Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001189.1 Hibiscus syriacus cultivar Beakdansim tig00002360_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: 166740
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:288 original size:18 final size:18
Alignment explanation
Indices: 276--310 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
266 CCGGTTTAAC
276 CGGTTTGACCGGTCTGAA
1 CGGTTTGACCGGTCTGAA
294 CGGTTTGACCGGTCTGA
1 CGGTTTGACCGGTCTGA
311 CCCGACCCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (18 bp):
CGGTTTGACCGGTCTGAA
Found at i:311 original size:9 final size:9
Alignment explanation
Indices: 274--312 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
264 AACCGGTTTA
*
274 ACCGGTTTG
1 ACCGGTCTG
283 ACCGGTCTG
1 ACCGGTCTG
* *
292 AACGGTTTG
1 ACCGGTCTG
301 ACCGGTCTG
1 ACCGGTCTG
310 ACC
1 ACC
313 CGACCCGACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:2230 original size:77 final size:78
Alignment explanation
Indices: 2131--2286 Score: 296
Period size: 77 Copynumber: 2.0 Consensus size: 78
2121 GAAACATGCG
*
2131 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATTGTTGAA
1 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
2196 CCAATTCTGCAAA
66 CCAATTCTGCAAA
2209 ACGCAAT-AAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
1 ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
2273 CCAATTCTGCAAA
66 CCAATTCTGCAAA
2286 A
1 A
2287 GTATGCCTAA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
77 70 0.91
78 7 0.09
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.25
Consensus pattern (78 bp):
ACGCAATAAAACCAGCAGCCCCAGTTATGAGGATGTTCTTAGGGGTATAGTTAGCCATAGTTGAA
CCAATTCTGCAAA
Found at i:10354 original size:57 final size:56
Alignment explanation
Indices: 10292--10399 Score: 146
Period size: 56 Copynumber: 1.9 Consensus size: 56
10282 ATGCACATAA
* *
10292 CATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCACCAGC
1 CATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCACTTGATGCACCAGC
* * *
10349 CATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCA
1 CATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCA
10400 TCGGTGCACT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
56 22 0.49
57 20 0.44
58 3 0.07
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (56 bp):
CATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCACTTGATGCACCAGC
Found at i:11774 original size:19 final size:17
Alignment explanation
Indices: 11750--11812 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
11740 ATCGATTTTC
11750 TTTTGAAAACAAAATTAGA
1 TTTTGAAAACAAAA-TA-A
*
11769 TTTTGAAAGCAAAA-AA
1 TTTTGAAAACAAAATAA
* *
11785 TTTTGAAAGCCAAATGAAA
1 TTTTGAAAACAAAAT--AA
11804 TTTTGAAAA
1 TTTTGAAAA
11813 GGATTTAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
16 14 0.37
17 1 0.03
19 23 0.61
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (17 bp):
TTTTGAAAACAAAATAA
Found at i:11789 original size:16 final size:18
Alignment explanation
Indices: 11768--11811 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
11758 ACAAAATTAG
11768 ATTTTGAAAG-CAAA-AA
1 ATTTTGAAAGCCAAAGAA
11784 ATTTTGAAAGCCAAATGAA
1 ATTTTGAAAGCCAAA-GAA
11803 ATTTTGAAA
1 ATTTTGAAA
11812 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.40
17 4 0.16
19 11 0.44
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.30
Consensus pattern (18 bp):
ATTTTGAAAGCCAAAGAA
Found at i:13085 original size:34 final size:30
Alignment explanation
Indices: 13047--13115 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
13037 CGATATAACA
13047 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
13081 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
13110 AATTTA
1 AATTTA
13116 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:13126 original size:29 final size:30
Alignment explanation
Indices: 13056--13115 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
13046 AAATTTAAGG
13056 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
13087 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
13116 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:13221 original size:21 final size:21
Alignment explanation
Indices: 13195--13251 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
13185 AGGGTGTCAA
13195 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
13216 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCACCCCTGC
13237 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
13252 TTGCACTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:13264 original size:22 final size:20
Alignment explanation
Indices: 13236--13294 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
13226 TGCATCCCTG
13236 TAGTGCATCCATGCACTTGCAC
1 TAGTGCATCCATGCACTT--AC
* *
13258 TAGTGCATCGATGCATCATAC
1 TAGTGCATCCATGCA-CTTAC
13279 -AGTGCATCCATGCACT
1 TAGTGCATCCATGCACT
13295 CAAACACCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 13 0.41
21 2 0.06
22 14 0.44
23 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (20 bp):
TAGTGCATCCATGCACTTAC
Found at i:13339 original size:20 final size:20
Alignment explanation
Indices: 13314--13381 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
13304 AATACAATTA
*
13314 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
**
13334 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTGCT
13355 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
13375 GTGCATC
1 GTGCATC
13382 CATACACGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 25 0.60
21 17 0.40
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:13394 original size:41 final size:41
Alignment explanation
Indices: 13314--13396 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
13304 AATACAATTA
* * *
13314 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATACATCAAGGCT
13355 GTGCATCGATGCATCCTGCTGTGCATCCATACA-CGAAGGCT
1 GTGCATCGATGCATCCTGCTGTGCATCCATACATC-AAGGCT
13396 G
1 G
13397 CAACGGCTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 37 0.97
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (41 bp):
GTGCATCGATGCATCCTGCTGTGCATCCATACATCAAGGCT
Found at i:13783 original size:34 final size:32
Alignment explanation
Indices: 13744--13813 Score: 77
Period size: 34 Copynumber: 2.1 Consensus size: 32
13734 TTTTGTAAAG
* * *
13744 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAGCCCG-G-AAAAACTA
* *
13778 GGGAAATGTTATAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
13810 GGGA
1 GGGA
13814 GTTGTAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 11 0.35
33 1 0.03
34 19 0.61
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTATAGCTTAGCCCGGAAAAACTA
Found at i:15032 original size:18 final size:19
Alignment explanation
Indices: 15009--15046 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
14999 ACCAATTTCG
15009 TCAAAAACAAA-C-AATTTT
1 TCAAAAA-AAATCGAATTTT
15027 TCAAAAAAAATCGAATTTT
1 TCAAAAAAAATCGAATTTT
15046 T
1 T
15047 TTTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 8 0.44
19 7 0.39
ACGTcount: A:0.53, C:0.13, G:0.03, T:0.32
Consensus pattern (19 bp):
TCAAAAAAAATCGAATTTT
Found at i:16741 original size:2 final size:2
Alignment explanation
Indices: 16734--16758 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16724 CAGCTTAAGC
16734 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 T
16759 TTAATCAATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17323 original size:65 final size:64
Alignment explanation
Indices: 17206--17410 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 64
17196 TTTCAGAGTA
* * * *
17206 ATGCACCGATGCACCGATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCACC-AACCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGCAT
*
17268 TTC
62 TTG
*
17271 ATGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATT
1 ATGCATCGATGCACCA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATT
17334 TG
63 TG
* * * * *
17336 ATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTG
*
17400 ATGTATCGATG
1 ATGCATCGATG
17411 TACTCTTAGT
Statistics
Matches: 119, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 43 0.36
65 67 0.56
66 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (64 bp):
ATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTG
Found at i:17429 original size:64 final size:63
Alignment explanation
Indices: 17254--17433 Score: 168
Period size: 65 Copynumber: 2.8 Consensus size: 63
17244 AATTAAATTG
* * * * *
17254 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAA
1 AACATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAA
* * * *
17319 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TG-
1 AACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGA
17382 A
63 A
* *
17383 AACATCGAATGCACTTGATGTATCGATGTACTCTTAG-TGCACCGATGCACT
1 AACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
17434 AAGGGTCCAA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
64 43 0.43
65 51 0.52
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (63 bp):
AACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAA
Found at i:20878 original size:29 final size:30
Alignment explanation
Indices: 20845--20920 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
20835 TTGGCTTATA
* *
20845 ATATTTTATTCTTATCTTT-ACTTAAAACT
1 ATATTTTATTCTTATCTTTAAATTAAAAAT
**
20874 ATATTTTAAAAC-TAT-TTTAAATTAAAAAT
1 ATATTTT-ATTCTTATCTTTAAATTAAAAAT
*
20903 ATATTTTATTATTATCTT
1 ATATTTTATTCTTATCTT
20921 AGCTTTTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
28 4 0.11
29 28 0.78
30 4 0.11
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (30 bp):
ATATTTTATTCTTATCTTTAAATTAAAAAT
Found at i:20982 original size:31 final size:31
Alignment explanation
Indices: 20947--21010 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
20937 TTAAAAATAT
*
20947 ATATATTTTTTTAAATAAAAATAAGAGTAAA
1 ATATATATTTTTAAATAAAAATAAGAGTAAA
* * * *
20978 ATATATATTTTTATATTAAATTAATAGTAAA
1 ATATATATTTTTAAATAAAAATAAGAGTAAA
21009 AT
1 AT
21011 TTTTAAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (31 bp):
ATATATATTTTTAAATAAAAATAAGAGTAAA
Found at i:21105 original size:31 final size:31
Alignment explanation
Indices: 21064--21158 Score: 99
Period size: 31 Copynumber: 3.1 Consensus size: 31
21054 AAGTGATGAT
21064 AAAGATAAAATATATATCAATAAATTAA-A-ATA
1 AAAGA-AAAATATAT-TCAATAAATTAAGACA-A
*
21096 AAAGAAAAATATATTTAATAAATTAAGACAA
1 AAAGAAAAATATATTCAATAAATTAAGACAA
* * *
21127 AAATAAAAATAT-TT-AATAACTTAAAACAA
1 AAAGAAAAATATATTCAATAAATTAAGACAA
21156 AAA
1 AAA
21159 TAAAGAGATA
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.28
30 13 0.23
31 22 0.39
32 6 0.11
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAGAAAAATATATTCAATAAATTAAGACAA
Found at i:21144 original size:29 final size:30
Alignment explanation
Indices: 21068--21162 Score: 122
Period size: 29 Copynumber: 3.2 Consensus size: 30
21058 GATGATAAAG
* *
21068 ATAAAATATATATCAATAAATTAAAATAAAA
1 ATAAAATATAT-TTAATAAATTAAAACAAAA
*
21099 GA-AAAATATATTTAATAAATTAAGACAAAA
1 -ATAAAATATATTTAATAAATTAAAACAAAA
*
21129 ATAAAA-ATATTTAATAACTTAAAACAAAA
1 ATAAAATATATTTAATAAATTAAAACAAAA
21158 ATAAA
1 ATAAA
21163 GAGATAATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
29 27 0.47
30 20 0.35
31 9 0.16
32 1 0.02
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.27
Consensus pattern (30 bp):
ATAAAATATATTTAATAAATTAAAACAAAA
Found at i:30291 original size:29 final size:29
Alignment explanation
Indices: 30249--30305 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
30239 AGTAATCTTG
*
30249 CAGGTCGCCATGTAATCAAAACGACCAAA
1 CAGGTAGCCATGTAATCAAAACGACCAAA
*
30278 CAGGTAGCCATGTAATCAGAACGACCAA
1 CAGGTAGCCATGTAATCAAAACGACCAA
30306 GCAAAGGTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.26, G:0.19, T:0.14
Consensus pattern (29 bp):
CAGGTAGCCATGTAATCAAAACGACCAAA
Found at i:30951 original size:22 final size:22
Alignment explanation
Indices: 30926--30969 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
30916 ATTAGTTTGT
*
30926 TAGTTTGTTAGTTTAGGGTTTA
1 TAGTTTATTAGTTTAGGGTTTA
30948 TAGTTTATTAGTTTAGGGTTTA
1 TAGTTTATTAGTTTAGGGTTTA
30970 GGGTTTAGGG
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:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (22 bp):
TAGTTTATTAGTTTAGGGTTTA
Found at i:30968 original size:7 final size:7
Alignment explanation
Indices: 30958--30982 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30948 TAGTTTATTA
30958 GTTTAGG
1 GTTTAGG
30965 GTTTAGG
1 GTTTAGG
30972 GTTTAGG
1 GTTTAGG
30979 GTTT
1 GTTT
30983 CCGAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (7 bp):
GTTTAGG
Found at i:30975 original size:22 final size:22
Alignment explanation
Indices: 30927--30976 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
30917 TTAGTTTGTT
* *
30927 AGTTTGTTAGTTTAGGGTTTAT
1 AGTTTATTAGTTTAGGGTTTAG
30949 AGTTTATTAGTTTAGGGTTTAG
1 AGTTTATTAGTTTAGGGTTTAG
*
30971 GGTTTA
1 AGTTTA
30977 GGGTTTCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (22 bp):
AGTTTATTAGTTTAGGGTTTAG
Found at i:31184 original size:35 final size:35
Alignment explanation
Indices: 31106--31191 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
31096 AAATTTAGTT
31106 AATTAGTTTATTAGTTTAAGTTATATTATAATAAAA
1 AATTAGTTTATTAG-TTAAGTTATATTATAATAAAA
* *
31142 AA-CAGTTTATTAGTTAATTTA-AGTTAT-ATAAAA
1 AATTAGTTTATTAGTTAAGTTATA-TTATAATAAAA
*
31175 GAATTAGTTTGTTAGTT
1 -AATTAGTTTATTAGTT
31192 TAGGGTTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
33 7 0.16
34 13 0.30
35 21 0.49
36 2 0.05
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.47
Consensus pattern (35 bp):
AATTAGTTTATTAGTTAAGTTATATTATAATAAAA
Found at i:31201 original size:7 final size:7
Alignment explanation
Indices: 31189--31220 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
31179 TAGTTTGTTA
31189 GTTTAGG
1 GTTTAGG
31196 GTTTAGG
1 GTTTAGG
31203 GTTTAGG
1 GTTTAGG
31210 GTTTAGG
1 GTTTAGG
31217 GTTT
1 GTTT
31221 CCACTCATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.41, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:31252 original size:7 final size:7
Alignment explanation
Indices: 31242--31356 Score: 52
Period size: 7 Copynumber: 16.6 Consensus size: 7
31232 ATATATACTA
31242 TAAACCC
1 TAAACCC
31249 TAAACCC
1 TAAACCC
*
31256 T-AACCT
1 TAAACCC
* *
31262 TAAATCA
1 TAAACCC
**
31269 TAAACTA
1 TAAACCC
*
31276 TAAATCC
1 TAAACCC
* *
31283 TATACCA
1 TAAACCC
*
31290 TAAACCT
1 TAAACCC
**
31297 TAAACTA
1 TAAACCC
31304 TAAACCC
1 TAAACCC
**
31311 TAAACAA
1 TAAACCC
*
31318 TAAACCT
1 TAAACCC
**
31325 TAAATTC
1 TAAACCC
* *
31332 TAAATCA
1 TAAACCC
*
31339 TAAACTC
1 TAAACCC
31346 TAAACCC
1 TAAACCC
31353 TAAA
1 TAAA
31357 TTAATAAACT
Statistics
Matches: 77, Mismatches: 30, Indels: 2
0.71 0.28 0.02
Matches are distributed among these distances:
6 5 0.06
7 72 0.94
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCC
Found at i:31281 original size:14 final size:14
Alignment explanation
Indices: 31249--31356 Score: 67
Period size: 14 Copynumber: 7.8 Consensus size: 14
31239 CTATAAACCC
* *
31249 TAAACCCTAACCT-
1 TAAACCATAAACTA
*
31262 TAAATCATAAACTA
1 TAAACCATAAACTA
* *
31276 TAAATCC-TATACCA
1 TAAA-CCATAAACTA
*
31290 TAAACCTTAAACTA
1 TAAACCATAAACTA
* *
31304 TAAACCCTAAACAA
1 TAAACCATAAACTA
* * *
31318 TAAACCTTAAATTC
1 TAAACCATAAACTA
* *
31332 TAAATCATAAACTC
1 TAAACCATAAACTA
*
31346 TAAACCCTAAA
1 TAAACCATAAA
31357 TTAATAAACT
Statistics
Matches: 73, Mismatches: 19, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
13 12 0.16
14 60 0.82
15 1 0.01
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAAACTA
Found at i:31300 original size:28 final size:28
Alignment explanation
Indices: 31269--31343 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
31259 CCTTAAATCA
* *
31269 TAAACTATAAATCCTATACCATAAACCT
1 TAAACTATAAATCCTAAACAATAAACCT
*
31297 TAAACTATAAACCCTAAACAATAAACCT
1 TAAACTATAAATCCTAAACAATAAACCT
* * *
31325 TAAATTCTAAATCATAAAC
1 TAAACTATAAATCCTAAAC
31344 TCTAAACCCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAACTATAAATCCTAAACAATAAACCT
Found at i:31357 original size:21 final size:21
Alignment explanation
Indices: 31297--31366 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
31287 CCATAAACCT
*
31297 TAAACTATAAACCCTAAA-CAA
1 TAAACTCTAAACCCTAAATC-A
**
31318 TAAAC-CTTAAATTCTAAATCA
1 TAAACTC-TAAACCCTAAATCA
*
31339 TAAACTCTAAACCCTAAATTAA
1 TAAACTCTAAACCCTAAA-TCA
31361 TAAACT
1 TAAACT
31367 AACAAACTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
21 29 0.74
22 10 0.26
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACTCTAAACCCTAAATCA
Found at i:31395 original size:7 final size:7
Alignment explanation
Indices: 31383--31477 Score: 57
Period size: 7 Copynumber: 13.7 Consensus size: 7
31373 CTAAATTATA
31383 GTTTAGG
1 GTTTAGG
*
31390 GTTTAGA
1 GTTTAGG
31397 GTTTAGG
1 GTTTAGG
*
31404 GTTTAAG
1 GTTTAGG
*
31411 GTTTATG
1 GTTTAGG
** *
31418 GACTAAG
1 GTTTAGG
**
31425 GTTTATA
1 GTTTAGG
*
31432 GTTTATG
1 GTTTAGG
* *
31439 ATTTAAG
1 GTTTAGG
*
31446 G-TTAGA
1 GTTTAGG
31452 GTTTAGG
1 GTTTAGG
*
31459 GTTTAAG
1 GTTTAGG
31466 GTTTAGG
1 GTTTAGG
*
31473 ATTTA
1 GTTTA
31478 TAGTATATGC
Statistics
Matches: 66, Mismatches: 21, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
6 4 0.06
7 62 0.94
ACGTcount: A:0.25, C:0.01, G:0.29, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:31456 original size:20 final size:20
Alignment explanation
Indices: 31421--31468 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31411 GTTTATGGAC
* *
31421 TAAGGTTTATAGTTTATGATT
1 TAAGG-TTAGAGTTTAGGATT
*
31442 TAAGGTTAGAGTTTAGGGTT
1 TAAGGTTAGAGTTTAGGATT
31462 TAAGGTT
1 TAAGGTT
31469 TAGGATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 19 0.79
21 5 0.21
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (20 bp):
TAAGGTTAGAGTTTAGGATT
Found at i:31538 original size:35 final size:35
Alignment explanation
Indices: 31499--31571 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
31489 ACACGAGTGG
*
31499 AAACCTAAAACCTTAAATCATAAACACTAAACACT
1 AAACCTAAAACCATAAATCATAAACACTAAACACT
* * * * *
31534 AAACCTTAAATCATAAATTATAAACCCTAAACCCT
1 AAACCTAAAACCATAAATCATAAACACTAAACACT
31569 AAA
1 AAA
31572 TCATAAACTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (35 bp):
AAACCTAAAACCATAAATCATAAACACTAAACACT
Found at i:31557 original size:21 final size:21
Alignment explanation
Indices: 31533--31620 Score: 59
Period size: 21 Copynumber: 4.1 Consensus size: 21
31523 CACTAAACAC
* * *
31533 TAAACCTTAAATCATAAATTA
1 TAAACCCTAAACCATAAATCA
*
31554 TAAACCCTAAACCCTAAATCA
1 TAAACCCTAAACCATAAATCA
** * *
31575 TAAACTATAAACCTTAAACTAA
1 TAAACCCTAAACCATAAA-TCA
* ** *
31597 CAAACTATAAACCCTAAATCA
1 TAAACCCTAAACCATAAATCA
31618 TAA
1 TAA
31621 CTTAAACGTG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
21 36 0.67
22 18 0.33
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACCATAAATCA
Found at i:31585 original size:14 final size:14
Alignment explanation
Indices: 31512--31595 Score: 57
Period size: 14 Copynumber: 6.0 Consensus size: 14
31502 CCTAAAACCT
31512 TAAATCATAAAC-A
1 TAAATCATAAACTA
31525 CTAAA-CACTAAACCT-
1 -TAAATCA-TAAA-CTA
*
31540 TAAATCATAAATTA
1 TAAATCATAAACTA
* * **
31554 TAAACCCTAAACCC
1 TAAATCATAAACTA
31568 TAAATCATAAACTA
1 TAAATCATAAACTA
* *
31582 TAAACCTTAAACTA
1 TAAATCATAAACTA
31596 ACAAACTATA
Statistics
Matches: 53, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
13 3 0.06
14 47 0.89
15 3 0.06
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAATCATAAACTA
Found at i:31587 original size:28 final size:28
Alignment explanation
Indices: 31506--31614 Score: 115
Period size: 28 Copynumber: 4.1 Consensus size: 28
31496 TGGAAACCTA
* *
31506 AAACCTTAAATCATAAAC-ACTAAACACT
1 AAACCCTAAATCATAAACTA-TAAACCCT
* *
31534 AAACCTTAAATCATAAATTATAAACCCT
1 AAACCCTAAATCATAAACTATAAACCCT
*
31562 AAACCCTAAATCATAAACTATAAACCTT
1 AAACCCTAAATCATAAACTATAAACCCT
31590 AAA--CT-AA-C--AAACTATAAACCCT
1 AAACCCTAAATCATAAACTATAAACCCT
31612 AAA
1 AAA
31615 TCATAACTTA
Statistics
Matches: 74, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
22 16 0.22
24 1 0.01
25 2 0.03
26 2 0.03
28 52 0.70
29 1 0.01
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.23
Consensus pattern (28 bp):
AAACCCTAAATCATAAACTATAAACCCT
Found at i:31700 original size:33 final size:34
Alignment explanation
Indices: 31640--31706 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
31630 GAATTTTCCC
31640 CTTAAACAACTAATACACTATTCTTTTA-TATAA
1 CTTAAACAACTAATACACTATTCTTTTATTATAA
31673 CTTAAACTAACTAATGA-ACTATT-TTTTATTATAA
1 CTTAAAC-AACTAAT-ACACTATTCTTTTATTATAA
31707 TATAACTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 12 0.39
34 18 0.58
35 1 0.03
ACGTcount: A:0.42, C:0.15, G:0.01, T:0.42
Consensus pattern (34 bp):
CTTAAACAACTAATACACTATTCTTTTATTATAA
Found at i:31933 original size:37 final size:37
Alignment explanation
Indices: 31885--31988 Score: 106
Period size: 37 Copynumber: 2.8 Consensus size: 37
31875 TAAACTAATA
* *
31885 AACTAACAAACTAATTTTTTTAAAATATAACTGAAAT
1 AACTAATAAACTAATTTTTTTATAATATAACTGAAAT
* * *
31922 AACTAATAAACTATTTTTTATTATAACATAACTTAAAT
1 AACTAATAAACTAATTTTT-TTATAATATAACTGAAAT
*
31960 ---TAATTAACTAAATTTTTTATATAATATAA
1 AACTAATAAACT-AATTTTTT-TATAATATAA
31989 ATTCAACAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
35 9 0.16
36 15 0.27
37 17 0.30
38 15 0.27
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (37 bp):
AACTAATAAACTAATTTTTTTATAATATAACTGAAAT
Found at i:32134 original size:2 final size:2
Alignment explanation
Indices: 32127--32173 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
32117 GAATTTAATA
32127 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
32169 AT AT A
1 AT AT A
32174 ATTGTATAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32562 original size:29 final size:29
Alignment explanation
Indices: 32529--32588 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
32519 ATGGGACCTT
*
32529 TGCTTGGTCGTTTTGATTACATGGCGACC
1 TGCTTGGTCGTTTTGATTACACGGCGACC
32558 TGCTTGGTCGTTTTGATTACACGGCGACC
1 TGCTTGGTCGTTTTGATTACACGGCGACC
32587 TG
1 TG
32589 TAAGATTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.13, C:0.22, G:0.28, T:0.37
Consensus pattern (29 bp):
TGCTTGGTCGTTTTGATTACACGGCGACC
Found at i:35184 original size:14 final size:15
Alignment explanation
Indices: 35165--35193 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35155 CTCTTTTCTT
35165 AATATTAA-AAAATA
1 AATATTAATAAAATA
35179 AATATTAATAAAATA
1 AATATTAATAAAATA
35194 TTTATCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATTAATAAAATA
Found at i:37263 original size:17 final size:18
Alignment explanation
Indices: 37241--37297 Score: 62
Period size: 17 Copynumber: 3.1 Consensus size: 18
37231 TATTTATTTC
37241 ATAATAATAAT-ATAAAT
1 ATAATAATAATAATAAAT
*
37258 ATAATAATAATAATAAAAA
1 ATAATAATAATAAT-AAAT
*
37277 ACAAATTAATAATAATAAAT
1 A-TAA-TAATAATAATAAAT
37297 A
1 A
37298 AAACAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 11 0.33
18 2 0.06
19 4 0.12
20 6 0.18
21 10 0.30
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAATAATAATAATAAAT
Found at i:37264 original size:9 final size:10
Alignment explanation
Indices: 37241--37298 Score: 52
Period size: 9 Copynumber: 6.1 Consensus size: 10
37231 TATTTATTTC
37241 ATAAT-AATA
1 ATAATAAATA
37250 AT-ATAAAT-
1 ATAATAAATA
37258 ATAAT-AATA
1 ATAATAAATA
*
37267 ATAATAAAAA
1 ATAATAAATA
* *
37277 ACAAATTAATA
1 A-TAATAAATA
37288 ATAATAAATA
1 ATAATAAATA
37298 A
1 A
37299 AACAAATGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
8 7 0.18
9 12 0.32
10 12 0.32
11 7 0.18
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (10 bp):
ATAATAAATA
Found at i:37272 original size:14 final size:13
Alignment explanation
Indices: 37243--37298 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
37233 TTTATTTCAT
37243 AATAATAAT-ATA
1 AATAATAATAATA
37255 AAT-ATAATAAT-
1 AATAATAATAATA
* *
37266 AATAATAAAAAACA
1 AATAAT-AATAATA
37280 AATTAATAATAATA
1 AA-TAATAATAATA
37294 AATAA
1 AATAA
37299 AACAAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
11 8 0.23
12 7 0.20
13 7 0.20
14 9 0.26
15 4 0.11
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:37288 original size:21 final size:22
Alignment explanation
Indices: 37262--37323 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
37252 ATAAATATAA
37262 TAATAATAATAAAAAACAAAT-
1 TAATAATAATAAAAAACAAATG
37283 TAATAATAATAAATAAAACAAATG
1 TAATAATAAT-AA-AAAACAAATG
* * *
37307 AAATAAAAAAAAAAAAC
1 TAATAATAATAAAAAAC
37324 TAGTGTCTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 10 0.29
22 7 0.20
23 11 0.31
24 7 0.20
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.19
Consensus pattern (22 bp):
TAATAATAATAAAAAACAAATG
Found at i:37291 original size:24 final size:24
Alignment explanation
Indices: 37254--37323 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
37244 ATAATAATAT
37254 AAATATAATAATAATAATAAAAAAC
1 AAATATAATAATAATAA-AAAAAAC
*
37279 AAAT-TAATAATAATAAATAAAAC
1 AAATATAATAATAATAAAAAAAAC
37302 AAATGA-AATAA-AA-AAAAAAAAC
1 AAAT-ATAATAATAATAAAAAAAAC
37324 TAGTGTCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
22 8 0.20
23 12 0.29
24 17 0.41
25 4 0.10
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.20
Consensus pattern (24 bp):
AAATATAATAATAATAAAAAAAAC
Found at i:37304 original size:23 final size:24
Alignment explanation
Indices: 37241--37305 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
37231 TATTTATTTC
* *
37241 ATAAT-AATAATATAAATATAATA
1 ATAATAAATAAAACAAATATAATA
*
37264 ATAATAATAAAAAACAAAT-TAATA
1 ATAATAA-ATAAAACAAATATAATA
37288 ATAATAAATAAAACAAAT
1 ATAATAAATAAAACAAAT
37306 GAAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.42
24 13 0.36
25 8 0.22
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAATAAATAAAACAAATATAATA
Found at i:38273 original size:16 final size:17
Alignment explanation
Indices: 38252--38285 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
38242 CTTGATTCAA
38252 TTTTCC-TTTTTCTTTT
1 TTTTCCTTTTTTCTTTT
38268 TTTTCCTTTTTTCTTTT
1 TTTTCCTTTTTTCTTTT
38285 T
1 T
38286 CTTTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCCTTTTTTCTTTT
Found at i:38284 original size:13 final size:13
Alignment explanation
Indices: 38264--38296 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
38254 TTCCTTTTTC
38264 TTTT-TTTTCCTT
1 TTTTCTTTTCCTT
*
38276 TTTTCTTTTTCTT
1 TTTTCTTTTCCTT
38289 TTTTCTTT
1 TTTTCTTT
38297 GTTGGATGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTCCTT
Found at i:43077 original size:17 final size:17
Alignment explanation
Indices: 43057--43094 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
43047 AATGAAATAT
43057 AAAT-ATAAATACTATAA
1 AAATAATAAATA-TATAA
*
43074 AAATAATAAGTATATAA
1 AAATAATAAATATATAA
43091 AAAT
1 AAAT
43095 TTGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (17 bp):
AAATAATAAATATATAA
Found at i:43691 original size:14 final size:15
Alignment explanation
Indices: 43672--43700 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43662 CTCTTTTCTT
43672 AATATTAA-AAAATA
1 AATATTAATAAAATA
43686 AATATTAATAAAATA
1 AATATTAATAAAATA
43701 TTTATCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATTAATAAAATA
Found at i:43910 original size:2 final size:2
Alignment explanation
Indices: 43903--43934 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
43893 ATTTAAACAA
43903 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
43935 GACTAAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45765 original size:3 final size:3
Alignment explanation
Indices: 45757--45807 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
45747 TATTTATTTC
* *
45757 ATA ATA ATA AT- ATA AT- ATA ATA ATA ATA ATA A-A ACA A-A TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45801 ATA ATA A
1 ATA ATA A
45808 ATAAAACAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 7 0.17
3 35 0.83
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:45781 original size:19 final size:17
Alignment explanation
Indices: 45757--45812 Score: 67
Period size: 19 Copynumber: 3.1 Consensus size: 17
45747 TATTTATTTC
45757 ATAATAATAATATAATATA
1 ATAATAATAATA-AATA-A
*
45776 ATAATAATAATAAAACAA
1 ATAATAATAAT-AAATAA
45794 ATTAATAATAATAAATAA
1 A-TAATAATAATAAATAA
45812 A
1 A
45813 ACAAATGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 24 0.73
20 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:45785 original size:22 final size:22
Alignment explanation
Indices: 45774--45839 Score: 82
Period size: 22 Copynumber: 3.0 Consensus size: 22
45764 TAATATAATA
45774 TAATAATAATAATAAAACAAAT
1 TAATAATAATAATAAAACAAAT
45796 TAATAATAATAAATAAAACAAAT
1 TAATAATAAT-AATAAAACAAAT
* *
45819 GAAATAA-AAAAATAAAA-AAAT
1 -TAATAATAATAATAAAACAAAT
45840 AAACTAGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.10
22 17 0.43
23 14 0.35
24 5 0.12
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.23
Consensus pattern (22 bp):
TAATAATAATAATAAAACAAAT
Found at i:48900 original size:3 final size:3
Alignment explanation
Indices: 48892--48975 Score: 105
Period size: 3 Copynumber: 28.0 Consensus size: 3
48882 CCATATTAAT
* * * * * * *
48892 TTA TTA TTA TTA TAA TCA TAA TTA TCA TTA TTA TAA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48940 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48976 AATACATTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:49421 original size:16 final size:16
Alignment explanation
Indices: 49400--49432 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
49390 TGCAAAAAAA
49400 AGACAAACG-GAGACAG
1 AGACAAA-GAGAGACAG
49416 AGACAAAGAGAGACAG
1 AGACAAAGAGAGACAG
49432 A
1 A
49433 AAATACACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.55, C:0.15, G:0.30, T:0.00
Consensus pattern (16 bp):
AGACAAAGAGAGACAG
Found at i:62121 original size:16 final size:18
Alignment explanation
Indices: 62102--62147 Score: 69
Period size: 16 Copynumber: 2.6 Consensus size: 18
62092 CTATTTCAAG
62102 TTCAATTTATTT-GAAA-
1 TTCAATTTATTTCGAAAT
62118 TTCAATTTATTTTCGAAAT
1 TTCAATTTA-TTTCGAAAT
62137 TTCAATTTATT
1 TTCAATTTATT
62148 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 6 0.22
19 9 0.33
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (18 bp):
TTCAATTTATTTCGAAAT
Found at i:62142 original size:19 final size:17
Alignment explanation
Indices: 62102--62147 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 17
62092 CTATTTCAAG
62102 TTCAATTTA-TTTGAAA
1 TTCAATTTATTTTGAAA
62118 TTCAATTTATTTTCGAAA
1 TTCAATTTATTTT-GAAA
62136 TTTCAATTTATT
1 -TTCAATTTATT
62148 CTTCTATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.33
17 3 0.11
18 4 0.15
19 11 0.41
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (17 bp):
TTCAATTTATTTTGAAA
Found at i:63045 original size:82 final size:83
Alignment explanation
Indices: 62908--63134 Score: 402
Period size: 82 Copynumber: 2.7 Consensus size: 83
62898 ACCTTAACTG
*
62908 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGTCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
*
62973 AATCAATCATTGAATTT-
66 AACCAATCATTGAATTTA
62990 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
63055 AACCAATCATTGAATTTA
66 AACCAATCATTGAATTTA
* * *
63073 GAAGATGAATTTGCTGATAGCATCTTCTGGAAGTGATCTTTGAGTTATCTGATCTGGTTTGG
1 GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
63135 TAGGAACTAT
Statistics
Matches: 139, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 80 0.58
83 59 0.42
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (83 bp):
GAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AACCAATCATTGAATTTA
Found at i:64073 original size:113 final size:113
Alignment explanation
Indices: 63886--64985 Score: 1512
Period size: 113 Copynumber: 9.6 Consensus size: 113
63876 TAGATTGACA
*
63886 TTTCCAGAGAAAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
63951 AGAATTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
63999 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
64064 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCC
66 AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
*
64112 TTTCCAGA-AAGAGTTCATAAAGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
64176 AAGAATTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
65 AAGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
64225 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* *
64290 AGAACTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
* *
64338 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAAAAGTTTATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
64403 AGAGCTTGTTCAACCTTTTGC-TCAAATCCATCACTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCAT-GAATTCATCACTTGATGGATCAGCT
*
64451 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * *
64516 AGAATTTGTTCAACCTTTTACATGAATTCATCACTTGATGGATCATCT
66 AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
* *
64564 TTTCCAGAGGAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* ** * * *
64629 AGAATTTGTTCAACCTTTTGTTTAAATCCATCATTTGATGGATCAGCT
66 AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
* *
64677 TTTCCAGAGAAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * ** * * * * *
64742 AGAATTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATTAACA
66 AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
* * * ** *
64790 TTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCAT-CTGAA-GAAGAAGAAGTTCATAATAA
1 TTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAGTTCATAATGA
* * * *
64852 GAAGAGCTTGTTCAACTTTTTGCAT-AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCT
64 GAAGAACTTGTTCAACCTTTTGCATGAATTC-ATCAC---------TTGA-T-GGATCAG-CT
* ** * *
64914 TTTCTAGAG-AAGTTCATAATGAGAAGAACTCATCAAAAACAAAGGATGAAGAAGTTCATAATGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC-TGAA-GAAGGAAGAAGAAGTTCATAATGA
64978 GAAGAACT
64 GAAGAACT
64986 CATCAAGAGC
Statistics
Matches: 886, Mismatches: 78, Indels: 33
0.89 0.08 0.03
Matches are distributed among these distances:
111 5 0.01
112 47 0.05
113 764 0.86
114 4 0.00
121 3 0.00
122 1 0.00
123 28 0.03
124 6 0.01
125 3 0.00
126 25 0.03
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTGCATGAATTCATCACTTGATGGATCAGCT
Found at i:65251 original size:3 final size:3
Alignment explanation
Indices: 65243--65323 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
65233 CCATATTAAT
* * * * * * *
65243 TTA TTA TTA TTA TAA TCA TAA TTA TCA TTA TTA TAA TTA TTA TAA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65291 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65324 AATACATTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:65343 original size:9 final size:9
Alignment explanation
Indices: 65271--65345 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
65261 TAATTATCAT
*
65271 TATTATAAT
1 TATTATAAA
65280 TATTATAAA
1 TATTATAAA
* *
65289 TATTATTAT
1 TATTATAAA
* *
65298 TATTATTAT
1 TATTATAAA
* *
65307 TATTATTAT
1 TATTATAAA
65316 TATTATTAAA
1 TATTA-TAAA
*
65326 TA-CATTAAA
1 TATTA-TAAA
65335 TATTATAAA
1 TATTATAAA
65344 TA
1 TA
65346 ATAAAAAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
9 52 0.91
10 5 0.09
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (9 bp):
TATTATAAA
Found at i:65766 original size:16 final size:16
Alignment explanation
Indices: 65745--65777 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65735 TGCAAAAAAA
65745 AGACAAACG-GAGACAG
1 AGACAAA-GAGAGACAG
65761 AGACAAAGAGAGACAG
1 AGACAAAGAGAGACAG
65777 A
1 A
65778 AAATACACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.55, C:0.15, G:0.30, T:0.00
Consensus pattern (16 bp):
AGACAAAGAGAGACAG
Found at i:69372 original size:22 final size:22
Alignment explanation
Indices: 69344--69387 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
69334 AATGTCAAGC
69344 CATAGGCTCCTTCAGCTTGTAA
1 CATAGGCTCCTTCAGCTTGTAA
69366 CATAGGCTCCTTCAGCTTGTAA
1 CATAGGCTCCTTCAGCTTGTAA
69388 AATCTTCCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (22 bp):
CATAGGCTCCTTCAGCTTGTAA
Found at i:70762 original size:3 final size:3
Alignment explanation
Indices: 70754--70784 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
70744 CTTCAAACAT
70754 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
70785 ATGTCAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:77660 original size:14 final size:14
Alignment explanation
Indices: 77628--77669 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
77618 AAGATTGAGC
*
77628 TGAATATAAACGAA
1 TGAACATAAACGAA
* *
77642 CGAACATAAATGAA
1 TGAACATAAACGAA
77656 TGAACATAAACGAA
1 TGAACATAAACGAA
77670 CAGATTATCG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (14 bp):
TGAACATAAACGAA
Found at i:86536 original size:3 final size:3
Alignment explanation
Indices: 86525--86588 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
86515 TTTTTTTCCG
** *
86525 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
86570 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
86589 CAATTTTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:86566 original size:32 final size:32
Alignment explanation
Indices: 86523--86586 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
86513 TTTTTTTTTC
*
86523 CGTTATTTTATTATTATTATTATTA-TTATTAT
1 CGTTATCTTATTATT-TTATTATTATTTATTAT
86555 CGTTATCTTATTATTTTATTATTATTTATTAT
1 CGTTATCTTATTATTTTATTATTATTTATTAT
86587 TACAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
CGTTATCTTATTATTTTATTATTATTTATTAT
Found at i:86790 original size:48 final size:49
Alignment explanation
Indices: 86707--86825 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 49
86697 GCAACCCGTT
* * *
86707 AGATTAGGGTTTCAAACCCTAAATCATATTAGGGTTTTAAACCCTAAATC
1 AGATTAGGGTTTC-AACCCTAAAACATATTAGGGTTTCAAACCCTAAAAC
*
86757 TGATTAGGGTTTCAA-CCTAAAACA-ATTTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAACCCTAAAACATA-TTAGGGTTTCAAACCCTAAAAC
86805 AGATTA-GGTTTCAAACCCTAA
1 AGATTAGGGTTTC-AACCCTAA
86826 TCCCCTACTC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
47 7 0.11
48 35 0.57
49 7 0.11
50 12 0.20
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.30
Consensus pattern (49 bp):
AGATTAGGGTTTCAACCCTAAAACATATTAGGGTTTCAAACCCTAAAAC
Found at i:86814 original size:24 final size:25
Alignment explanation
Indices: 86707--86825 Score: 156
Period size: 25 Copynumber: 4.9 Consensus size: 25
86697 GCAACCCGTT
*
86707 AGATTAGGGTTTCAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
* * *
86732 ATATTAGGGTTTTAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
*
86757 TGATTAGGGTTTC-AA-CCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
86780 A-ATTTAGGGTTTCAAACCCTAAAAC
1 AGA-TTAGGGTTTCAAACCCTAAAAC
86805 AGATTA-GGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
86826 TCCCCTACTC
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.01
23 17 0.20
24 19 0.23
25 45 0.54
26 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.30
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAAAC
Found at i:100129 original size:16 final size:16
Alignment explanation
Indices: 100095--100155 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
100085 TATTACACCT
**
100095 AAAAAAAAA-AAAAAA
1 AAAAAAAAAGAAAATG
*
100110 AAAAAAAAAGGAAATG
1 AAAAAAAAAGAAAATG
**
100126 AAAAAATGAGAAAATG
1 AAAAAAAAAGAAAATG
*
100142 -AAAAAGAAGAAAAT
1 AAAAAAAAAGAAAAT
100156 AAATAAAGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
15 21 0.57
16 16 0.43
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAAAAAAGAAAATG
Found at i:101154 original size:43 final size:43
Alignment explanation
Indices: 101106--101260 Score: 177
Period size: 43 Copynumber: 3.5 Consensus size: 43
101096 CTGACCGACT
*
101106 TCCTCATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
* * * ** *
101149 TCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-
1 TCCTCATCACGTAGGAGCCGTGTCA--ACC-ATAGATAACCAG-CCG
* *
101195 TCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCG
1 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
*
101238 TCCTCATCACGTAGGAACCGTGT
1 TCCTCATCACGTAGGAGCCGTGT
101261 TATCACCTTT
Statistics
Matches: 89, Mismatches: 18, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
42 1 0.01
43 51 0.57
44 3 0.03
45 3 0.03
46 30 0.34
47 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCG
Found at i:101260 original size:89 final size:89
Alignment explanation
Indices: 101109--101308 Score: 323
Period size: 89 Copynumber: 2.2 Consensus size: 89
101099 ACCGACTTCC
* *
101109 TCATCACGTAGGAGCCATGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
101174 TCACCTTTA-GATGGCCAGA-TCTCT
66 TCACCTTTAGGA-GGCCAGAGT-TCT
101198 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
*
101263 TCACCTTTAGGAGGCCAGAGTTTT
66 TCACCTTTAGGAGGCCAGAGTTCT
* *
101287 TCATCATGTATGAACCGTGTCA
1 TCATCACGTATGAGCCGTGTCA
101309 TCCCCAGACC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
89 101 0.97
90 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (89 bp):
TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCTTTAGGAGGCCAGAGTTCT
Found at i:101655 original size:3 final size:3
Alignment explanation
Indices: 101644--101707 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
101634 TTTTTTTCCG
** *
101644 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
101689 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
101708 CAATTTTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:101685 original size:32 final size:32
Alignment explanation
Indices: 101642--101705 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
101632 TTTTTTTTTC
*
101642 CGTTATTTTATTATTATTATTATTA-TTATTAT
1 CGTTATCTTATTATT-TTATTATTATTTATTAT
101674 CGTTATCTTATTATTTTATTATTATTTATTAT
1 CGTTATCTTATTATTTTATTATTATTTATTAT
101706 TACAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
CGTTATCTTATTATTTTATTATTATTTATTAT
Found at i:101786 original size:15 final size:15
Alignment explanation
Indices: 101766--101803 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
101756 CCAATCCCGG
101766 AGCCCAACAACCTGA
1 AGCCCAACAACCTGA
101781 AGCCCAACAACCTGA
1 AGCCCAACAACCTGA
101796 AGCCCAAC
1 AGCCCAAC
101804 TCAGAATGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.39, C:0.42, G:0.13, T:0.05
Consensus pattern (15 bp):
AGCCCAACAACCTGA
Found at i:101872 original size:25 final size:25
Alignment explanation
Indices: 101843--101962 Score: 172
Period size: 25 Copynumber: 4.8 Consensus size: 25
101833 AACCCGTTAG
*
101843 ATTAGGGTTTCAAACCCTAAATCAT
1 ATTAGGGTTTCAAACCCTAAAACAT
* *
101868 ATTAGGGTTTTAAACCCTAAATC-T
1 ATTAGGGTTTCAAACCCTAAAACAT
101892 GATTAGGGTTTCAAACCCTAAAACA-
1 -ATTAGGGTTTCAAACCCTAAAACAT
*
101917 ATTTAGGGTTTCAAACCCTAAAACAG
1 A-TTAGGGTTTCAAACCCTAAAACAT
101943 ATTAGGGTTTCAAACCCTAA
1 ATTAGGGTTTCAAACCCTAA
101963 TCCCCTACTC
Statistics
Matches: 88, Mismatches: 3, Indels: 8
0.89 0.03 0.08
Matches are distributed among these distances:
24 2 0.02
25 85 0.97
26 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (25 bp):
ATTAGGGTTTCAAACCCTAAAACAT
Found at i:101905 original size:50 final size:50
Alignment explanation
Indices: 101841--101962 Score: 192
Period size: 50 Copynumber: 2.4 Consensus size: 50
101831 GCAACCCGTT
* * *
101841 AGATTAGGGTTTCAAACCCTAAATC-ATATTAGGGTTTTAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAACAAT-TTAGGGTTTCAAACCCTAAAAC
*
101891 TGATTAGGGTTTCAAACCCTAAAACAATTTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAACAATTTAGGGTTTCAAACCCTAAAAC
101941 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
101963 TCCCCTACTC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
50 64 0.97
51 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (50 bp):
AGATTAGGGTTTCAAACCCTAAAACAATTTAGGGTTTCAAACCCTAAAAC
Found at i:102286 original size:27 final size:26
Alignment explanation
Indices: 102262--102316 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
102252 GAGCAAAGAT
102262 AAAAAGAAC-AGAAAAACGAAAAAAG
1 AAAAAGAACGAGAAAAACGAAAAAAG
* *
102287 AAAGAGAACGGAGAGAAACGAAAAAA-
1 AAAAAGAAC-GAGAAAAACGAAAAAAG
102313 AAAA
1 AAAA
102317 GGAAAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 8 0.32
26 3 0.12
27 14 0.56
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (26 bp):
AAAAAGAACGAGAAAAACGAAAAAAG
Found at i:112493 original size:14 final size:14
Alignment explanation
Indices: 112474--112505 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
112464 AGCTATAGTA
112474 TATTATCATAAATT
1 TATTATCATAAATT
*
112488 TATTATCATAACTT
1 TATTATCATAAATT
112502 TATT
1 TATT
112506 TCAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATCATAAATT
Found at i:116141 original size:21 final size:20
Alignment explanation
Indices: 116117--116177 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
116107 GGCAACCAAC
116117 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAAT-TTTTTCAAAG
* *
116138 TTTGATAAA-TATTTC----
1 TTTGAAAAATTTTTTCAAAG
116153 TTTGAAAAATATTTTTCAAAG
1 TTTGAAAAAT-TTTTTCAAAG
116174 TTTG
1 TTTG
116178 GTAGATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 8 0.27
17 5 0.17
19 5 0.17
21 12 0.40
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (20 bp):
TTTGAAAAATTTTTTCAAAG
Found at i:118206 original size:17 final size:18
Alignment explanation
Indices: 118184--118227 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
118174 TGGATGGCCA
*
118184 AAATGGTGGAAAGT-CAG
1 AAATGGAGGAAAGTACAG
*
118201 AAATGGAGGAGAGTACAG
1 AAATGGAGGAAAGTACAG
118219 AAATAGGAG
1 AAAT-GGAG
118228 ATTCAGAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 7 0.30
19 4 0.17
ACGTcount: A:0.45, C:0.05, G:0.36, T:0.14
Consensus pattern (18 bp):
AAATGGAGGAAAGTACAG
Found at i:122715 original size:218 final size:220
Alignment explanation
Indices: 122133--123044 Score: 1473
Period size: 218 Copynumber: 4.2 Consensus size: 220
122123 TTCTCTAGTC
*
122133 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCATATGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCATATGCCCCCTATTTCTTCAGAGAG
122198 TATAAGACTCGAACAATCTTC-ACTGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACT
66 TATAAGACTCGAACAATCTTCAAC-GATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACT
* * *
122262 CGAACAATCTTCATCGATCGCGTCCGCCCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCT
130 CGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCT
*
122327 TCAACAATCGTGTCTGCCCCCCTATTT
195 TCAACAATCGCGTCTG-CCCCCTATTT
* *
122354 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCATATGCCCCCTATTTCTTCAGAGAG
122419 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
66 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
122484 GAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
131 GAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
*
122549 CAACGATCGCGTCTGCCCCCTATTT
196 CAACAATCGCGTCTGCCCCCTATTT
* * * *
122574 CTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGCGTATGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCATATGCCCCCTATTTCTTCAGAGAG
*
122637 TATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
66 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
*
122702 GAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAATATAAGACTCGAACAATCTT
131 GAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
**
122767 CAATGATCGCGTCTGCCCCCTATTT
196 CAACAATCGCGTCTGCCCCCTATTT
* * *
122792 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCATCTGCCCCCTATTTATTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCATATGCCCCCTATTTCTTCAGAGAG
* *
122855 TATAAGACCCAAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGAC-C
66 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
* * * * *
122919 -CACCATCTTCAACGATCGCGTCTGCCCCTTATTTATTCAGAGAGTATAAGAC-C-CACAATCTT
131 GAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
* * *
122981 CAACAATCGTGTATGCTCCCTATTT
196 CAACAATCGCGTCTGCCCCCTATTT
*
123006 CTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
123045 TTGGGAAACC
Statistics
Matches: 652, Mismatches: 35, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
214 47 0.07
215 1 0.00
216 63 0.10
217 1 0.00
218 309 0.47
219 2 0.00
220 28 0.04
221 199 0.31
222 2 0.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (220 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCATATGCCCCCTATTTCTTCAGAGAG
TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
GAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT
CAACAATCGCGTCTGCCCCCTATTT
Found at i:123045 original size:55 final size:55
Alignment explanation
Indices: 122133--123044 Score: 1428
Period size: 55 Copynumber: 16.7 Consensus size: 55
122123 TTCTCTAGTC
* * * *
122133 CTTCAGAGAGTATAAGACTCGAACAATCTTTAACAATCGCATATGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
122188 CTTCAGAGAGTATAAGACTCGAACAATCTTC-ACTGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-GATCGCGTCTGCCCCCTATTT
* *
122243 CTTCAGAGAGTATAAGACTCGAACAATCTTCATCGATCGCGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * *
122298 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCTGCCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTG-CCCCCTATTT
*
122354 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
122409 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
122464 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
122519 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * * * *
122574 CTTCAGAGAGTATAAGAC-C-CATAATCTTCATCAATCGCGTATGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
*
122627 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
122682 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* *
122737 CTTCAGAGAATATAAGACTCGAACAATCTTCAATGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * *
122792 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCATCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * *
122845 ATTCAGAGAGTATAAGACCCAAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * *
122900 CTTCAGAGAGTATAAGAC-C-CACCATCTTCAACGATCGCGTCTGCCCCTTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * * * * *
122953 ATTCAGAGAGTATAAGAC-C-CACAATCTTCAACAATCGTGTATGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* *
123006 CTTCAGAGAGTATGAGACTCGAACAATCTTCAACAATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
123045 TTGGGAAACC
Statistics
Matches: 798, Mismatches: 50, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
53 187 0.23
54 6 0.01
55 551 0.69
56 54 0.07
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
Found at i:124054 original size:8 final size:8
Alignment explanation
Indices: 124041--124101 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
124031 TCTTGAACCC
124041 TCATTTTT
1 TCATTTTT
124049 TCATTTTTTTAT
1 TCA---TTTT-T
124061 TCATTTTT
1 TCATTTTT
124069 T-ATTTTT
1 TCATTTTT
124076 AT-ATTTTT
1 -TCATTTTT
124084 T-ATTTTT
1 TCATTTTT
124091 TCATTTTT
1 TCATTTTT
124099 TCA
1 TCA
124102 CTCATTTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
7 14 0.30
8 21 0.45
9 4 0.09
11 4 0.09
12 4 0.09
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.75
Consensus pattern (8 bp):
TCATTTTT
Found at i:124073 original size:7 final size:7
Alignment explanation
Indices: 124063--124099 Score: 56
Period size: 7 Copynumber: 5.0 Consensus size: 7
124053 TTTTTTATTC
124063 ATTTTTT
1 ATTTTTT
124070 ATTTTTAT
1 ATTTTT-T
124078 ATTTTTT
1 ATTTTTT
124085 ATTTTTT
1 ATTTTTT
124092 CATTTTTT
1 -ATTTTTT
124100 CACTCATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.50
8 14 0.50
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (7 bp):
ATTTTTT
Found at i:124083 original size:15 final size:15
Alignment explanation
Indices: 124043--124099 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
124033 TTGAACCCTC
124043 ATTTTTTCA--TTTT
1 ATTTTTTCATTTTTT
*
124056 -TTTATTCATTTTTT
1 ATTTTTTCATTTTTT
124070 ATTTTTAT-ATTTTTT
1 ATTTTT-TCATTTTTT
124085 ATTTTTTCATTTTTT
1 ATTTTTTCATTTTTT
124100 CACTCATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
12 7 0.19
14 5 0.14
15 24 0.65
16 1 0.03
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTTCATTTTTT
Found at i:124110 original size:13 final size:12
Alignment explanation
Indices: 124091--124124 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
124081 TTTTATTTTT
124091 TCATTTTTTCAC
1 TCATTTTTTCAC
124103 TCATTTTTTCAC
1 TCATTTTTTCAC
124115 TCATTTTTTC
1 TCATTTTTTC
124125 TTCTTCTTCT
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:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (12 bp):
TCATTTTTTCAC
Found at i:140707 original size:20 final size:19
Alignment explanation
Indices: 140671--140715 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
140661 TTTTAATTTT
** *
140671 TTAAAAAAATATCAAATTA
1 TTAAAAAAATAAAAAATAA
140690 TTAATAAAAATAAAAAATAA
1 TTAA-AAAAATAAAAAATAA
140710 TTAAAA
1 TTAAAA
140716 TATATAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
TTAAAAAAATAAAAAATAA
Found at i:140715 original size:16 final size:16
Alignment explanation
Indices: 140691--140733 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
140681 ATCAAATTAT
*
140691 TAATAAAAATAAAAAA
1 TAATTAAAATAAAAAA
* *
140707 TAATTAAAATATATAA
1 TAATTAAAATAAAAAA
140723 TAATTTAAAAT
1 TAA-TTAAAAT
140734 TCTTAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATTAAAATAAAAAA
Found at i:141524 original size:20 final size:20
Alignment explanation
Indices: 141499--141540 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
141489 GTAGTGTTTG
141499 TACTCTGTAGAACTTTCACA
1 TACTCTGTAGAACTTTCACA
141519 TACTCTGTAGAACTTTCACA
1 TACTCTGTAGAACTTTCACA
141539 TA
1 TA
141541 TAAGCTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (20 bp):
TACTCTGTAGAACTTTCACA
Found at i:145841 original size:29 final size:29
Alignment explanation
Indices: 145772--145882 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
145762 GAAACATTCG
* * * *
145772 AGTGACCAAAATAGAAGTAAATTAAAAGTTT
1 AGTGACTAAAATAAAAATAAA-T-AAATTTT
* *
145803 AGTGAGTAAATTAAAAATAAATAAATTTT
1 AGTGACTAAAATAAAAATAAATAAATTTT
145832 AGTGACTAAAATAAAAATAAATAAATTTT
1 AGTGACTAAAATAAAAATAAATAAATTTT
* *
145861 AGTGACTAAAATAGAAGTAAAT
1 AGTGACTAAAATAAAAATAAAT
145883 TGAAAAAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
29 53 0.76
30 1 0.01
31 16 0.23
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.29
Consensus pattern (29 bp):
AGTGACTAAAATAAAAATAAATAAATTTT
Found at i:150036 original size:12 final size:12
Alignment explanation
Indices: 150004--150038 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
149994 AGTAATTAAA
*
150004 TTATATATATAT
1 TTATATATTTAT
*
150016 ATATATATTTAT
1 TTATATATTTAT
150028 TTATATATTTA
1 TTATATATTTA
150039 AAATAATGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATATATTTAT
Found at i:150280 original size:21 final size:21
Alignment explanation
Indices: 150242--150282 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
150232 GTTGGATTAG
*
150242 GTCAGGTCATAATCAAATCAT
1 GTCAGGTCAGAATCAAATCAT
* *
150263 GTCAGGTCAGAGTTAAATCA
1 GTCAGGTCAGAATCAAATCA
150283 GATGAGGTTA
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:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (21 bp):
GTCAGGTCAGAATCAAATCAT
Found at i:155203 original size:37 final size:37
Alignment explanation
Indices: 155145--155263 Score: 163
Period size: 37 Copynumber: 3.3 Consensus size: 37
155135 TCCCATTATC
* * *
155145 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
*
155181 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
* *
155217 A-TTTTCAAATAAACATTTACCAAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
155253 ATTTTTCAAAG
1 ATTTTTCAAAG
155264 TTGGTTGCCA
Statistics
Matches: 73, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.37
36 18 0.25
37 28 0.38
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAACA
Found at i:155231 original size:35 final size:36
Alignment explanation
Indices: 155144--155262 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 36
155134 ATCCCATTAT
*
155144 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTG-AAAAC
* *
155180 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
*
155216 CA-TTTTCAAATAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
155251 CAATTTTTCAAA
1 C-ATTTTTCAAA
155263 GTTGGTTGCC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.44
36 14 0.19
37 28 0.37
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAACAAACATTTACCAAACTTTGAAAAC
Found at i:155787 original size:25 final size:25
Alignment explanation
Indices: 155698--155779 Score: 155
Period size: 25 Copynumber: 3.3 Consensus size: 25
155688 ACATATTCTG
*
155698 CTTCAGTTGTGGAGAGAGCAACTAT
1 CTTCTGTTGTGGAGAGAGCAACTAT
155723 CTTCTGTTGTGGAGAGAGCAACTAT
1 CTTCTGTTGTGGAGAGAGCAACTAT
155748 CTTCTGTTGTGGAGAGAGCAACTAT
1 CTTCTGTTGTGGAGAGAGCAACTAT
155773 CTTCTGT
1 CTTCTGT
155780 AGTTGAGAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
25 56 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (25 bp):
CTTCTGTTGTGGAGAGAGCAACTAT
Found at i:158617 original size:15 final size:15
Alignment explanation
Indices: 158597--158628 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
158587 AAAATCTTTC
*
158597 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
158612 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
158627 TT
1 TT
158629 CGATCTGCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.25, G:0.16, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:159897 original size:35 final size:37
Alignment explanation
Indices: 159853--159935 Score: 125
Period size: 35 Copynumber: 2.3 Consensus size: 37
159843 TTGAAAAATT
159853 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAA-CA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
* * *
159889 A-TTTTCAAATAAATATTTACCGAACTTTGAAAACCA
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
159925 ATTTTTCAAAG
1 ATTTTTCAAAG
159936 TTGGTTGTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 29 0.71
36 4 0.10
37 8 0.20
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.34
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:165773 original size:7 final size:8
Alignment explanation
Indices: 165750--165778 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
165740 ATTGTAAAAA
165750 TATATTTT
1 TATATTTT
165758 TATATTTT
1 TATATTTT
165766 TATA-TTT
1 TATATTTT
165773 TATATT
1 TATATT
165779 GATAAAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TATATTTT
Done.