Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008295.1 Hibiscus syriacus cultivar Beakdansim tig00110962_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: 741301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:2904 original size:22 final size:22
Alignment explanation
Indices: 2876--2956 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
2866 GGATCAGCCT
** *
2876 GTGCAGCCCGCTTCCAACATTC
1 GTGCAGCCTACTTCCAGCATTC
*
2898 GTGCAGCCTACTTCTAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
2920 GTGCA-CCTACTTCCAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
* *
2941 GTGCAACCTTCTTCCA
1 GTGCAGCCTACTTCCA
2957 CCATCCGTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 20 0.38
22 32 0.62
ACGTcount: A:0.19, C:0.37, G:0.16, T:0.28
Consensus pattern (22 bp):
GTGCAGCCTACTTCCAGCATTC
Found at i:3220 original size:29 final size:28
Alignment explanation
Indices: 3186--3252 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
3176 GATATTTTAT
*
3186 TTTATAAAAAGTTT-TACACTTTATTATAA
1 TTTATAAAAAGTTTGTA-A-TTCATTATAA
*
3215 TTTATAAACAATTTTGTAATTCATTATAA
1 TTTATAAA-AAGTTTGTAATTCATTATAA
3244 TTTATAAAA
1 TTTATAAAA
3253 CCTTTTGTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 25 0.74
30 6 0.18
31 2 0.06
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (28 bp):
TTTATAAAAAGTTTGTAATTCATTATAA
Found at i:3933 original size:21 final size:22
Alignment explanation
Indices: 3892--3933 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3882 AACTAGCGGG
3892 AAATAGGATCCTAAAAATTTAT
1 AAATAGGATCCTAAAAATTTAT
* *
3914 AAATGGGATCC-AAAAGTTTA
1 AAATAGGATCCTAAAAATTTA
3934 ATTTTCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (22 bp):
AAATAGGATCCTAAAAATTTAT
Found at i:4391 original size:25 final size:25
Alignment explanation
Indices: 4358--4406 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
4348 TATCTCTGAT
4358 TTTTTAAAATTTAATAATAAAATTG
1 TTTTTAAAATTTAATAATAAAATTG
4383 TTTTTAAAATTTAATAATAAAATT
1 TTTTTAAAATTTAATAATAAAATT
4407 AATAACCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
TTTTTAAAATTTAATAATAAAATTG
Found at i:4408 original size:12 final size:13
Alignment explanation
Indices: 4362--4411 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
4352 TCTGATTTTT
4362 TAAAATTTAATAA
1 TAAAATTTAATAA
**
4375 TAAAATTGT--TTT
1 TAAAATT-TAATAA
4387 TAAAATTTAATAA
1 TAAAATTTAATAA
4400 TAAAA-TTAATAA
1 TAAAATTTAATAA
4412 CCATGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
11 1 0.03
12 15 0.50
13 13 0.43
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
TAAAATTTAATAA
Found at i:8544 original size:21 final size:21
Alignment explanation
Indices: 8490--8544 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
8480 GGTACATGGC
* *
8490 GAATCCAGGCAAAGAGCATTG
1 GAATACAGTCAAAGAGCATTG
* *
8511 GAATACAGT-AAAGAGGATTT
1 GAATACAGTCAAAGAGCATTG
8531 GAGATACA-TCAAAG
1 GA-ATACAGTCAAAG
8545 GGACCTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (21 bp):
GAATACAGTCAAAGAGCATTG
Found at i:14877 original size:2 final size:2
Alignment explanation
Indices: 14870--14916 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
14860 GGAAAAGATC
14870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14912 TA TA T
1 TA TA T
14917 GATTTCAAAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15904 original size:21 final size:21
Alignment explanation
Indices: 15880--15931 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
15870 AAACCAGAAA
* * *
15880 ATATGTCCATACAATCTACGT
1 ATATATCCAAACAATCTACAT
15901 ATATATCCAAACAATCTACAT
1 ATATATCCAAACAATCTACAT
15922 ATATATCCAA
1 ATATATCCAA
15932 CCAAATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (21 bp):
ATATATCCAAACAATCTACAT
Found at i:25852 original size:12 final size:12
Alignment explanation
Indices: 25808--25854 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
25798 AGGAATTATC
*
25808 TTTTTAGGATTTA
1 TTTTTAGTA-TTA
*
25821 TTTTTTGTATT-
1 TTTTTAGTATTA
*
25832 TTCTTAGTATTA
1 TTTTTAGTATTA
25844 TTTTTAGTATT
1 TTTTTAGTATT
25855 CTAGGGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
11 9 0.32
12 12 0.43
13 7 0.25
ACGTcount: A:0.19, C:0.02, G:0.11, T:0.68
Consensus pattern (12 bp):
TTTTTAGTATTA
Found at i:37322 original size:33 final size:33
Alignment explanation
Indices: 37280--37374 Score: 181
Period size: 33 Copynumber: 2.9 Consensus size: 33
37270 AGTTGACAAG
*
37280 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTAGTGGCCAACTTA
37313 TTGGAAATTTCATCTTGGTTAGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTAGTGGCCAACTTA
37346 TTGGAAATTTCATCTTGGTTAGTGGCCAA
1 TTGGAAATTTCATCTTGGTTAGTGGCCAA
37375 ACTTTGAACA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTAGTGGCCAACTTA
Found at i:39407 original size:18 final size:18
Alignment explanation
Indices: 39384--39418 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
39374 TTAATCTCAT
39384 TAAAAATAAATATAATAA
1 TAAAAATAAATATAATAA
39402 TAAAAATAAATATAATA
1 TAAAAATAAATATAATA
39419 GTATAAAGAA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATAAATATAATAA
Found at i:41195 original size:20 final size:20
Alignment explanation
Indices: 41148--41197 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
41138 TCGATATTTT
*
41148 CAAGAGTTTCAAAACTATCT
1 CAAGAGTTTCAAAACTATCC
*
41168 CAAGAGTTTCAAAACTTTCC
1 CAAGAGTTTCAAAACTATCC
41188 CTAA-AGTTTC
1 C-AAGAGTTTC
41198 GATACTTTAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.32
Consensus pattern (20 bp):
CAAGAGTTTCAAAACTATCC
Found at i:42196 original size:32 final size:32
Alignment explanation
Indices: 42153--42217 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
42143 TTCTCCACCA
*
42153 ACATAGAAGCATCATTTTTTGGTTTCCATTCT
1 ACATAGAAGCATCATTTTTTGCTTTCCATTCT
*
42185 ACATAGGAGCATCATTTTTTGCTTTCCATTCT
1 ACATAGAAGCATCATTTTTTGCTTTCCATTCT
42217 A
1 A
42218 TCTTTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.43
Consensus pattern (32 bp):
ACATAGAAGCATCATTTTTTGCTTTCCATTCT
Found at i:52368 original size:15 final size:15
Alignment explanation
Indices: 52350--52378 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52340 GAAGGACATG
52350 CAGATAAATGACAAA
1 CAGATAAATGACAAA
52365 CAGATAAATGACAA
1 CAGATAAATGACAA
52379 GCATAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
CAGATAAATGACAAA
Found at i:53279 original size:21 final size:21
Alignment explanation
Indices: 53238--53280 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
53228 TTCTGGGTTG
*
53238 TGTGCATCGATGCATATTCAA
1 TGTGCATCGATGCATACTCAA
*
53259 TGTGTATCGATGCACT-CTCAA
1 TGTGCATCGATGCA-TACTCAA
53280 T
1 T
53281 TAAAGGAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
TGTGCATCGATGCATACTCAA
Found at i:57310 original size:63 final size:64
Alignment explanation
Indices: 57226--57445 Score: 234
Period size: 64 Copynumber: 3.5 Consensus size: 64
57216 TTGAAGGTGT
** * *
57226 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CTATTAATAATAAA-ACATCGAATGCAATTAGTG
57289 C
64 C
**
57290 ATCGATGCAT-AGTAGTGCATCGATGCATCCTATTAATAAGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAATAAAACATCGAATGCAATTAGTGC
* * * * * * *
57353 ATCGATGAATAAGGCA-TGCATCGATGCATCCCAGTAATAATAAAACATCAAATACATTTTA-TG
1 ATCGATGCATAA-GTAGTGCATCGATGCATCCTATTAATAATAAAACATCGAATGCA-ATTAGTG
57416 C
64 C
* *
57417 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
57446 ACCTTCATTA
Statistics
Matches: 132, Mismatches: 18, Indels: 12
0.81 0.11 0.07
Matches are distributed among these distances:
63 52 0.39
64 75 0.57
65 5 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCTATTAATAATAAAACATCGAATGCAATTAGTGC
Found at i:58245 original size:30 final size:29
Alignment explanation
Indices: 58204--58269 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
58194 GTGGTCCTTA
*
58204 TGGACAGTTACCAAGGATCTTTATGACCTC
1 TGGATAGTTACC-AGGATCTTTATGACCTC
* * *
58234 TGGATAGTTACCGGGGTCTTTGTGACCTC
1 TGGATAGTTACCAGGATCTTTATGACCTC
58263 TGGATAG
1 TGGATAG
58270 GTCCTTCGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (29 bp):
TGGATAGTTACCAGGATCTTTATGACCTC
Found at i:63258 original size:29 final size:30
Alignment explanation
Indices: 63185--63264 Score: 126
Period size: 30 Copynumber: 2.7 Consensus size: 30
63175 GCATATGCCC
*
63185 ATCTTTATGACCTCTGGACAGTTACCGAGG
1 ATCTTTATGACCTCTGGATAGTTACCGAGG
63215 ATCTTTATGACCTCTGGATAGTTACCG-GG
1 ATCTTTATGACCTCTGGATAGTTACCGAGG
* *
63244 GTCTTTGTGACCTCTGGATAG
1 ATCTTTATGACCTCTGGATAG
63265 GTCCTTTGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 21 0.45
30 26 0.55
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (30 bp):
ATCTTTATGACCTCTGGATAGTTACCGAGG
Found at i:65300 original size:20 final size:20
Alignment explanation
Indices: 65275--65313 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
65265 TCATATGTTA
*
65275 AAGAATGCATCGATGCACTG
1 AAGAATGCACCGATGCACTG
*
65295 AAGAATGCACCTATGCACT
1 AAGAATGCACCGATGCACT
65314 TCAATGGTAA
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:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
AAGAATGCACCGATGCACTG
Found at i:73037 original size:14 final size:14
Alignment explanation
Indices: 73015--73047 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
73005 CTTGACATCT
*
73015 TCTCCCTCTCTATC
1 TCTCTCTCTCTATC
73029 TCTCTCTCTCTATC
1 TCTCTCTCTCTATC
73043 TCTCT
1 TCTCT
73048 TGTTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.45, G:0.00, T:0.48
Consensus pattern (14 bp):
TCTCTCTCTCTATC
Found at i:75632 original size:45 final size:46
Alignment explanation
Indices: 75568--75669 Score: 170
Period size: 45 Copynumber: 2.2 Consensus size: 46
75558 AACAATATTT
* *
75568 AATTAATTTGAATAAAAGAATGTTAAG-TAATCTAATTTTTTATCA
1 AATTAATTTGAATAAAAGAATGTTAAGTTAATCTAATTTTTCAGCA
75613 AATTAATTTGAATAAAAGAATGTTAAGTTAATCTAATTTTTCAGCA
1 AATTAATTTGAATAAAAGAATGTTAAGTTAATCTAATTTTTCAGCA
*
75659 AATGAATTTGA
1 AATTAATTTGA
75670 GTGAAATAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 27 0.51
46 26 0.49
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (46 bp):
AATTAATTTGAATAAAAGAATGTTAAGTTAATCTAATTTTTCAGCA
Found at i:75667 original size:46 final size:45
Alignment explanation
Indices: 75572--75669 Score: 160
Period size: 46 Copynumber: 2.2 Consensus size: 45
75562 ATATTTAATT
* * *
75572 AATTTGAATAAAAGAATGTTAAGTAATCTAATTTTTTATCAAATT
1 AATTTGAATAAAAGAATGTTAAGTAATCTAATTTTTCAGCAAATG
75617 AATTTGAATAAAAGAATGTTAAGTTAATCTAATTTTTCAGCAAATG
1 AATTTGAATAAAAGAATGTTAAG-TAATCTAATTTTTCAGCAAATG
75663 AATTTGA
1 AATTTGA
75670 GTGAAATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
45 23 0.47
46 26 0.53
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (45 bp):
AATTTGAATAAAAGAATGTTAAGTAATCTAATTTTTCAGCAAATG
Found at i:76090 original size:18 final size:18
Alignment explanation
Indices: 76045--76090 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
76035 AAAAAAATCT
*
76045 AAATGTAAAAGTATTAAAA
1 AAAT-TAAAATTATTAAAA
76064 AAATT-AAATTATTAAAA
1 AAATTAAAATTATTAAAA
76081 AAATTAAAAT
1 AAATTAAAAT
76091 ATAAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 16 0.64
18 5 0.20
19 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
AAATTAAAATTATTAAAA
Found at i:79461 original size:19 final size:16
Alignment explanation
Indices: 79447--79497 Score: 68
Period size: 15 Copynumber: 3.1 Consensus size: 16
79437 GATTTTTCAA
79447 CAGGTTTAACTTTTTT
1 CAGGTTTAACTTTTTT
79463 CTTTAGGTTTAACTTTTTT
1 C---AGGTTTAACTTTTTT
79482 -AGGTTTAACTTTTTT
1 CAGGTTTAACTTTTTT
79497 C
1 C
79498 TTTCTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 15 0.48
16 1 0.03
19 15 0.48
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.59
Consensus pattern (16 bp):
CAGGTTTAACTTTTTT
Found at i:88940 original size:14 final size:14
Alignment explanation
Indices: 88921--88976 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
88911 CGTTCGTGAA
88921 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
88935 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
88948 --TT-GTTTATGTT
1 CGTTCGATTATGTT
88959 CGTTCGATTATGTT
1 CGTTCGATTATGTT
88973 CGTT
1 CGTT
88977 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:88955 original size:24 final size:24
Alignment explanation
Indices: 88922--88983 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
88912 GTTCGTGAAC
* *
88922 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
88946 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
88970 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
88984 ATTCATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:88993 original size:24 final size:23
Alignment explanation
Indices: 88922--88990 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 23
88912 GTTCGTGAAC
* *
88922 GTTCGATTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
88946 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTC-ATTAT
*
88970 GTTCGTTTATGTTCATTCATT
1 GTTCGTTTATGTTCGTTCATT
88991 TATATTTAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 3 0.08
24 37 0.93
ACGTcount: A:0.13, C:0.12, G:0.20, T:0.55
Consensus pattern (23 bp):
GTTCGTTTATGTTCGTTCATTAT
Found at i:89736 original size:10 final size:10
Alignment explanation
Indices: 89721--89795 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
89711 GGGTCTCCAA
89721 CGTTTATGTT
1 CGTTTATGTT
89731 CGTTTATGTT
1 CGTTTATGTT
89741 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* * **
89752 ATGCTCGTGTT
1 -CGTTTATGTT
89763 CGTTTATGTT
1 CGTTTATGTT
89773 CG----TGTT
1 CGTTTATGTT
89779 CGTTTATGTT
1 CGTTTATGTT
89789 CGTTTAT
1 CGTTTAT
89796 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.67
11 7 0.14
12 3 0.06
ACGTcount: A:0.09, C:0.13, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:89752 original size:16 final size:16
Alignment explanation
Indices: 89727--89791 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
89717 CCAACGTTTA
89727 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
89743 TGTTCATTTATGCTCG
1 TGTTCGTTTATGTTCG
89759 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
89775 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
89791 T
1 T
89792 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.14, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:89884 original size:16 final size:16
Alignment explanation
Indices: 89863--89893 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
89853 AAAAAAAAAT
89863 TTCGTTTATGTTCGTG
1 TTCGTTTATGTTCGTG
89879 TTCGTTTATGTTCGT
1 TTCGTTTATGTTCGT
89894 CTATTTATTA
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:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TTCGTTTATGTTCGTG
Found at i:98199 original size:41 final size:40
Alignment explanation
Indices: 98140--98233 Score: 143
Period size: 40 Copynumber: 2.3 Consensus size: 40
98130 TTAAATCAAT
* * *
98140 TAAGGATCTAATTGAGAAAATCTTATTTTTATTTGATAAAA
1 TAAGGATATAATTAAG-AAATCTTACTTTTATTTGATAAAA
*
98181 TAAGGATATTATTAAGAAATCTTACTTTTATTTGATAAAA
1 TAAGGATATAATTAAGAAATCTTACTTTTATTTGATAAAA
98221 TAAGGATATAATT
1 TAAGGATATAATT
98234 GTCTAATTGC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.73
41 13 0.27
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (40 bp):
TAAGGATATAATTAAGAAATCTTACTTTTATTTGATAAAA
Found at i:99148 original size:24 final size:24
Alignment explanation
Indices: 99121--99176 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
99111 GGCTCGATTT
99121 TCTTCCAATAGTCAGACCTTTTAA
1 TCTTCCAATAGTCAGACCTTTTAA
*
99145 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAATAGTCAGACCTTTTAA
*
99169 -ATTCCAAT
1 TCTTCCAAT
99177 TACTTACATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (24 bp):
TCTTCCAATAGTCAGACCTTTTAA
Found at i:100067 original size:2 final size:2
Alignment explanation
Indices: 100062--100106 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
100052 ACACAGACGC
*
100062 AT AT AT GT AT AT -T 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
100103 AT AT
1 AT AT
100107 CATACCTCAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:101610 original size:19 final size:19
Alignment explanation
Indices: 101586--101638 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
101576 AGGGAAACAA
*
101586 AAAGAAGAAATTCAAAATT
1 AAAGAATAAATTCAAAATT
101605 AAAGAATAAATTCAAAATT
1 AAAGAATAAATTCAAAATT
101624 AAAGAATAAATTCAA
1 AAAGAATAAATTCAA
101639 TAACCATGGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.23
Consensus pattern (19 bp):
AAAGAATAAATTCAAAATT
Found at i:103496 original size:39 final size:39
Alignment explanation
Indices: 103453--103532 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
103443 TTTTAACATT
103453 TATTTTTTTATTTTTTAAAATTAAATTAAATTACATAAA
1 TATTTTTTTATTTTTTAAAATTAAATTAAATTACATAAA
*
103492 TATTTTTTTATTTTTTAAAATTACATTAAATTACATAAA
1 TATTTTTTTATTTTTTAAAATTAAATTAAATTACATAAA
103531 TA
1 TA
103533 ATAAACTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (39 bp):
TATTTTTTTATTTTTTAAAATTAAATTAAATTACATAAA
Found at i:107494 original size:127 final size:127
Alignment explanation
Indices: 107267--108044 Score: 1385
Period size: 127 Copynumber: 6.1 Consensus size: 127
107257 CACATGACGA
*
107267 CGCGTTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
1 CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
107332 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
66 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
* * *
107394 TGCGTTCCCAGGGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
1 CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
107459 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
66 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
* *
107521 CGCGTTCCCGGGGGCGCGCATTCTATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
1 CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
* *
107586 CACTTATGTCCCCCGGGAACTATTTATGTCAATACCTATTATTACTTAGGGGACCGTGAAGG
66 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
* * *
107648 CACGTTCCCGGGGGCGTGCCTTCCATTATTTTGTCAGAGAATATATTATCATTACCCTATTATGT
1 CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
* *
107713 CACTTATATCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAAGGGACCGTGAAGG
66 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
* * *
107775 TGCGTTCCCGGGGGCACGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
1 CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
107840 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
66 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
* *
107902 CGCATTTCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
1 CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
*
107967 CACTTATGTCCCTCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
66 CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
108029 CGCGTTCCCGGGGGCG
1 CGCGTTCCCGGGGGCG
108045 ACTTCCTGGG
Statistics
Matches: 615, Mismatches: 36, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 615 1.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (127 bp):
CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCCTATTATGT
CACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGACCGTGAAGG
Found at i:108503 original size:34 final size:34
Alignment explanation
Indices: 108465--108565 Score: 157
Period size: 34 Copynumber: 3.0 Consensus size: 34
108455 GAATTTAATG
* *
108465 TTAAATTTTGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
* * *
108499 TTAAATTTCGAATAATATTATTTGTATTTTAATT
1 TTAAATTTCGAATACTATAATTTGTATTTTAAAT
108533 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATACTATAATTTGTATTTTAAA
108566 AACATTTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 59 1.00
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATACTATAATTTGTATTTTAAAT
Found at i:109109 original size:21 final size:20
Alignment explanation
Indices: 109079--109148 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
109069 GGTATAAAAC
* *
109079 CCTGCGGGCTAGGCATGTAA
1 CCTGCAGGCTAGGAATGTAA
109099 CCTGGCAGGCTAGGAATGTAA
1 CCT-GCAGGCTAGGAATGTAA
*
109120 CCCTGCGGGCTAGGAATGTAA
1 -CCTGCAGGCTAGGAATGTAA
109141 CCCTGCAG
1 -CCTGCAG
109149 AGATGACATA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19
Consensus pattern (20 bp):
CCTGCAGGCTAGGAATGTAA
Found at i:110995 original size:30 final size:30
Alignment explanation
Indices: 110929--111024 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 30
110919 TAATTAGCAC
* * *
110929 AAAAAATAATTA-ATTAATA-AATTTAAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
*
110957 AAATAATAATTATATAAATATTATTTTAAT
1 AAAAAATAATTATATAAATATTATTTTAAT
* * *
110987 AAAAAATAA-TATTTATATAATTATATTAAT
1 AAAAAATAATTATATAAAT-ATTATTTTAAT
*
111017 ATAAAATA
1 AAAAAATA
111025 TAATATCTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
28 11 0.20
29 13 0.23
30 32 0.57
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAAAATAATTATATAAATATTATTTTAAT
Found at i:111003 original size:33 final size:32
Alignment explanation
Indices: 110952--111040 Score: 92
Period size: 33 Copynumber: 2.7 Consensus size: 32
110942 TTAATAAATT
* *
110952 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATATTTATATAAA-ATTATATTAA
110986 TAAAAAATAATATTTATAT--AATTATATTAA
1 TAAAAAATAATATTTATATAAAATTATATTAA
* *
111016 TATAAAATATAATATCTATTTAAAA
1 TA-AAAA-ATAATATTTATATAAAA
111041 AAAATAACTG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
30 11 0.23
31 5 0.11
32 11 0.23
33 14 0.30
34 6 0.13
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (32 bp):
TAAAAAATAATATTTATATAAAATTATATTAA
Found at i:111867 original size:18 final size:18
Alignment explanation
Indices: 111844--111884 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
111834 GTTCTGTTAT
111844 AGAAGCATTCTACTTACA
1 AGAAGCATTCTACTTACA
111862 AGAAGCATTCTACTTACA
1 AGAAGCATTCTACTTACA
111880 AGAAG
1 AGAAG
111885 AATTAAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (18 bp):
AGAAGCATTCTACTTACA
Found at i:114001 original size:7 final size:7
Alignment explanation
Indices: 113984--114021 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
113974 GCTGATAAAC
113984 ATTAA-T
1 ATTAATT
113990 ATTAATT
1 ATTAATT
113997 ATTAATT
1 ATTAATT
114004 ATTAATT
1 ATTAATT
114011 ATTAATT
1 ATTAATT
114018 ATTA
1 ATTA
114022 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTAATT
Found at i:115233 original size:17 final size:17
Alignment explanation
Indices: 115186--115240 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
115176 GCAGACTAGC
*
115186 TTTTGTCTTAAAAATGA-
1 TTTTTTCTT-AAAATGAT
115203 TTTTTTCTTAAAATGAT
1 TTTTTTCTTAAAATGAT
*
115220 TTTTTTCTTAAAATTAT
1 TTTTTTCTTAAAATGAT
115237 TTTT
1 TTTT
115241 AAAAGGCAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.20
17 28 0.80
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTTTTCTTAAAATGAT
Found at i:118513 original size:11 final size:11
Alignment explanation
Indices: 118497--118538 Score: 84
Period size: 11 Copynumber: 3.8 Consensus size: 11
118487 GATGCTAAGG
118497 AATGAGAAAGA
1 AATGAGAAAGA
118508 AATGAGAAAGA
1 AATGAGAAAGA
118519 AATGAGAAAGA
1 AATGAGAAAGA
118530 AATGAGAAA
1 AATGAGAAA
118539 TGAAGAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.10
Consensus pattern (11 bp):
AATGAGAAAGA
Found at i:118556 original size:18 final size:18
Alignment explanation
Indices: 118504--118556 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
118494 AGGAATGAGA
*
118504 AAGAAATGAGAAAGAAATG
1 AAGAAATGA-AAGGAAATG
118523 -AGAAA-GAAATGAGAAATG
1 AAGAAATGAAA-G-GAAATG
118541 AAGAAATGAAAGGAAA
1 AAGAAATGAAAGGAAA
118557 GGTAATTCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 15 0.52
19 6 0.21
20 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.26, T:0.09
Consensus pattern (18 bp):
AAGAAATGAAAGGAAATG
Found at i:120724 original size:1 final size:1
Alignment explanation
Indices: 120720--120786 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
120710 GAAAAAAAGG
* * * * * * * * *
120720 AAAAACAAAAAAAAAAGAAAAAAAAGAAAAAAAGAAAAGAAAAGAAAAGAAAAAAAGAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
120785 AA
1 AA
120787 GAGAAAAGAG
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.87, C:0.01, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:120735 original size:19 final size:18
Alignment explanation
Indices: 120711--120793 Score: 68
Period size: 17 Copynumber: 4.7 Consensus size: 18
120701 CTATCAGGGG
*
120711 AAAAAAAGGAAAAACAAA
1 AAAAAAAGGAAAAAAAAA
*
120729 AAAAAAA-GAAAAAAAAG
1 AAAAAAAGGAAAAAAAAA
*
120746 AAAAAAA-G--AAAAGAA
1 AAAAAAAGGAAAAAAAAA
*
120761 AAGAAAA-GAAAAAAAGAA
1 AAAAAAAGGAAAAAAA-AA
120779 AAAGAAAAGAGAAAA
1 AAA-AAAAG-GAAAA
120794 GAGAAAAGAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
15 12 0.23
17 20 0.38
18 11 0.21
19 4 0.08
21 5 0.10
ACGTcount: A:0.84, C:0.01, G:0.14, T:0.00
Consensus pattern (18 bp):
AAAAAAAGGAAAAAAAAA
Found at i:120752 original size:23 final size:23
Alignment explanation
Indices: 120726--120812 Score: 104
Period size: 22 Copynumber: 3.6 Consensus size: 23
120716 AAGGAAAAAC
120726 AAAAAAAAAAGAAAA-AAAAGAA
1 AAAAAAAAAAGAAAAGAAAAGAA
*
120748 AAAAAGAAAAGAAAAGAAAAGAA
1 AAAAAAAAAAGAAAAGAAAAGAA
120771 AAAAAGAAAAAGAAAAGAGAAAAGAGA
1 AAAAA-AAAAAG-AAA-AGAAAAGA-A
*
120798 AAAGAAAAGAAGAAA
1 AAA-AAAAAAAGAAA
120813 TTTTTTTGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
22 14 0.25
23 12 0.21
24 5 0.09
25 3 0.05
26 11 0.20
27 9 0.16
28 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAGAAAAGAAAAGAA
Found at i:120762 original size:18 final size:18
Alignment explanation
Indices: 120710--120812 Score: 99
Period size: 18 Copynumber: 5.7 Consensus size: 18
120700 TCTATCAGGG
120710 GAAAAAAAGGAAAA-ACAAA
1 GAAAAAAA-GAAAAGA-AAA
120729 -AAAAAAAGAAAA-AAAA
1 GAAAAAAAGAAAAGAAAA
120745 GAAAAAAAGAAAAGAAAA
1 GAAAAAAAGAAAAGAAAA
120763 GAAAAGAAA-AAAAGAAAAA
1 GAAAA-AAAGAAAAG-AAAA
*
120782 GAAAAGAGAA-AAGAGAAAA
1 GAAAA-A-AAGAAAAGAAAA
*
120801 GAAAAGAAGAAA
1 GAAAAAAAGAAA
120813 TTTTTTTGAA
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
16 3 0.04
17 20 0.27
18 23 0.31
19 23 0.31
20 6 0.08
ACGTcount: A:0.82, C:0.01, G:0.17, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAAAAGAAAA
Found at i:120773 original size:43 final size:43
Alignment explanation
Indices: 120721--120808 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 43
120711 AAAAAAAGGA
120721 AAAACAAAAAAAAAAGAAAAAAAAGA-AAAAAAGAAAAGAAAAG
1 AAAACAAAAAAAAAA-AAAAAAAAGAGAAAAAAGAAAAGAAAAG
* * * *
120764 AAAAGAAAAAAAGAAAAAGAAAAGAGAAAAGAGAAAAGAAAAG
1 AAAACAAAAAAAAAAAAAAAAAAGAGAAAAAAGAAAAGAAAAG
120807 AA
1 AA
120809 GAAATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 9 0.22
43 31 0.77
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.00
Consensus pattern (43 bp):
AAAACAAAAAAAAAAAAAAAAAAGAGAAAAAAGAAAAGAAAAG
Found at i:120787 original size:5 final size:5
Alignment explanation
Indices: 120727--120808 Score: 86
Period size: 5 Copynumber: 17.4 Consensus size: 5
120717 AGGAAAAACA
*
120727 AAAAA AAAAG AAAA- AAAAG -AAA- AAAAG AAAAG AAAAG AAAAG -AAA-
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
* *
120772 AAAAG AAAAAG AAAAG AGAA- AAGAG AAAAG AAAAG AA
1 AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
120809 GAAATTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 18 0.28
5 42 0.65
6 5 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:120800 original size:19 final size:19
Alignment explanation
Indices: 120730--120812 Score: 89
Period size: 17 Copynumber: 4.2 Consensus size: 19
120720 AAAAACAAAA
120730 AAAAAAGAAAA-AAAAGA-
1 AAAAAAGAAAAGAAAAGAG
120747 AAAAAAGAAAAGAAAAGAAAAG
1 AAAAAAGAAAAGAAAAG---AG
120769 AAAAAAAGAAAAAGAAAAGAG
1 -AAAAAAG-AAAAGAAAAGAG
*
120790 AAAAGAGAAAAGAAAAGAAG
1 AAAAAAGAAAAGAAAAG-AG
120810 AAA
1 AAA
120813 TTTTTTTGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
17 11 0.19
18 5 0.09
19 10 0.18
20 11 0.19
21 3 0.05
23 7 0.12
24 10 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAGAAAAGAG
Found at i:122218 original size:51 final size:52
Alignment explanation
Indices: 122110--122301 Score: 239
Period size: 52 Copynumber: 3.7 Consensus size: 52
122100 TATATTATCT
*
122110 ATGTG-GGTCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCC
1 ATGTGAGG-CATCTTGAAGGTTCACATCAGCATGAAAAAGACAGAAGTAATCC
* *
122162 ATGTGAGGCATCTTGAAGGTTCACATTAGCAT-AAAAAGATAGAAGTAATCC
1 ATGTGAGGCATCTTGAAGGTTCACATCAGCATGAAAAAGACAGAAGTAATCC
* *
122213 ATGTGAGGCATCTTGAAGGTTCACATCAGCATGGAAAAA-ACATATA-TTATCC
1 ATGTGAGGCATCTTGAAGGTTCACATCAGCAT-GAAAAAGACAGA-AGTAATCC
* * * * *
122265 ATGTGGGGCATCCTGAAGGCTCACACCAACATGAAAA
1 ATGTGAGGCATCTTGAAGGTTCACATCAGCATGAAAA
122302 GGTTGGGATA
Statistics
Matches: 124, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
51 54 0.44
52 62 0.50
53 8 0.06
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (52 bp):
ATGTGAGGCATCTTGAAGGTTCACATCAGCATGAAAAAGACAGAAGTAATCC
Found at i:122302 original size:103 final size:103
Alignment explanation
Indices: 122110--122302 Score: 248
Period size: 103 Copynumber: 1.9 Consensus size: 103
122100 TATATTATCT
*
122110 ATGTGGGTCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGCATCT
1 ATGTGGGTCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGCATCC
* ** *
122175 TGAAGGTTCACATTAGCATAAAAAGATAGAAGTAATCC
66 TGAAGGCTCACACCAACATAAAAAGATAGAAGTAATCC
* * * *
122213 ATGTGAGG-CATCTTGAAGGTTCACATCAGCATGGAAAAA-ACATATA-TTATCCATGTGGGGCA
1 ATGTG-GGTCATCTTGAAGGCTCACATCAGCAT-GAAAAAGACAGA-AGTAATCCATGTGAGGCA
*
122275 TCCTGAAGGCTCACACCAACATGAAAAG
63 TCCTGAAGGCTCACACCAACATAAAAAG
122303 GTTGGGATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
103 68 0.88
104 9 0.12
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (103 bp):
ATGTGGGTCATCTTGAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGAGGCATCC
TGAAGGCTCACACCAACATAAAAAGATAGAAGTAATCC
Found at i:123985 original size:86 final size:86
Alignment explanation
Indices: 123833--124052 Score: 307
Period size: 86 Copynumber: 2.6 Consensus size: 86
123823 ATATTCGACT
* * *
123833 GAGGAATATACCACATGGCTTTCCTGTGAAGGGGAGTCATCTAAAGATCATCTCACTTGGTCCAG
1 GAGGAATATACCACATGGTTTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTCGGTCCAG
*
123898 ACCCACTAAGGGGAACCACCC
66 ACCCACTAAGAGGAACCACCC
* * *
123919 GAGGAATATACCACATGGTTTTCCTATGAAGTGGAGTCATCCAAA-ATTCATCTCACTCGGTTCA
1 GAGGAATATACCACATGGTTTTCCTGTGAAGGGGAGTCATCCAAAGA-TCATCTCACTCGGTCCA
* * *
123983 GACCCGCTAAGAGGAATCACCT
65 GACCCACTAAGAGGAACCACCC
* * *
124005 GAGGAGTATACCACATGGTTTTCCCGTGAAGGGGAGTTATCCAAAGAT
1 GAGGAATATACCACATGGTTTTCCTGTGAAGGGGAGTCATCCAAAGAT
124053 ACTCGTTAAG
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
85 1 0.01
86 115 0.98
87 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Consensus pattern (86 bp):
GAGGAATATACCACATGGTTTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTCGGTCCAG
ACCCACTAAGAGGAACCACCC
Found at i:124442 original size:85 final size:85
Alignment explanation
Indices: 124286--124447 Score: 218
Period size: 85 Copynumber: 1.9 Consensus size: 85
124276 CGATTCACAG
* **
124286 CATAGCTCAAGGCGAGAAGGGTCATCTGTCAACACAAACCTTCAAGTTTGATTACATTCAGTTCC
1 CATAACTCAAGGCGAGAAGGGTCATCTGTCAACACAAACCTTCAAGTTTGATTACATTCAACTCC
*
124351 AGGACATGTCAAGTTTACAA
66 AGGACATATCAAGTTTACAA
* * * *
124371 CATAACTCAAGGCGAGAAGGGTTATTTGTCAACA-AACATCTTCAAGTTTGATTCCATTCAACTC
1 CATAACTCAAGGCGAGAAGGGTCATCTGTCAACACAA-ACCTTCAAGTTTGATTACATTCAACTC
* *
124435 GATGACATATCAA
65 CAGGACATATCAA
124448 CTACATGGTA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
84 2 0.03
85 64 0.97
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (85 bp):
CATAACTCAAGGCGAGAAGGGTCATCTGTCAACACAAACCTTCAAGTTTGATTACATTCAACTCC
AGGACATATCAAGTTTACAA
Found at i:125179 original size:46 final size:45
Alignment explanation
Indices: 124974--125309 Score: 242
Period size: 46 Copynumber: 7.7 Consensus size: 45
124964 GATAACCAGC
* * *
124974 CGTCATCATCACGTAGGAACCATGTTATCACCTATAGATGACCTGA
1 CGTCCTCATCACGTAGGAACCGTGTCATCACC-ATAGATGACCTGA
* * *
125020 CGTCCTCATCACGTAGGAACCGCGTCATCA--AT-CA--ACATGA
1 CGTCCTCATCACGTAGGAACCGTGTCATCACCATAGATGACCTGA
* * * *
125060 TC-TCCTCATCACGTAGGAACCGTGTCA-AATCC--AGATAACCAGC
1 -CGTCCTCATCACGTAGGAACCGTGTCATCA-CCATAGATGACCTGA
* *
125103 CGTCTTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGA
1 CGTCCTCATCACGTAGGAACCGTGTCATCACC-ATAGATGACCTGA
*
125149 CGTCCTCATCACGTAGGAACCGTGTCATCA-C-T---CGACCTGA
1 CGTCCTCATCACGTAGGAACCGTGTCATCACCATAGATGACCTGA
* ** * ** * *
125189 TC-TCCTCATCAAGTAGGAGTCATGTCA--ACCCCAGATAACC-AA
1 -CGTCCTCATCACGTAGGAACCGTGTCATCACCATAGATGACCTGA
* * *
125231 CTGTCCTCATCACGTAGGAACCGTGTTATCATCTATAGATGGCCTG-
1 C-GTCCTCATCACGTAGGAACCGTGTCATCA-CCATAGATGACCTGA
*
125277 CAGTCCTCATCACGCAGGAACCGTGTCATCACC
1 C-GTCCTCATCACGTAGGAACCGTGTCATCACC
125310 CGACTAAATT
Statistics
Matches: 222, Mismatches: 44, Indels: 49
0.70 0.14 0.16
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 57 0.26
41 4 0.02
42 3 0.01
43 54 0.24
44 1 0.00
45 3 0.01
46 97 0.44
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (45 bp):
CGTCCTCATCACGTAGGAACCGTGTCATCACCATAGATGACCTGA
Found at i:125190 original size:129 final size:129
Alignment explanation
Indices: 124960--125390 Score: 546
Period size: 129 Copynumber: 3.3 Consensus size: 129
124950 AATTTGTCAC
* *
124960 TCCAGATAACCAGCCGTCATCATCACGTAGGAACCATGTTATCACCTATAGATGACCTGACGTCC
1 TCCAGATAACCAGCCGTCTTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCC
* * * * * *
125025 TCATCACGTAGGAACCGCGTCATCAATCAACATGATCTCCTCATCACGTAGGAACCGTGTCAAA
66 TCATCACGTAGGAACCGTGTCATCACTCGACCTGATCTCCTCATCAAGTAGGAATCGTGTCAAA
125089 TCCAGATAACCAGCCGTCTTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCC
1 TCCAGATAACCAGCCGTCTTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCC
* * *
125154 TCATCACGTAGGAACCGTGTCATCACTCGACCTGATCTCCTCATCAAGTAGGAGTCATGTCAAC
66 TCATCACGTAGGAACCGTGTCATCACTCGACCTGATCTCCTCATCAAGTAGGAATCGTGTCAAA
* * * * * *
125218 CCCAGATAACCAACTGTCCTCATCACGTAGGAACCGTGTTATCATCTATAGATGGCCTG-CAGTC
1 TCCAGATAACCAGCCGTCTTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGAC-GTC
* * * * * * *
125282 CTCATCACGCAGGAACCGTGTCATCACCCGA-CTAAATTTCCTCATTATGTAGGAATCGTGT-TA
65 CTCATCACGTAGGAACCGTGTCATCACTCGACCT-GATCTCCTCATCAAGTAGGAATCGTGTCAA
125345 A
129 A
* * * *
125346 TCCTTGATAACCAGAAC-TCTTCATCACGTATGAGCCGTGTTATCA
1 TCC-AGATAACCAG-CCGTCTTCATCACGTAGGAACCGTGTTATCA
125391 TCATTCCTAA
Statistics
Matches: 263, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
128 6 0.02
129 257 0.98
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (129 bp):
TCCAGATAACCAGCCGTCTTCATCACGTAGGAACCGTGTTATCACCTATAGATGACCTGACGTCC
TCATCACGTAGGAACCGTGTCATCACTCGACCTGATCTCCTCATCAAGTAGGAATCGTGTCAAA
Found at i:127332 original size:2 final size:2
Alignment explanation
Indices: 127325--127354 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
127315 TACGTGTATG
127325 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
127355 TAACTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:127471 original size:23 final size:23
Alignment explanation
Indices: 127444--127490 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
127434 TTTGATAATA
127444 TTTTTAGTATTGTTATCCGAACG
1 TTTTTAGTATTGTTATCCGAACG
127467 TTTTTAGTATTGTTATCCGAACG
1 TTTTTAGTATTGTTATCCGAACG
127490 T
1 T
127491 CTTTCAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.17, T:0.49
Consensus pattern (23 bp):
TTTTTAGTATTGTTATCCGAACG
Found at i:128069 original size:16 final size:17
Alignment explanation
Indices: 128034--128071 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
128024 GCAGACTAGC
*
128034 TTTTGTCTTACAAATGA
1 TTTTTTCTTACAAATGA
*
128051 TTTTTTCTTA-AAATTA
1 TTTTTTCTTACAAATGA
128067 TTTTT
1 TTTTT
128072 AAAAGACAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.26, C:0.08, G:0.05, T:0.61
Consensus pattern (17 bp):
TTTTTTCTTACAAATGA
Found at i:129309 original size:18 final size:18
Alignment explanation
Indices: 129276--129310 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
129266 TCAGATTTAA
*
129276 ATTTCAATTCATTCATAT
1 ATTTCAATTCACTCATAT
*
129294 ATTTCAATTCCCTCATA
1 ATTTCAATTCACTCATA
129311 AACATTTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTCAATTCACTCATAT
Found at i:131969 original size:2 final size:2
Alignment explanation
Indices: 131964--132032 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
131954 AAGGGAAATA
131964 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
132006 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
132033 ATTTTTTAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:136126 original size:23 final size:22
Alignment explanation
Indices: 136087--136131 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
136077 TTATTATATT
*
136087 TTTAATATTTTGTATTTAATTTA
1 TTTAATATTTTGAATTT-ATTTA
136110 TTTAAGTATTTT-AATTTATTTA
1 TTTAA-TATTTTGAATTTATTTA
136132 ATGTTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTAATATTTTGAATTTATTTA
Found at i:142125 original size:49 final size:51
Alignment explanation
Indices: 142064--142175 Score: 124
Period size: 53 Copynumber: 2.2 Consensus size: 51
142054 GATACCTGCA
* *
142064 CCGCGCCT-TATATAATTTTATC-AG-TTAAAAGTATGGCGCGGCCCCTG-C
1 CCGCG-CTATATATAATTATATCAAGATTAAAAGTAAGGCGCGGCCCCTGAC
* *
142112 CTCGCGCTATATATAATTATGTCAGAGAATTAAAGGTAAGGCGCGGCCCCTGAC
1 C-CGCGCTATATATAATTATATCA-AG-ATTAAAAGTAAGGCGCGGCCCCTGAC
142166 CCGCGCTATA
1 CCGCGCTATA
142176 CCCTACGTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
48 3 0.06
49 16 0.30
51 2 0.04
53 30 0.57
54 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (51 bp):
CCGCGCTATATATAATTATATCAAGATTAAAAGTAAGGCGCGGCCCCTGAC
Found at i:144103 original size:2 final size:2
Alignment explanation
Indices: 144096--144135 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
144086 AATTTGATAA
144096 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
144136 TAAAATGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:144654 original size:21 final size:19
Alignment explanation
Indices: 144583--144654 Score: 60
Period size: 20 Copynumber: 3.7 Consensus size: 19
144573 GGTTTGTTTA
144583 AATTTTT-AAATTT-TATT
1 AATTTTTGAAATTTATATT
*
144600 AATTTTT-AATTTTTTATATT
1 AATTTTTGAA--ATTTATATT
*
144620 AATTTTTGAGATTTATATTT
1 AATTTTTGAAATTTATA-TT
*
144640 TATTTTTAGAAATTT
1 AATTTTT-GAAATTT
144655 CAAATATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
17 9 0.20
19 9 0.20
20 19 0.43
21 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
AATTTTTGAAATTTATATT
Found at i:148236 original size:14 final size:14
Alignment explanation
Indices: 148219--148275 Score: 53
Period size: 14 Copynumber: 4.1 Consensus size: 14
148209 TTTTTTCGTG
148219 TTTGTTTTACGTAA
1 TTTGTTTTACGTAA
* *
148233 TTTGTTTTTCGAAA
1 TTTGTTTTACGTAA
** * *
148247 AATGTTTTCCGT-G
1 TTTGTTTTACGTAA
148260 TTTGTTTTACGTAA
1 TTTGTTTTACGTAA
148274 TT
1 TT
148276 CATTTTCCGG
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (14 bp):
TTTGTTTTACGTAA
Found at i:148502 original size:21 final size:23
Alignment explanation
Indices: 148459--148509 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
148449 CATTTTCATC
148459 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
148483 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
*
148504 ATAATA
1 AAAATA
148510 ATATAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
23 8 0.31
24 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:148523 original size:22 final size:23
Alignment explanation
Indices: 148476--148569 Score: 68
Period size: 22 Copynumber: 3.9 Consensus size: 23
148466 TATTTATTAA
* *
148476 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
148497 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
148520 -ATATTTTTAATATTATATAAAATAATC
1 AATATTTATAATA--ATAT--AAT-ATT
148547 AATTATATTATAATAATATAATA
1 AA-TAT-TTATAATAATATAATA
148570 AGATATTATA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
21 11 0.19
22 15 0.26
23 4 0.07
24 4 0.07
25 1 0.02
26 6 0.10
27 2 0.03
28 5 0.09
29 3 0.05
30 7 0.12
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:148604 original size:22 final size:27
Alignment explanation
Indices: 148565--148651 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
148555 TATAATAATA
*
148565 TAATAAGATATTATA-TTTTTAT-T-T
1 TAATAATATATTATATTTTTTATATAT
148589 TAATAATATA-TA-ATTTTTTATATAT
1 TAATAATATATTATATTTTTTATATAT
* *
148614 TAATAATGA-ATAATATTATTTATATATT
1 TAATAAT-ATATTATATTTTTTATATA-T
148642 TAAATAATAT
1 T-AATAATAT
148652 TTTAGTAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
22 1 0.02
23 9 0.18
24 10 0.20
25 9 0.18
26 2 0.04
27 11 0.22
28 3 0.06
29 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATAATATATTATATTTTTTATATAT
Found at i:148610 original size:57 final size:57
Alignment explanation
Indices: 148507--148644 Score: 133
Period size: 57 Copynumber: 2.4 Consensus size: 57
148497 AATATTTATA
148507 ATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATAT-TATAATAAT
1 ATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATATAT-TAATAAT
* ***
148564 ATAATA-AGATATTATATTTTT-ATTTTA-ATAATATATAATTTTTTATATATTAATAAT
1 ATAATATA-ATATTATATTTTTAATATTATATAA-A-ATAATCAATTATATATTAATAAT
* *
148621 GAATAATATTAT-TTATATATTTAA
1 --ATAATATAATATTATATTTTTAA
148645 ATAATATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
55 4 0.06
56 7 0.10
57 37 0.55
58 10 0.15
59 9 0.13
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (57 bp):
ATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATATATTAATAAT
Found at i:148626 original size:25 final size:26
Alignment explanation
Indices: 148565--148651 Score: 92
Period size: 24 Copynumber: 3.3 Consensus size: 26
148555 TATAATAATA
* *
148565 TAATAAGATATTATATTTTTAT-T-T
1 TAATAATATATAATATTTTTATATAT
148589 TAATAATATATAAT-TTTTTATATAT
1 TAATAATATATAATATTTTTATATAT
148614 TAATAATGA-ATAATATTATTTATATATT
1 TAATAAT-ATATAATATT-TTTATATA-T
148642 TAAATAATAT
1 T-AATAATAT
148652 TTTAGTAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.13
24 13 0.25
25 13 0.25
26 3 0.06
27 8 0.15
28 3 0.06
29 6 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TAATAATATATAATATTTTTATATAT
Found at i:148637 original size:79 final size:79
Alignment explanation
Indices: 148461--148637 Score: 177
Period size: 84 Copynumber: 2.2 Consensus size: 79
148451 TTTTCATCAA
*
148461 AATATTATTTATTAAAATATTTAAAATATATTTATTAATATTTATAATAATATAATATTATATTT
1 AATATTATTTA-TAAAATA-TTAAAAGATATTTATTAATATTTATAATAATATAATA-TATATTT
148526 TTAATATTATATAAAAT
63 TTAATATTATATAAAAT
**
148543 AATCAATTATATTATAATAATA-TAATAAGATATTATATTTTTATTT-TAATAATAT-ATA-AT-
1 AAT--ATTAT-TTATAA-AATATTAA-AAGATATT-TATTAATATTTATAATAATATAATATATA
148603 TTTTTATATATTA-ATAATGAAT
60 TTTTTA-ATATTATATAA--AAT
148625 AATATTATTTATA
1 AATATTATTTATA
148638 TATTTAAATA
Statistics
Matches: 83, Mismatches: 3, Indels: 21
0.78 0.03 0.20
Matches are distributed among these distances:
79 5 0.06
80 15 0.18
81 8 0.10
82 9 0.11
83 6 0.07
84 24 0.29
85 16 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (79 bp):
AATATTATTTATAAAATATTAAAAGATATTTATTAATATTTATAATAATATAATATATATTTTTA
ATATTATATAAAAT
Found at i:148835 original size:88 final size:88
Alignment explanation
Indices: 148667--148837 Score: 206
Period size: 90 Copynumber: 1.9 Consensus size: 88
148657 TAAAGATATT
* * * * * *
148667 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
148732 TAATTTATAATATTTTATTTCAC
66 TAATTTATAATATTTTATTTCAC
*
148755 TAAAATATACCAATATTAATATTTTTATTAATAAAACTATAAAAATAATA-TTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
148818 AA-ATTATTT-TAATATTTTAT
62 AATATAATTTATAATATTTTAT
148838 AATAATAATA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
88 20 0.28
89 8 0.11
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (88 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
TAATTTATAATATTTTATTTCAC
Found at i:148858 original size:21 final size:22
Alignment explanation
Indices: 148832--148872 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
148822 TATTTTAATA
148832 TTTTATAAT-AATAATATTAAG
1 TTTTATAATAAATAATATTAAG
*
148853 TTTTATGATAAATAATATTA
1 TTTTATAATAAATAATATTA
148873 TTTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TTTTATAATAAATAATATTAAG
Found at i:149017 original size:15 final size:15
Alignment explanation
Indices: 148991--149061 Score: 92
Period size: 15 Copynumber: 4.9 Consensus size: 15
148981 GTAATTTATT
148991 TTCCAG-AATTCAAA
1 TTCCAGTAATTCAAA
**
149005 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
*
149020 TTTCAGTAATTCAAA
1 TTCCAGTAATTCAAA
149035 TT-CAGTAATTCAAA
1 TTCCAGTAATTCAAA
*
149049 TTACAGTAATTCA
1 TTCCAGTAATTCA
149062 TTTTCCGGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
14 20 0.40
15 30 0.60
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:149040 original size:29 final size:30
Alignment explanation
Indices: 148981--149061 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 30
148971 TTCCAGAAAT
* *
148981 GTAATTTATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTACAGTAATTCAAATTCCA
*
149010 GTAATTCATTTTTCAGTAATTCAAATT-CA
1 GTAATTCATTTTACAGTAATTCAAATTCCA
**
149039 GTAATTCAAATTACAGTAATTCA
1 GTAATTCATTTTACAGTAATTCA
149062 TTTTCCGGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 36 0.78
30 10 0.22
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTACAGTAATTCAAATTCCA
Found at i:150282 original size:15 final size:15
Alignment explanation
Indices: 150262--150295 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
150252 TGAGACATTA
150262 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
150277 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
150292 CCCG
1 CCCG
150296 TCCAGCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.68, G:0.21, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:152148 original size:39 final size:39
Alignment explanation
Indices: 152094--152174 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
152084 TATGGGGAGT
*
152094 AGGAGATGGGAATGCAGCAGGATGCTGTTGATAAGGTGG
1 AGGAGATGGGAATGCAGCAGGATGCTGTTGATAAGGCGG
* *
152133 AGGAGATTGGAATGCAGCAGGATGTTGTTGATAAGGCGG
1 AGGAGATGGGAATGCAGCAGGATGCTGTTGATAAGGCGG
152172 AGG
1 AGG
152175 TGGTGGTGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.07, G:0.43, T:0.21
Consensus pattern (39 bp):
AGGAGATGGGAATGCAGCAGGATGCTGTTGATAAGGCGG
Found at i:153436 original size:23 final size:23
Alignment explanation
Indices: 153392--153436 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
153382 AACATATTAG
**
153392 GTAGCGCTTATATAATGTAATAT
1 GTAGCGCTTATATAATAAAATAT
153415 GTAGCGCTTATATAATAAAATA
1 GTAGCGCTTATATAATAAAATA
153437 GACATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (23 bp):
GTAGCGCTTATATAATAAAATAT
Found at i:153498 original size:87 final size:87
Alignment explanation
Indices: 153352--153514 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
153342 TATATTATAT
*
153352 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATATGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
153417 AGCGCTTATATAATAAAATAGA
66 AGCACTTATATAATAAAATAGA
*
153439 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
153504 AGCACTTATAT
66 AGCACTTATAT
153515 TGACCTATTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCACTTATATAATAAAATAGA
Found at i:155948 original size:21 final size:21
Alignment explanation
Indices: 155924--155971 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
155914 TTTGGGATTA
155924 ACACTTGTTATAAATGTATCG
1 ACACTTGTTATAAATGTATCG
155945 ACACTTGTTATAAATGTATCG
1 ACACTTGTTATAAATGTATCG
155966 ACACTT
1 ACACTT
155972 TTCCGCGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
ACACTTGTTATAAATGTATCG
Found at i:156119 original size:219 final size:220
Alignment explanation
Indices: 155737--156169 Score: 654
Period size: 219 Copynumber: 2.0 Consensus size: 220
155727 CACAAAGTAG
* * **
155737 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTATACACCAAAAGTATCGACACT
1 AATGTATCGACACTTTTCAGCGCACTTGGTTAAGAAATACATTATACACCAAAAGTATCGACACT
* *
155802 TGTTTTATTTGTGTCGATAATTTTTATACACTTGTTTTCTCAAAAATCAGTATATTTAGACCAGT
66 TGTTTTATTTGTGTCGATAATTTTTATACACCTGTTTTCTCAAAAACCAGTATATTTAGACCAGT
* * *
155867 TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATTAACACTTGT
131 TAAATTGCTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCAACACTTCT
155932 TATAAATGTATCGACACTTGTTATA
196 TATAAATGTATCGACACTTGTTATA
* * **
155957 AATGTATCGACACTTTTCCGCGCACTTGGTTAAGAAATACATTCTGGACCAAAAGTATCGACACT
1 AATGTATCGACACTTTTCAGCGCACTTGGTTAAGAAATACATTATACACCAAAAGTATCGACACT
* * * *
156022 TG-TTTAGTTT-TGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGG
66 TGTTTTA-TTTGTGTCGATAATTTTTATACACCTGTTTTCTCAAAAACCAGTATATTTAGACCAG
* * * *
156085 TTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTTGGATCGACACTTC
130 TTAAATTGCTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCAACACTTC
156150 TTATAAATGTATCGACACTT
195 TTATAAATGTATCGACACTT
156170 TTTAGTGCAC
Statistics
Matches: 191, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
219 129 0.68
220 62 0.32
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.41
Consensus pattern (220 bp):
AATGTATCGACACTTTTCAGCGCACTTGGTTAAGAAATACATTATACACCAAAAGTATCGACACT
TGTTTTATTTGTGTCGATAATTTTTATACACCTGTTTTCTCAAAAACCAGTATATTTAGACCAGT
TAAATTGCTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCAACACTTCT
TATAAATGTATCGACACTTGTTATA
Found at i:156321 original size:199 final size:199
Alignment explanation
Indices: 155737--156965 Score: 1735
Period size: 199 Copynumber: 6.1 Consensus size: 199
155727 CACAAAGTAG
* * **
155737 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTATACACCAAAAGTATCGACACT
1 AATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
* * * * * *
155802 TGTTTTATTTGTGTCGATAATTTTTATACACTTGTTTTCTCAAAAATCAGTATATTTAGACCAGT
66 TGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGT
**
155867 TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATTAACACTTGT
131 TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGT
155932 TATA
196 TATA
*
155936 AATGTATCGACACTTGTTATAAATGTATCGACACTTTTCCGCGCACTTGGTTAAGAAATACATTC
1 AATGTATCGACACTT-TT-T---CG--T-G-CAC--TT--G-G---TT--TT--GAAATACATTC
156001 TGGACCAAAAGTATCGACACTTG-TTTAGTTT-TGTCGATACTTTTTGTACACCTGTTTTCTCAA
45 TGGACCAAAAGTATCGACACTTGTTTTA-TTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAA
* * *
156064 AAACCGGTATATTTAGACCGGTTACATTGCTAATTTACCTATTACATTATAATTATGGGTTTCGA
109 AAACCGGTATATTTAGACCGGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGA
* *
156129 TGTTTTTTGGATCGACACTTCTTATA
174 TGTTTTTGGGATCGACACTTGTTATA
*
156155 AATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
1 AATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
* *
156220 TGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTATCAAAAACCAGTATATTTAGACCGGT
66 TGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGT
* * *
156285 TAAATTATTAATTTACCTATTACAACAAAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGT
131 TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGT
156350 TATA
196 TATA
**
156354 AATGTATCGACA-TTTTTCCGTGCACTTGGTTAAGAAATACATTCTGGACCAAAAGTATCGACAC
1 AATGTATCGACACTTTTT-CGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACAC
* * * * *
156418 TTGTTTTAGTTATGTCGATACTTTTTGTACACCTGTTTTCTTAAAAACCGGTATATTTAGATCAG
65 TTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGG
* * *
156483 TTAAATTGTTAATTTACCTATTACCTCATAATTATGGGTTTCGGTGTTTTTGGGATCGATACTTG
130 TTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTG
156548 TTATA
195 TTATA
*
156553 AATGTATCGACACTTTTCCGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
1 AATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
** **
156618 TGTTTTATTTGTGTCGATACTTTTTGTACATATGTTTTCTCAAAAATTGGTATATTTAGACCGGT
66 TGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGT
* * *
156683 TAAATTGTTAATTTATCTATTACATCATAATTATGTGTTTCGATATTTTTGGGATCGACACTTGT
131 TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGT
156748 TATA
196 TATA
* *
156752 AATATATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
1 AATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
* * * *
156817 TGTTTTAGTTGTGTCAATATTTTTTGTACACCTATTTTCTCAAAAACCGGTATATTTAGACCGGT
66 TGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGT
** * * * *
156882 TACGTTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATATTTTTTGGATCGACACTTCT
131 TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGT
156947 TATA
196 TATA
*
156951 AATGTATCAACACTT
1 AATGTATCGACACTT
156966 CTTATAAATG
Statistics
Matches: 922, Mismatches: 82, Indels: 52
0.87 0.08 0.05
Matches are distributed among these distances:
198 42 0.05
199 679 0.74
200 8 0.01
201 1 0.00
202 2 0.00
204 1 0.00
205 1 0.00
206 2 0.00
207 1 0.00
208 5 0.01
210 5 0.01
211 1 0.00
212 2 0.00
213 1 0.00
214 1 0.00
216 2 0.00
217 1 0.00
218 4 0.00
219 129 0.14
220 34 0.04
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.41
Consensus pattern (199 bp):
AATGTATCGACACTTTTTCGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACT
TGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGT
TAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTGT
TATA
Found at i:156965 original size:21 final size:21
Alignment explanation
Indices: 156939--156984 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
156929 TTTTGGATCG
156939 ACACTTCTTATAAATGTATCA
1 ACACTTCTTATAAATGTATCA
*
156960 ACACTTCTTATAAATGTATCC
1 ACACTTCTTATAAATGTATCA
156981 ACAC
1 ACAC
156985 ATAAGTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (21 bp):
ACACTTCTTATAAATGTATCA
Found at i:157381 original size:19 final size:19
Alignment explanation
Indices: 157357--157406 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
157347 TTACATTCAC
*
157357 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
157376 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
157395 ATACAAAATTAA
1 ATACAAAATTAA
157407 CCCTACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:158818 original size:18 final size:18
Alignment explanation
Indices: 158795--158833 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
158785 TTCTCCTCAT
* *
158795 TTCCTCCATCTTTTCTTC
1 TTCCTCAATCTTCTCTTC
158813 TTCCTCAATCTTCTCTTC
1 TTCCTCAATCTTCTCTTC
158831 TTC
1 TTC
158834 AAAATTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.38, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCAATCTTCTCTTC
Found at i:159552 original size:22 final size:21
Alignment explanation
Indices: 159524--159580 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
159514 AACCTGCATT
*
159524 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
159546 TATAATAACTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
159570 TATAAAAAAAC
1 TATAATAAAAC
159581 AAAAACATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
24 18 0.60
25 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:160830 original size:19 final size:20
Alignment explanation
Indices: 160802--160851 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
160792 CATTTATACA
*
160802 ACCTAAAATATCA-TTTTCT
1 ACCTATAATATCATTTTTCT
*
160821 ACCTATAATATCATTTTTTT
1 ACCTATAATATCATTTTTCT
*
160841 ACATATAATAT
1 ACCTATAATAT
160852 TAAATAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.46
Consensus pattern (20 bp):
ACCTATAATATCATTTTTCT
Found at i:161909 original size:181 final size:182
Alignment explanation
Indices: 161232--162618 Score: 1961
Period size: 182 Copynumber: 7.6 Consensus size: 182
161222 TACGCGTACT
* * *
161232 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTAATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
* * *
161297 ATTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACACT
66 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
*
161362 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
161414 TATTAAATTATCGACGCTTTCAACATATAC-ATATCTTTTTACCGGTTTTGTCATTTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGAGACC
*
161478 TG-TTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTTAAAGTATCGAC
65 -GATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA-TTTTTTTAAAGTATCGAC
* * *
161542 ACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATCGATAATTA
128 ACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * * *
161597 TATTAAAATATTGACACCTTCAATATATCCGGTAG-TTATTTACCTGTTTTGTCATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACC
* * * ** *
161661 GATTTTGTCATATTTTTAGCTGTTATATTATTATGGATAGATACATTTTCATAAAGTGTCGACAC
65 GATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
161726 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
* **
161779 TATTAAATTATCGACACTTTCAACATATCCAGTAGCGTTTTACCAATTTTGTCA-TTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
*
161843 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCAACACT
66 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* *
161908 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
161960 TATTAAAGTATCGACACTTTCAACATATCCGGTAG-TTATTTACCTGTTTTGTCATTTTGAGATT
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGA-C
* * * ** *
162024 GGA-TTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACA
64 CGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACA
* *
162088 TTTTTTAAGCGCTATAACTTCTTCT-TTTTAAATT-CAGAAAGTGTCGATACTTA
129 CTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTA
162141 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
* * * *
162206 GTTTTGTCATATTTTTACATGTAATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACA-T
66 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* *
162270 TTTATAGGCTCTATAACTTCTTCTCTTTTAATTTCCAAAAGTGTCGATACTTA
131 TTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * * *
162323 TATTAAAGTATCGACACTGTCAACATATCCGGTAG-TTATTTATCTGTTTTGTCATTTTGAGA-C
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGT-TTTACCGGTTTTGTCATTTTGAGACC
** * * ** *
162386 GATTTTGTCATATTTTTAGTTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACAC
65 GATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
*
162451 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAAGTGTCGATACTTA
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTC-CAAAAGTGTCGATACTTA
* *
162505 TATTAAATTATCGACACCTTCAACATAGCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
1 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
* * *
162570 ATTTTGTCATATTTTTACCTGTAATATTGCTATGGAGCGATACATTTTT
66 ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
162619 CATTTGTATC
Statistics
Matches: 1069, Mismatches: 113, Indels: 45
0.87 0.09 0.04
Matches are distributed among these distances:
180 8 0.01
181 421 0.39
182 428 0.40
183 195 0.18
184 17 0.02
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
ATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:162040 original size:363 final size:364
Alignment explanation
Indices: 161232--162618 Score: 2189
Period size: 363 Copynumber: 3.8 Consensus size: 364
161222 TACGCGTACT
*** * *
161232 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTAATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
* * * * *
161297 ATTTTATCATATTTTTA-CATGTTATATTGTTATGGATCGATACATTTT-TTAAAAGTATCGACA
66 ATTTTGTCATATTTTTAGC-TGTTATATTATTATAGATCGATACATTTTCAT-AAAGTGTCGACA
*
161360 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTCGATACTTATATTAAATTA
129 CTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTCGATACTTATATTAAATTA
* * * * *
161424 TCGACGCTTTCAACATATACA-TATCTTTTTACCGGTTTTGTCATTTTTGAGACCTG-TTTTATC
193 TCGACACTTTCAACATATCCAGTAGCGTTTTACCGGTTTTGTCA-TTTTGAGACC-GATTTTGTC
*
161487 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTTAAAGTATCGACACTTTATAGG
256 ATATTTTTACCTGTAATATTGTTATGGATCGATACA-TTTTTTTAAAGTATCGACACTTTATAGG
* *
161552 CGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATCGATAATTA
320 CGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * * *
161597 TATTAAAATATTGACACCTTCAATATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
* *
161662 ATTTTGTCATATTTTTAGCTGTTATATTATTATGGATAGATACATTTTCATAAAGTGTCGACACT
66 ATTTTGTCATATTTTTAGCTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACT
161727 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
**
161792 ACACTTTCAACATATCCAGTAGCGTTTTACCAATTTTGTCA-TTTGAGACCGATTTTGTCATATT
196 ACACTTTCAACATATCCAGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTCATATT
* *
161856 TTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCAACACTTTATAGGCGCTAT
261 TTTACCTGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGGCGCTAT
*
161921 AACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTA
326 AACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
**
161960 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGATTG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGA-CC
* *
162025 GA-TTTGTCATATTTTTAGCTGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACAT
65 GATTTTGTCATATTTTTAGCTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACAC
*
162089 TTTTTAAGCGCTATAACTTCTTCT-TTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
130 TTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATC
* *
162153 GACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGGTTTTGTCATAT
195 GACACTTTCAACATATCCAGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTCATAT
* * * *
162218 TTTTACATGTAATATTGTTATGGATCGATACATTTTTTAAAAGTATCGACATTTTATAGGCTCTA
260 TTTTACCTGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGGCGCTA
*
162283 TAACTTCTTCTCTTTTAATTTCCAAAAGTGTCGATACTTA
325 TAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
162323 TATTAAAGTATCGACACTGTCAACATATCCGGTAGTTATTTATCTGTTTTGTCATTTTGAGA-CG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
*
162387 ATTTTGTCATATTTTTAGTTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACT
66 ATTTTGTCATATTTTTAGCTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACT
162452 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAAGTGTCGATACTTATATTAAATTATC
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAG-AAAGTGTCGATACTTATATTAAATTATC
* * *
162517 GACACCTTCAACATAGCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTCATAT
195 GACACTTTCAACATATCCAGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTCATAT
* *
162582 TTTTACCTGTAATATTGCTATGGAGCGATACATTTTT
260 TTTTACCTGTAATATTGTTATGGATCGATACATTTTT
162619 CATTTGTATC
Statistics
Matches: 950, Mismatches: 62, Indels: 21
0.92 0.06 0.02
Matches are distributed among these distances:
361 2 0.00
362 161 0.17
363 399 0.42
364 179 0.19
365 189 0.20
366 20 0.02
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (364 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTGAGACCG
ATTTTGTCATATTTTTAGCTGTTATATTATTATAGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
ACACTTTCAACATATCCAGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCGATTTTGTCATATT
TTTACCTGTAATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTTATAGGCGCTAT
AACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:167401 original size:3 final size:3
Alignment explanation
Indices: 167393--167423 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
167383 GATCAACATG
167393 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
167424 TTAAAATATG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:168349 original size:13 final size:13
Alignment explanation
Indices: 168331--168355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
168321 AAGTACAATA
168331 ATAAATAAAGAAC
1 ATAAATAAAGAAC
168344 ATAAATAAAGAA
1 ATAAATAAAGAA
168356 AAATAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
ATAAATAAAGAAC
Found at i:170606 original size:143 final size:143
Alignment explanation
Indices: 170165--170602 Score: 580
Period size: 143 Copynumber: 3.1 Consensus size: 143
170155 ACTTTTCAGC
* *
170165 AGAAACTTTTCAATGCCCAATTAATTATCTTAAGCAAATTTTTAGTGATATATCAACTAATTT-T
1 AGAAACTTTTCAGTGCCCAATTAATTATCTTAAGCAAATTTTCAGTGATATATCAACTAATTTCT
** * * *
170229 AACAAACTTTTCTCTTGTGATATATCACTTCATATCAGAAAAA-GATGTATTTTTCATAGGCAAA
66 -ACAAACTTTTCAGTGGTGATATATCACTTCATATCAGAAAAACG-TGCATTTATCATAGGCAAA
170293 ATAATGTACCATGGCT
129 ATAATGTACCATGG-T
* * *
170309 -GAAAAC-TTTCAGTGCCCAATTAATTATCTTAAGCAATTTTTCTGTGATATATCAACTTATTTC
1 AG-AAACTTTTCAGTGCCCAATTAATTATCTTAAGCAAATTTTCAGTGATATATCAACTAATTTC
* *
170372 AACAAACTTTT-AGTGGTGATATATCACTTCATATCATAAAAACGTGCATTTATCATAGGCAAAA
65 TACAAACTTTTCAGTGGTGATATATCACTTCATATCAGAAAAACGTGCATTTATCATAGGCAAAA
* * *
170436 TAATGCATCATGGC
130 TAATGTACCATGGT
* * * * * * * *
170450 ATAAACTTTTTAGTGACTAATTAATTATCTTCAGTAACTTTTCAGTGATATATCAACTCATTTCT
1 AGAAACTTTTCAGTGCCCAATTAATTATCTTAAGCAAATTTTCAGTGATATATCAACTAATTTCT
* *
170515 ATAAACTTTTCAGTGGTGATATATCACTTCATATCAGAAAAACGTGCATTTCTCATAGGCAAAAT
66 ACAAACTTTTCAGTGGTGATATATCACTTCATATCAGAAAAACGTGCATTTATCATAGGCAAAAT
170580 AATGTACCATGGT
131 AATGTACCATGGT
170593 AGAAACTTTT
1 AGAAACTTTT
170603 TAGTTCACAA
Statistics
Matches: 256, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
141 4 0.02
142 114 0.45
143 134 0.52
144 4 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (143 bp):
AGAAACTTTTCAGTGCCCAATTAATTATCTTAAGCAAATTTTCAGTGATATATCAACTAATTTCT
ACAAACTTTTCAGTGGTGATATATCACTTCATATCAGAAAAACGTGCATTTATCATAGGCAAAAT
AATGTACCATGGT
Found at i:173732 original size:18 final size:18
Alignment explanation
Indices: 173711--173745 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
173701 ATATAAAATT
*
173711 AAATATTTTATAATTAAA
1 AAATAGTTTATAATTAAA
173729 AAATAGTTTATAATTAA
1 AAATAGTTTATAATTAA
173746 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AAATAGTTTATAATTAAA
Found at i:173770 original size:18 final size:18
Alignment explanation
Indices: 173719--173772 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
173709 TTAAATATTT
* * *
173719 TATAATTAAAAAATAGTT
1 TATAATTATAAAATAATA
*
173737 TATAATTAATTTAAATAATA
1 TATAATT-A-TAAAATAATA
173757 TATAATTATAAAATAA
1 TATAATTATAAAATAA
173773 AATTTTATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
18 14 0.48
19 2 0.07
20 13 0.45
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
TATAATTATAAAATAATA
Found at i:177618 original size:31 final size:31
Alignment explanation
Indices: 177553--177697 Score: 256
Period size: 31 Copynumber: 4.7 Consensus size: 31
177543 GCTCGTATAA
*
177553 ATGTCCCGAAGAACCTAGGTAAACAGT-CAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
177583 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
177614 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
* *
177645 ATATCCCGAAGAACATAGGTAATCAGTCCAT
1 ATGTCCCGAAGAACATAGGTAAACAGTCCAT
177676 ATGTCCCGAAGAACATAGGTAA
1 ATGTCCCGAAGAACATAGGTAA
177698 CCCTCGAATC
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
30 26 0.24
31 84 0.76
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
ATGTCCCGAAGAACATAGGTAAACAGTCCAT
Found at i:177859 original size:18 final size:18
Alignment explanation
Indices: 177838--177890 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
177828 TTCATATTGT
177838 TTCTTTTATAATCACATG
1 TTCTTTTATAATCACATG
177856 TTCTTTTAT-AT--CAT-
1 TTCTTTTATAATCACATG
*
177870 TTATTTTATAATCACATG
1 TTCTTTTATAATCACATG
177888 TTC
1 TTC
177891 CTTCTCTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 8 0.28
15 5 0.17
17 5 0.17
18 11 0.38
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (18 bp):
TTCTTTTATAATCACATG
Found at i:180238 original size:23 final size:24
Alignment explanation
Indices: 180184--180238 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
180174 CTCAAGTGAA
* *
180184 AATTAAATAAAAATATTACAAACT
1 AATTAAATAAAAATAATAAAAACT
*
180208 AAAT-AATAAAAATAATAAAAAC-
1 AATTAAATAAAAATAATAAAAACT
180230 AATTAAATA
1 AATTAAATA
180239 CAAACATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 3 0.12
23 20 0.77
24 3 0.12
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.25
Consensus pattern (24 bp):
AATTAAATAAAAATAATAAAAACT
Found at i:180249 original size:13 final size:14
Alignment explanation
Indices: 180221--180255 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
180211 TAATAAAAAT
*
180221 AATAAAAACAATTA
1 AATACAAACAATTA
180235 AATACAAAC-ATTA
1 AATACAAACAATTA
180248 AATACAAA
1 AATACAAA
180256 TGTTACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (14 bp):
AATACAAACAATTA
Found at i:180675 original size:21 final size:21
Alignment explanation
Indices: 180651--180701 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
180641 ACCATGGTGG
*
180651 CATCGGAAACAGCTGCAGTGC
1 CATCTGAAACAGCTGCAGTGC
* * *
180672 CATCTGAAACGGCTGCGGTGG
1 CATCTGAAACAGCTGCAGTGC
180693 CATCTGAAA
1 CATCTGAAA
180702 TGAATACGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.18
Consensus pattern (21 bp):
CATCTGAAACAGCTGCAGTGC
Found at i:187589 original size:42 final size:42
Alignment explanation
Indices: 187530--187615 Score: 147
Period size: 42 Copynumber: 2.0 Consensus size: 42
187520 TACACTATTA
*
187530 TATTTCTAAAGGATACAGGATGCGTTAA-TCATGCCTTAATCT
1 TATTTCTAAAGGATACAGGATGCATTAACT-ATGCCTTAATCT
187572 TATTTCTAAAGGATACAGGATGCATTAACTATGCCTTAATCT
1 TATTTCTAAAGGATACAGGATGCATTAACTATGCCTTAATCT
187614 TA
1 TA
187616 GCGCAACTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (42 bp):
TATTTCTAAAGGATACAGGATGCATTAACTATGCCTTAATCT
Found at i:190059 original size:61 final size:59
Alignment explanation
Indices: 189991--190107 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 59
189981 AAACTATGTT
* * * * *
189991 TCTCATTCTAAAATGGTCTTTAATGTTTTTTAACATTTTAATTTCATCCTCAAATTATTAC
1 TCTCATTCTAAAATGATCCTTAA--ATTTTGAACATTTTAAATTCATCCTCAAATTATTAC
*
190052 TCTCATTCTAAACTGATCCTTAAATTTTGAACATTTTAAATTCATCCTCAAATTAT
1 TCTCATTCTAAAATGATCCTTAAATTTTGAACATTTTAAATTCATCCTCAAATTAT
190108 AACCCCAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 30 0.60
61 20 0.40
ACGTcount: A:0.32, C:0.18, G:0.04, T:0.46
Consensus pattern (59 bp):
TCTCATTCTAAAATGATCCTTAAATTTTGAACATTTTAAATTCATCCTCAAATTATTAC
Found at i:190216 original size:28 final size:29
Alignment explanation
Indices: 190165--190232 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 29
190155 ATCTCTCGAA
*
190165 ATCATTCAAAAGTTTAAGAATGAAATTGG
1 ATCATTCAAAAATTTAAGAATGAAATTGG
* * *
190194 ATCATT-AAAAATTTCAGGATGAAATTGA
1 ATCATTCAAAAATTTAAGAATGAAATTGG
*
190222 AACATTCAAAA
1 ATCATTCAAAA
190233 CGTTGTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (29 bp):
ATCATTCAAAAATTTAAGAATGAAATTGG
Found at i:191605 original size:22 final size:22
Alignment explanation
Indices: 191575--191616 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
191565 AGTCGAGGGT
* *
191575 TTCATAGGTCCTTCTGGACATA
1 TTCACAGGTCCTTCGGGACATA
191597 TTCACAGGTCCTTCGGGACA
1 TTCACAGGTCCTTCGGGACA
191617 AATTTCATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.31
Consensus pattern (22 bp):
TTCACAGGTCCTTCGGGACATA
Found at i:192928 original size:19 final size:19
Alignment explanation
Indices: 192904--192941 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
192894 TCTTTGCTTC
192904 GTGGGCAAGTGAGAATTTG
1 GTGGGCAAGTGAGAATTTG
192923 GTGGGCAAGTGAGAATTTG
1 GTGGGCAAGTGAGAATTTG
192942 AGGATGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.42, T:0.26
Consensus pattern (19 bp):
GTGGGCAAGTGAGAATTTG
Found at i:194584 original size:28 final size:28
Alignment explanation
Indices: 194512--194586 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 28
194502 TTGACGATTT
*
194512 ATACATATTTTACTATTCATTACTGTTC
1 ATACATATTTTACTGTTCATTACTGTTC
* *
194540 ATACATATTTGACTGTTTATTACTGTTC
1 ATACATATTTTACTGTTCATTACTGTTC
* *
194568 ATACGTATTTTATTGTTCA
1 ATACATATTTTACTGTTCA
194587 CAAATACGTT
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:0.27, C:0.15, G:0.08, T:0.51
Consensus pattern (28 bp):
ATACATATTTTACTGTTCATTACTGTTC
Found at i:196977 original size:42 final size:42
Alignment explanation
Indices: 196931--197015 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
196921 TCACGATCGA
196931 TCAAATGAATTTAAACGATTAAGTATTTTAGATTATAGGGAT
1 TCAAATGAATTTAAACGATTAAGTATTTTAGATTATAGGGAT
196973 TCAAATGAATTTAAACGATTAAGTATTTTAGATTATAGGGAT
1 TCAAATGAATTTAAACGATTAAGTATTTTAGATTATAGGGAT
197015 T
1 T
197016 AAGGATTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (42 bp):
TCAAATGAATTTAAACGATTAAGTATTTTAGATTATAGGGAT
Found at i:207244 original size:32 final size:32
Alignment explanation
Indices: 207208--207329 Score: 145
Period size: 32 Copynumber: 3.8 Consensus size: 32
207198 CATATACTAG
**
207208 CAGTGTTGCATTCAGTTAATGCACAATACAAT
1 CAGTGTTGCATTCAAATAATGCACAATACAAT
* ***
207240 CAGTGTTGCATTCAAATAATGCACAAGAGTGT
1 CAGTGTTGCATTCAAATAATGCACAATACAAT
* * **
207272 CAGTGTCGCATTTAGTTAATGCACAATACAAT
1 CAGTGTTGCATTCAAATAATGCACAATACAAT
*
207304 CAGCGTTGCATTCAAATAATGCACAA
1 CAGTGTTGCATTCAAATAATGCACAA
207330 GAGTGTCAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
CAGTGTTGCATTCAAATAATGCACAATACAAT
Found at i:207289 original size:64 final size:64
Alignment explanation
Indices: 207208--207356 Score: 253
Period size: 64 Copynumber: 2.3 Consensus size: 64
207198 CATATACTAG
* * *
207208 CAGTGTTGCATTCAGTTAATGCACAATACAATCAGTGTTGCATTCAAATAATGCACAAGAGTGT
1 CAGTGTCGCATTTAGTTAATGCACAATACAATCAGCGTTGCATTCAAATAATGCACAAGAGTGT
207272 CAGTGTCGCATTTAGTTAATGCACAATACAATCAGCGTTGCATTCAAATAATGCACAAGAGTGT
1 CAGTGTCGCATTTAGTTAATGCACAATACAATCAGCGTTGCATTCAAATAATGCACAAGAGTGT
* *
207336 CAATGTCGCATTTAGATAATG
1 CAGTGTCGCATTTAGTTAATG
207357 TGTAGCAGTT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (64 bp):
CAGTGTCGCATTTAGTTAATGCACAATACAATCAGCGTTGCATTCAAATAATGCACAAGAGTGT
Found at i:207347 original size:32 final size:32
Alignment explanation
Indices: 207239--207356 Score: 119
Period size: 32 Copynumber: 3.7 Consensus size: 32
207229 CACAATACAA
*
207239 TCAGTGTTGCATTCAAATAATGCACAAGAGTG
1 TCAGTGTCGCATTCAAATAATGCACAAGAGTG
* ** * ***
207271 TCAGTGTCGCATTTAGTTAATGCACAATACAA
1 TCAGTGTCGCATTCAAATAATGCACAAGAGTG
* *
207303 TCAGCGTTGCATTCAAATAATGCACAAGAGTG
1 TCAGTGTCGCATTCAAATAATGCACAAGAGTG
* * *
207335 TCAATGTCGCATTTAGATAATG
1 TCAGTGTCGCATTCAAATAATG
207357 TGTAGCAGTT
Statistics
Matches: 64, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (32 bp):
TCAGTGTCGCATTCAAATAATGCACAAGAGTG
Found at i:211831 original size:13 final size:13
Alignment explanation
Indices: 211810--211848 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
211800 AATTTATATT
*
211810 ATATTAAATTAAA
1 ATATAAAATTAAA
211823 ATATAAAATTAAA
1 ATATAAAATTAAA
211836 ATATAAAATTAAA
1 ATATAAAATTAAA
211849 TCATATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATAAAATTAAA
Found at i:211835 original size:6 final size:6
Alignment explanation
Indices: 211815--211848 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
211805 ATATTATATT
211815 AAATTA AAATATA AAATTA AAATATA AAATTA AA
1 AAATTA AAAT-TA AAATTA AAAT-TA AAATTA AA
211849 TCATATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 14 0.54
7 12 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATTA
Found at i:221810 original size:6 final size:6
Alignment explanation
Indices: 221799--221823 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
221789 GAAGAGGGTT
221799 CATCGG CATCGG CATCGG CATCGG C
1 CATCGG CATCGG CATCGG CATCGG C
221824 CTCAAGTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.32, T:0.16
Consensus pattern (6 bp):
CATCGG
Found at i:222693 original size:19 final size:19
Alignment explanation
Indices: 222669--222705 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
222659 ATGACCAACA
*
222669 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
222688 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
222706 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:222754 original size:20 final size:20
Alignment explanation
Indices: 222731--222865 Score: 85
Period size: 20 Copynumber: 6.6 Consensus size: 20
222721 GTTTCCAGAT
222731 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTTTGACTA
** * *
222751 TCGCATTGCGATTTT-CCAAA
1 TCGCAACGCGATTTTGAC-TA
*** **
222771 TTCGCATTACGATTTTGTAAAA
1 -TCGCAACGCGATTTTG-ACTA
*
222793 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
**
222813 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTTTGAC-T-A
*
222834 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGACTA
*
222854 TCGCAATGCGAT
1 TCGCAACGCGAT
222866 AATACAAAAT
Statistics
Matches: 90, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
19 3 0.03
20 42 0.47
21 41 0.46
22 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTTGACTA
Found at i:222804 original size:21 final size:20
Alignment explanation
Indices: 222731--222889 Score: 68
Period size: 21 Copynumber: 7.8 Consensus size: 20
222721 GTTTCCAGAT
**
222731 TCGCAACGCGATTTTGACTA
1 TCGCAACGCGATTTTGAAAA
** * *
222751 TCGCATTGCGATTTTCCAAAT
1 TCGCAACGCGATTTT-GAAAA
***
222772 TCGCATTACGATTTTGTAAAA
1 TCGCAACGCGATTTTG-AAAA
* **
222793 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGAAAA
**
222813 TCGCAACGCGATAAT-ACATAA
1 TCGCAACGCGATTTTGA-A-AA
* **
222834 TCGCAACGCGATTCTGACTA
1 TCGCAACGCGATTTTGAAAA
* * **
222854 TCGCAATGCGATAATACAAAA
1 TCGCAACGCGAT-TTTGAAAA
*
222875 TCGCAATGCGATTTT
1 TCGCAACGCGATTTT
222890 CAAAGCGCCA
Statistics
Matches: 101, Mismatches: 32, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
19 1 0.01
20 41 0.41
21 58 0.57
22 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTTTGAAAA
Found at i:222817 original size:41 final size:41
Alignment explanation
Indices: 222789--222887 Score: 153
Period size: 41 Copynumber: 2.4 Consensus size: 41
222779 ACGATTTTGT
*
222789 AAAATCGCAACGCGATTCTGACTATCGCAACGCGATAATAC
1 AAAATCGCAACGCGATTCTGACTATCGCAACACGATAATAC
* **
222830 ATAATCGCAACGCGATTCTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATTCTGACTATCGCAACACGATAATAC
*
222871 AAAATCGCAATGCGATT
1 AAAATCGCAACGCGATT
222888 TTCAAAGCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGCGATTCTGACTATCGCAACACGATAATAC
Found at i:223057 original size:22 final size:22
Alignment explanation
Indices: 223031--223081 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
223021 CTACGGCGAC
* *
223031 ATCCGTCCCCATCTCTGACGAA
1 ATCCGTCCCCATCTCCGAAGAA
223053 ATCCGTCCCCATCTCCGAAGAA
1 ATCCGTCCCCATCTCCGAAGAA
223075 ATCCGTC
1 ATCCGTC
223082 TATCTCCATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGAAGAA
Done.