT
Statistics
Matches: 109, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
39 6 0.06
40 62 0.57
41 38 0.35
42 3 0.03
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (40 bp):
ATCGCATTGCGATAGTCAGTATCGCGTTGCGAAAGTCAGT
Found at i:167569 original size:61 final size:61
Alignment explanation
Indices: 167453--167569 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
167443 GAAAGTCAGA
* * * *
167453 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCGTTGCAATTTTGTATT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTGTATT
* * * *
167514 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTT
167570 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTGTATT
Found at i:167585 original size:61 final size:61
Alignment explanation
Indices: 167453--167587 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
167443 GAAAGTCAGA
* * * * ** *
167453 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTAAGTATCTCGTTGCAATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTCCAAT
* * * *
167514 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTT-CCAAT
167576 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
167588 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGAAAGTAAGTATCGCATTGCAATTTTCCAAT
Found at i:169597 original size:17 final size:17
Alignment explanation
Indices: 169575--169607 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
169565 TACTACCATA
*
169575 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
169592 ATATTATATTTTATAT
1 ATATTATATTTTATAT
169608 AAATAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:170045 original size:15 final size:15
Alignment explanation
Indices: 170025--170061 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
170015 CATGCTTAAG
*
170025 GGGACCACTGGATGT
1 GGGACCACTGGACGT
170040 GGGACCACTGGACGT
1 GGGACCACTGGACGT
170055 GGGACCA
1 GGGACCA
170062 ATGTTGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.41, T:0.14
Consensus pattern (15 bp):
GGGACCACTGGACGT
Found at i:171219 original size:18 final size:18
Alignment explanation
Indices: 171196--171237 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
171186 CCAAGTCTAA
171196 TTCTTCTGTAGATTTGAC
1 TTCTTCTGTAGATTTGAC
171214 TTCTTCTGTAGATTTGAC
1 TTCTTCTGTAGATTTGAC
171232 TTCTTC
1 TTCTTC
171238 ATTCTTGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.52
Consensus pattern (18 bp):
TTCTTCTGTAGATTTGAC
Found at i:172247 original size:3 final size:3
Alignment explanation
Indices: 172183--172228 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
172173 GAATGTTTTT
*
172183 TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
172229 CATTAGAGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:173723 original size:17 final size:17
Alignment explanation
Indices: 173698--173742 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
173688 ATCGTTGGAA
*
173698 CACTTAGTGCATCGGTG
1 CACTAAGTGCATCGGTG
173715 CACTAAGTGTGCATCGGTG
1 CACTAA--GTGCATCGGTG
173734 CACTAAGTG
1 CACTAAGTG
173743 TGCATCGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 8 0.32
19 17 0.68
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (17 bp):
CACTAAGTGCATCGGTG
Found at i:173728 original size:19 final size:19
Alignment explanation
Indices: 173704--173754 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
173694 GGAACACTTA
173704 GTGCATCGGTGCACTAAGT
1 GTGCATCGGTGCACTAAGT
173723 GTGCATCGGTGCACTAAGT
1 GTGCATCGGTGCACTAAGT
*
173742 GTGCATCGATGCA
1 GTGCATCGGTGCA
173755 TAAAATGCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (19 bp):
GTGCATCGGTGCACTAAGT
Found at i:173898 original size:65 final size:64
Alignment explanation
Indices: 173742--173901 Score: 212
Period size: 65 Copynumber: 2.5 Consensus size: 64
173732 TGCACTAAGT
* * * *
173742 GTGCATCGATGCATAAAATGCATTCGATGTTTTTAATAAGCCTAACTGAATCGATGCATGGTGT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTAACTGAATCGATGCATGGAGA
* * * * *
173806 GTGCATCGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAT-AAACCTAACTGAATCGATGCATGGAGA
* *
173871 GTGCATCGATGCATAAACTGCTTTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
173902 CAATTTATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
64 34 0.41
65 49 0.59
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAACCTAACTGAATCGATGCATGGAGA
Found at i:173937 original size:20 final size:20
Alignment explanation
Indices: 173912--173949 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
173902 CAATTTATTC
*
173912 ATTGGTTCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
173932 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
173950 TCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:182587 original size:65 final size:64
Alignment explanation
Indices: 182443--182602 Score: 187
Period size: 65 Copynumber: 2.5 Consensus size: 64
182433 TGCACTAAGT
* * * *
182443 GTGCATCGATGCATAAAAG-GCATTCGATGTTTTTAATAAGCCTAACTGAATCGATGCATGGTGT
1 GTGCATCGATGCAT-AAAGTGCATTCGATGTTTTCAATAAACCTAACTGAATCGATGCATGGAGA
* * * * *
182507 GTGCATCGATGCATAAAGTGCAATCGATGTTTTCATTAAAACCTGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATAAAGTGCATTCGATGTTTTCAAT-AAACCTAACTGAATCGATGCATGGAGA
* * *
182572 GTGCATCGATACATAAACTACATTCGATGTT
1 GTGCATCGATGCATAAAGTGCATTCGATGTT
182603 CAATTTATTC
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 4 0.05
64 29 0.36
65 48 0.59
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATAAAGTGCATTCGATGTTTTCAATAAACCTAACTGAATCGATGCATGGAGA
Found at i:183961 original size:101 final size:101
Alignment explanation
Indices: 183797--183986 Score: 283
Period size: 101 Copynumber: 1.9 Consensus size: 101
183787 TTTGAATTTG
* * * *
183797 TTTGGCTAGTTGAAAGAATCTATCCATAAAGCCAGATCTTTTAACCATTTGCTTTAGAGGAATAA
1 TTTGGCTAGCTGAAAGAATCTATCCATAAAGCCAGAGCTTTCAACCAATTGCTTTAGAGGAATAA
*
183862 CTC-GTCTTTATTGTATGTATATATTATTTGCCTTTA
66 CTCAG-CTTTATTGTATATATATATTATTTGCCTTTA
* * * *
183898 TTTGGCTAGCTGAAGGAATCTATCCATAAAGCCAGGGCTTTCAACCAATTGTTTTATAGGAATAA
1 TTTGGCTAGCTGAAAGAATCTATCCATAAAGCCAGAGCTTTCAACCAATTGCTTTAGAGGAATAA
183963 CTCAGCTTTATTGTATATATATAT
66 CTCAGCTTTATTGTATATATATAT
183987 AATTACATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 78 0.99
102 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (101 bp):
TTTGGCTAGCTGAAAGAATCTATCCATAAAGCCAGAGCTTTCAACCAATTGCTTTAGAGGAATAA
CTCAGCTTTATTGTATATATATATTATTTGCCTTTA
Found at i:190763 original size:9 final size:9
Alignment explanation
Indices: 190741--190776 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
190731 CTCTAAATGG
*
190741 AAAAATAAAA
1 AAAAAT-AAC
190751 AAAAATAAC
1 AAAAATAAC
190760 AAAAATAAC
1 AAAAATAAC
190769 AAAAATAA
1 AAAAATAA
190777 GGTGGGTCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 19 0.76
10 6 0.24
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAC
Found at i:191772 original size:32 final size:32
Alignment explanation
Indices: 191731--191846 Score: 99
Period size: 32 Copynumber: 3.5 Consensus size: 32
191721 CAATACAGAC
*
191731 TCAACTTCACGACGAATGAGTCACCCACGATT
1 TCAACTTCACAACGAATGAGTCACCCACGATT
* * * **
191763 TCAACTTCACAACGAAGGATATCGTACCTAAAAGTT
1 TCAACTTCACAACGAATGA-GTC--ACCCACGA-TT
* * *
191799 TCGAC-TCAACGATGAATGAGTCACCCACGATT
1 TCAACTTC-ACAACGAATGAGTCACCCACGATT
191831 TCAACTTCACAACGAA
1 TCAACTTCACAACGAA
191847 CTATATCGTA
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
32 29 0.48
33 9 0.15
35 9 0.15
36 14 0.23
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (32 bp):
TCAACTTCACAACGAATGAGTCACCCACGATT
Found at i:191927 original size:74 final size:73
Alignment explanation
Indices: 191728--191967 Score: 271
Period size: 68 Copynumber: 3.4 Consensus size: 73
191718 ATTCAATACA
* *
191728 GACTCAACTTCACGACGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTACCTA
1 GACTTAACTTCACGACGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTACCCA
191793 AAAGTTTC
66 AAAGTTTC
* * **
191801 GAC-T--C--AACGATGAATGAGTCACCCACGATTTCAACTTCACAACGAACTATATCGTACCCA
1 GACTTAACTTCACGACGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTACCCA
191861 AAAGTTTC
66 AAAGTTTC
* * * * *
191869 GACTTAACTTCACGACGAAGGAGTTGCTCCC-TGATTTCAACTTCACAATGAAGGATATCGTGCC
1 GACTTAACTTCACGACGAATGAG-T-CACCCACGATTTCAACTTCACAACGAAGGATATCGTACC
* *
191933 CAATA-TATC
64 CAAAAGTTTC
*
191942 GACTTAACTTCAC-AGCAAATGAGTCA
1 GACTTAACTTCACGA-CGAATGAGTCA
191968 TCTACAACAA
Statistics
Matches: 139, Mismatches: 20, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
68 61 0.44
69 1 0.01
70 1 0.01
71 2 0.01
72 2 0.01
73 35 0.25
74 33 0.24
75 4 0.03
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (73 bp):
GACTTAACTTCACGACGAATGAGTCACCCACGATTTCAACTTCACAACGAAGGATATCGTACCCA
AAAGTTTC
Found at i:192645 original size:36 final size:35
Alignment explanation
Indices: 192573--192725 Score: 175
Period size: 36 Copynumber: 4.4 Consensus size: 35
192563 TCAAATATAG
* * ***
192573 TTTTT-AAAATATATAATATATAGTTTTTGGAA-A
1 TTTTTGAAAACATATAATATATGGTTTTAAAAACA
192606 TTTTTGAAAACATATAATATATGGTTTTAAAAAACA
1 TTTTTGAAAACATATAATATATGGTTTT-AAAAACA
* * *
192642 TTTTTGAAAACGTATAAGATATGGTTTTTAAAACA
1 TTTTTGAAAACATATAATATATGGTTTTAAAAACA
* * *
192677 TTTTTTGAAAACGTATAATATATGTTTTTGAAAACA
1 -TTTTTGAAAACATATAATATATGGTTTTAAAAACA
192713 TTTTTGAAAACAT
1 TTTTTGAAAACAT
192726 TTTTGAAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
33 5 0.05
34 20 0.19
35 20 0.19
36 59 0.57
ACGTcount: A:0.42, C:0.05, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTTTGAAAACATATAATATATGGTTTTAAAAACA
Found at i:192733 original size:83 final size:83
Alignment explanation
Indices: 192636--192807 Score: 258
Period size: 83 Copynumber: 2.1 Consensus size: 83
192626 ATGGTTTTAA
* *
192636 AAAACATTTTTG-AAAACGTATAAGATATGGTTTTTAAAACATTTTTTGAAAACGTATAATATA-
1 AAAACATTTTTGAAAAACGTATAAGATATGGTTTTAAAAAC-CTTTTTGAAAACGTATAATATAT
*
192699 TGTTTTTGAAAACATTTTTG
65 TG-TTTTAAAAACATTTTTG
* * *
192719 AAAACATTTTTGAAAAATGTATAATATATGGTTTTAAAAACCTTTTTGAAAACGTATAATATGTT
1 AAAACATTTTTGAAAAACGTATAAGATATGGTTTTAAAAACCTTTTTGAAAACGTATAATATATT
192784 GTTTTAAAAACATTTTTG
66 GTTTTAAAAACATTTTTG
192802 AAAACA
1 AAAACA
192808 CATATAATAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
83 54 0.67
84 27 0.33
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.41
Consensus pattern (83 bp):
AAAACATTTTTGAAAAACGTATAAGATATGGTTTTAAAAACCTTTTTGAAAACGTATAATATATT
GTTTTAAAAACATTTTTG
Found at i:192735 original size:13 final size:12
Alignment explanation
Indices: 192701--192734 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
192691 ATAATATATG
192701 TTTTTGAAAACA
1 TTTTTGAAAACA
192713 TTTTTGAAAACA
1 TTTTTGAAAACA
192725 TTTTTGAAAA
1 TTTTTGAAAA
192735 ATGTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:192788 original size:35 final size:35
Alignment explanation
Indices: 192714--192920 Score: 211
Period size: 36 Copynumber: 5.8 Consensus size: 35
192704 TTGAAAACAT
* *
192714 TTTTGAAAACATTTTTGAAAA-ATGTATAATATATGG
1 TTTTAAAAACATTTTTGAAAACA--TATAATATATAG
* * * *
192750 TTTTAAAAACCTTTTTGAAAACGTATAATATGTTG
1 TTTTAAAAACATTTTTGAAAACATATAATATATAG
192785 TTTTAAAAACATTTTTGAAAACACATATAATATATAG
1 TTTTAAAAACATTTTTG-AAA-ACATATAATATATAG
** * * * *
192822 TTTTGAAAATATTTTTTTGAAAACGTATAGTACATGG
1 TTTT-AAAA-ACATTTTTGAAAACATATAATATATAG
* *
192859 TTTTGAAAAC-GTTTTGAAAACATATAATATATAG
1 TTTTAAAAACATTTTTGAAAACATATAATATATAG
192893 TTTTAAAAACATATTTTGAAAACATATA
1 TTTTAAAAACAT-TTTTGAAAACATATA
192921 CATGTGTTTT
Statistics
Matches: 140, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
34 28 0.20
35 27 0.19
36 40 0.29
37 31 0.22
38 7 0.05
39 7 0.05
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.41
Consensus pattern (35 bp):
TTTTAAAAACATTTTTGAAAACATATAATATATAG
Found at i:192937 original size:36 final size:38
Alignment explanation
Indices: 192870--192963 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 38
192860 TTTGAAAACG
*
192870 TTTTGAAAACATATA-ATATATAGTTTTAAAAACAT-A-
1 TTTTGAAAACATATACATATATA-TTTTAAAAAAATGAT
* *
192906 TTTTGAAAACATATACATGTGT-TTTTAAAAAAAATGAT
1 TTTTGAAAACATATACATATATATTTT-AAAAAAATGAT
*
192944 TTTTGGAAACATAATACATA
1 TTTTGAAAACAT-ATACATA
192964 CTTACATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
35 4 0.08
36 22 0.46
37 5 0.10
38 11 0.23
39 6 0.12
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (38 bp):
TTTTGAAAACATATACATATATATTTTAAAAAAATGAT
Found at i:193025 original size:23 final size:24
Alignment explanation
Indices: 192989--193053 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
192979 TTTCGTCACA
*
192989 TTATATATTAATATTATTTTTAT-T
1 TTATTTATT-ATATTATTTTTATAT
*
193013 TTATTTATTATATTA-TATTATAT
1 TTATTTATTATATTATTTTTATAT
193036 TTATTTATTAT-TTATTTT
1 TTATTTATTATATTATTTT
193054 GTTTATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 8 0.22
23 20 0.56
24 8 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATTTATTATATTATTTTTATAT
Found at i:193058 original size:16 final size:18
Alignment explanation
Indices: 192992--193060 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 18
192982 CGTCACATTA
192992 TATATTA-ATATTATTT-T
1 TATATTATAT-TTATTTAT
193009 TAT-TT-TATTTATTATAT
1 TATATTATATTTATT-TAT
193026 TATATTATATTTATTTAT
1 TATATTATATTTATTTAT
*
193044 TAT-TTAT-TTTGTTTAT
1 TATATTATATTTATTTAT
193060 T
1 T
193061 TTTTTTCAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
15 5 0.11
16 14 0.30
17 11 0.24
18 8 0.17
19 8 0.17
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (18 bp):
TATATTATATTTATTTAT
Found at i:194265 original size:5 final size:5
Alignment explanation
Indices: 194255--194305 Score: 59
Period size: 5 Copynumber: 9.8 Consensus size: 5
194245 CCTTTTATTC
*
194255 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT- TTTTA TATTTA TATTTA TATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA -ATTTA -ATTTA -ATTT
194306 TTCAAATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
4 3 0.07
5 24 0.57
6 15 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (5 bp):
ATTTA
Found at i:195229 original size:15 final size:15
Alignment explanation
Indices: 195209--195274 Score: 98
Period size: 15 Copynumber: 4.4 Consensus size: 15
195199 TTTCGGAAAA
195209 TGAATTACTGAAATT
1 TGAATTACTGAAATT
195224 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
195239 TGAATTACTGGAAA-A
1 TGAATTACT-GAAATT
*
195254 TGAATTACTGGAATT
1 TGAATTACTGAAATT
195269 TGAATT
1 TGAATT
195275 TTGGAAAATG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
14 3 0.07
15 39 0.85
16 4 0.09
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:195286 original size:14 final size:15
Alignment explanation
Indices: 195203--195290 Score: 92
Period size: 15 Copynumber: 5.9 Consensus size: 15
195193 TTAGTTTTTC
195203 GGAAAATGAATTACT
1 GGAAAATGAATTACT
*
195218 -GAAATTTGAATTACT
1 GGAAA-ATGAATTACT
*
195233 -GAAATTTGAATTACT
1 GGAAA-ATGAATTACT
195248 GGAAAATGAATTACT
1 GGAAAATGAATTACT
** *
195263 GGAATTTGAATT-TT
1 GGAAAATGAATTACT
195277 GGAAAATGAATTAC
1 GGAAAATGAATTAC
195291 ATTTCCGGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
14 15 0.24
15 43 0.69
16 4 0.06
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.34
Consensus pattern (15 bp):
GGAAAATGAATTACT
Done.