Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008267.1 Hibiscus syriacus cultivar Beakdansim tig00110922_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: 60196
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:9038 original size:10 final size:10
Alignment explanation
Indices: 9023--9047 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9013 CAAATATAAC
9023 CTAAATGCAA
1 CTAAATGCAA
9033 CTAAATGCAA
1 CTAAATGCAA
9043 CTAAA
1 CTAAA
9048 ATATTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:13237 original size:16 final size:15
Alignment explanation
Indices: 13218--13247 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
13208 TTTAACTTGA
13218 TTCTTTTTCAATCATT
1 TTCTTTTT-AATCATT
13234 TTCTTTTTAATCAT
1 TTCTTTTTAATCAT
13248 CAATGGCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (15 bp):
TTCTTTTTAATCATT
Found at i:13870 original size:17 final size:18
Alignment explanation
Indices: 13848--13885 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
13838 TTTATATTTG
13848 TATAA-TTGAATCGAATA
1 TATAATTTGAATCGAATA
*
13865 TATAATTTTGAATTGAATA
1 TATAA-TTTGAATCGAATA
13884 TA
1 TA
13886 AAATCTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
19 13 0.72
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (18 bp):
TATAATTTGAATCGAATA
Found at i:14323 original size:14 final size:13
Alignment explanation
Indices: 14293--14340 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
14283 CATTCATAAT
*
14293 AAACAAACAAACCA
1 AAACAAAC-ATCCA
14307 AAATCAAACATCCA
1 AAA-CAAACATCCA
*
14321 AAACAAATATCCA
1 AAACAAACATCCA
*
14334 AACCAAA
1 AAACAAA
14341 TATTCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 15 0.50
14 10 0.33
15 5 0.17
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (13 bp):
AAACAAACATCCA
Found at i:14332 original size:13 final size:13
Alignment explanation
Indices: 14304--14349 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
14294 AACAAACAAA
*
14304 CCAAAATCAAACAT
1 CCAAAA-CAAATAT
14318 CCAAAACAAATAT
1 CCAAAACAAATAT
*
14331 CCAAACCAAATAT
1 CCAAAACAAATAT
*
14344 TCAAAA
1 CCAAAA
14350 TCCATCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 22 0.79
14 6 0.21
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (13 bp):
CCAAAACAAATAT
Found at i:15585 original size:12 final size:12
Alignment explanation
Indices: 15561--15590 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
15551 TGGTGGAATA
15561 GGAGGTGGATTT
1 GGAGGTGGATTT
*
15573 GGAGGTGGGTTT
1 GGAGGTGGATTT
15585 GGAGGT
1 GGAGGT
15591 AAGTTTGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.57, T:0.30
Consensus pattern (12 bp):
GGAGGTGGATTT
Found at i:16288 original size:20 final size:20
Alignment explanation
Indices: 16250--16288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16240 AAACCCGACT
* *
16250 AGGGGTATCGGTACCCATTG
1 AGGGGTATCGATACACATTG
16270 AGGGGTATCGATACACATT
1 AGGGGTATCGATACACATT
16289 CAAGGAGGGT
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:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (20 bp):
AGGGGTATCGATACACATTG
Found at i:22265 original size:13 final size:13
Alignment explanation
Indices: 22247--22273 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
22237 TCCAATATAA
22247 AATCTTAAAATTC
1 AATCTTAAAATTC
22260 AATCTTAAAATTC
1 AATCTTAAAATTC
22273 A
1 A
22274 TTAACACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:32878 original size:10 final size:10
Alignment explanation
Indices: 32863--32887 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32853 CAAATATAAC
32863 CTAAATGCAA
1 CTAAATGCAA
32873 CTAAATGCAA
1 CTAAATGCAA
32883 CTAAA
1 CTAAA
32888 ATATTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:33745 original size:20 final size:20
Alignment explanation
Indices: 33702--33748 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
33692 TCAAGGGGTA
*
33702 TCGATACTCATGGCCAGGTT
1 TCGATACTCATGGCCAGGTC
***
33722 TCGATACTCATGGGGTGGTC
1 TCGATACTCATGGCCAGGTC
33742 TCGATAC
1 TCGATAC
33749 CGATGACAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (20 bp):
TCGATACTCATGGCCAGGTC
Found at i:33849 original size:21 final size:21
Alignment explanation
Indices: 33825--33916 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
33815 AGGGGTAGAT
33825 TATCGATACTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAG
*
33846 TATCGATATTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAG
33867 TATCGATACT-CCCATAAGAG
1 TATCGATACTCCCCATAAGAG
*
33887 TATCGATACTCCCCAAAAGAG
1 TATCGATACTCCCCATAAGAG
33908 TATCGATAC
1 TATCGATAC
33917 CAAGACATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 20 0.30
21 47 0.70
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (21 bp):
TATCGATACTCCCCATAAGAG
Found at i:33893 original size:41 final size:42
Alignment explanation
Indices: 33825--33916 Score: 159
Period size: 41 Copynumber: 2.2 Consensus size: 42
33815 AGGGGTAGAT
* *
33825 TATCGATACTCCCCATAAGAGTATCGATATTCCCCATAAGAG
1 TATCGATACTCCCCATAAGAGTATCGATACTCCCCAAAAGAG
33867 TATCGATACT-CCCATAAGAGTATCGATACTCCCCAAAAGAG
1 TATCGATACTCCCCATAAGAGTATCGATACTCCCCAAAAGAG
33908 TATCGATAC
1 TATCGATAC
33917 CAAGACATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 38 0.79
42 10 0.21
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (42 bp):
TATCGATACTCCCCATAAGAGTATCGATACTCCCCAAAAGAG
Found at i:40133 original size:22 final size:22
Alignment explanation
Indices: 40108--40149 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
40098 CCCCCTTTGA
*
40108 AGGGGAACCGATTCCCCCCCAC
1 AGGGGAACCGATACCCCCCCAC
*
40130 AGGGGAATCGATACCCCCCC
1 AGGGGAACCGATACCCCCCC
40150 TGGGGTTCTG
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:0.24, C:0.43, G:0.24, T:0.10
Consensus pattern (22 bp):
AGGGGAACCGATACCCCCCCAC
Found at i:42971 original size:3 final size:3
Alignment explanation
Indices: 42963--43056 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
42953 TTTTTATCCA
42963 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
43011 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TA- TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43057 AATATATTAA
Statistics
Matches: 88, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 2 0.02
3 86 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:43550 original size:23 final size:25
Alignment explanation
Indices: 43520--43570 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
43510 AGAACGAGAC
* *
43520 AGAGAGACA-A-AAAAAAAGAATAG
1 AGAGAGACATAGAAAAAAAAAACAG
43543 AGAGAGACATAGAAAAAAAAAACAG
1 AGAGAGACATAGAAAAAAAAAACAG
43568 AGA
1 AGA
43571 AAATACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 9 0.38
24 1 0.04
25 14 0.58
ACGTcount: A:0.69, C:0.06, G:0.22, T:0.04
Consensus pattern (25 bp):
AGAGAGACATAGAAAAAAAAAACAG
Found at i:44393 original size:18 final size:19
Alignment explanation
Indices: 44353--44393 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
44343 TTAGATTTTT
*
44353 TTTTCGTTTATTTTATATG
1 TTTTCATTTATTTTATATG
44372 TTTTCATTTATTTTAT-TG
1 TTTTCATTTATTTTATATG
44390 TTTT
1 TTTT
44394 TAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.15, C:0.05, G:0.07, T:0.73
Consensus pattern (19 bp):
TTTTCATTTATTTTATATG
Found at i:44448 original size:12 final size:12
Alignment explanation
Indices: 44433--44460 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
44423 TTTTATTATA
44433 TTATTAAATATT
1 TTATTAAATATT
44445 TTATTAAATATT
1 TTATTAAATATT
44457 TTAT
1 TTAT
44461 AATATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATTAAATATT
Found at i:45175 original size:21 final size:23
Alignment explanation
Indices: 45150--45191 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45140 TCAAATTTTT
45150 TATTTAT-T-TATTATTTTATAA
1 TATTTATATGTATTATTTTATAA
*
45171 TATTTATATGTTTTATTTTAT
1 TATTTATATGTATTATTTTAT
45192 TTGCAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATATGTATTATTTTATAA
Found at i:45215 original size:13 final size:15
Alignment explanation
Indices: 45184--45220 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
45174 TTATATGTTT
45184 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
45199 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
45212 TA-TTTATTT
1 TATTTTATTT
45221 TTATGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:55826 original size:18 final size:18
Alignment explanation
Indices: 55805--55840 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55795 GCTTAAAGAG
* *
55805 AATAGAAAAAAAATAGAA
1 AATAAAAAAAAAAGAGAA
55823 AATAAAAAAAAAAGAGAA
1 AATAAAAAAAAAAGAGAA
55841 GAAAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (18 bp):
AATAAAAAAAAAAGAGAA
Found at i:55845 original size:16 final size:16
Alignment explanation
Indices: 55803--55846 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
55793 ATGCTTAAAG
* *
55803 AGAATAGAAAAAAAAT
1 AGAAAAGAAAAAAAAA
*
55819 AGAAAATAAAAAAAAA
1 AGAAAAGAAAAAAAAA
*
55835 AGAGAAGAAAAA
1 AGAAAAGAAAAA
55847 GAAAGGGGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (16 bp):
AGAAAAGAAAAAAAAA
Found at i:57224 original size:84 final size:84
Alignment explanation
Indices: 56970--57648 Score: 1234
Period size: 84 Copynumber: 8.2 Consensus size: 84
56960 ATATCTTAGT
56970 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57034 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
57053 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57117 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
57136 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57201 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
57220 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
57285 CTGATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
57304 -CAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57367 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
57386 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57451 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
57470 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57535 CTGA--TGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
57552 CCAATCA-TGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
57616 CT-ATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
57634 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
57649 AAAAGATGAA
Statistics
Matches: 582, Mismatches: 4, Indels: 19
0.96 0.01 0.03
Matches are distributed among these distances:
80 1 0.00
81 63 0.11
82 80 0.14
83 180 0.31
84 258 0.44
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:57411 original size:250 final size:251
Alignment explanation
Indices: 56970--57648 Score: 1239
Period size: 250 Copynumber: 2.7 Consensus size: 251
56960 ATATCTTAGT
56970 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57034 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
57099 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
131 AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
57164 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
196 GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
57220 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
57285 CTGATCTG-GTTGGACAGAA-CAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTG
66 CTGATCTGATTTGG-CAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTG
57348 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATT
130 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATT
57413 TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
195 TGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
57470 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57535 CTGA--TGATTTGGCAGAACCAATCA-TGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTG
* *
57597 GAAGTGTTCTTTGAGTTATCT-ATCTG-GTTGGACAGAACCAATCGTTGGAATT
130 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGG-CAGAACCAATCATT-GAATT
57649 AAAAGATGAA
Statistics
Matches: 418, Mismatches: 4, Indels: 15
0.96 0.01 0.03
Matches are distributed among these distances:
247 4 0.01
248 47 0.11
249 51 0.12
250 269 0.64
251 47 0.11
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (251 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCCAATAGCATCTTCTGG
AAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTT
GCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
Found at i:57416 original size:166 final size:168
Alignment explanation
Indices: 56970--57648 Score: 1234
Period size: 166 Copynumber: 4.1 Consensus size: 168
56960 ATATCTTAGT
56970 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57034 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
*
57098 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
131 GAAGTGTTCTTTGAGTTATCTGATCTGAGTTGGCAGAA
57136 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57201 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
57266 GAAGTGTTCTTTGAGTTATCTGATCTG-GTTGGACAGAA
131 GAAGTGTTCTTTGAGTTATCTGATCTGAGTTGG-CAGAA
57304 -CAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57367 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
*
57432 GAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAA
131 GAAGTGTTCTTTGAGTTATCTGATCTGAGTTGGCAGAA
57470 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
57535 CTGA--TGATTTGGCAGAACCAATCA-TGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
66 CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
57597 GAAGTGTTCTTTGAGTTATCT-ATCTG-GTTGGACAGAA
131 GAAGTGTTCTTTGAGTTATCTGATCTGAGTTGG-CAGAA
*
57634 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
57649 AAAAGATGAA
Statistics
Matches: 501, Mismatches: 4, Indels: 17
0.96 0.01 0.03
Matches are distributed among these distances:
163 4 0.01
164 18 0.04
165 64 0.13
166 181 0.36
167 149 0.30
168 85 0.17
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (168 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAACCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGAGTTGGCAGAA
Found at i:58666 original size:112 final size:113
Alignment explanation
Indices: 58356--59354 Score: 1755
Period size: 113 Copynumber: 8.9 Consensus size: 113
58346 TCAAATCCAC
* *
58356 TTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
58420 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58469 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58534 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCA-
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58581 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58646 AGTTCATAATGAGAAGAACTTGTTCAA-TTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
58693 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58758 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
*
58806 TTGATGGATCAACATTGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58870 AGTTCATAATGAG-AGAACTTGTTCAAC-TTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
58916 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
58981 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAA-TCATCA-
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *
59027 TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
59092 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
59140 TTGATGGATCAACATTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAG
1 TTGATGGATCAACATTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAG
* * * *
59205 AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCAC
65 AAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
* *** *
59254 TTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
* *
59319 AGTTCATAATGAGAAGAGCTTGTTCAAC-CTTTGTTT
66 AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
59355 GATACTATCA
Statistics
Matches: 853, Mismatches: 24, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
110 74 0.09
111 157 0.18
112 246 0.29
113 273 0.32
114 103 0.12
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (113 bp):
TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCAT
Found at i:58753 original size:224 final size:225
Alignment explanation
Indices: 58353--59354 Score: 1746
Period size: 224 Copynumber: 4.5 Consensus size: 225
58343 ATTTCAAATC
* *
58353 CACTTGATGGATCATTCATTGCCAGA-TAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
1 CACTTGATGGATCA-ACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG
58417 AAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAAC
65 AAGAAGTTCATAATGAGAAGAACTTGTTCAA-TTTTTGTTTAAATTCATCATTTGATGGATCAAC
58482 ATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
129 ATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
58547 AAGAACTTGTTCAACTTTTTGTTTAAATTCAT
194 AAGAACTTGTTCAACTTTTTGTTTAAATTCAT
58579 CA-TTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
58643 AGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTGTTTAAATTCATCATTTGATGGATCAACAT
66 AGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTGTTTAAATTCATCATTTGATGGATCAACAT
* *
58708 TGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAA
131 TGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
58773 GAACTTGTTCAACTTTTTGTTTAAATTCAT
196 GAACTTGTTCAACTTTTTGTTTAAATTCAT
* *
58803 CATTTGATGGATCAACATTGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGA
1 CACTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
*
58867 AGAAGTTCATAATGAG-AGAACTTGTTCAACTTTTGTTTAAATTCATCATTTGATGGATCAACAT
66 AGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTGTTTAAATTCATCATTTGATGGATCAACAT
58931 TGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
131 TGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
58996 GAACTTGTTCAACTTTTTGTTTAAA-TCAT
196 GAACTTGTTCAACTTTTTGTTTAAATTCAT
* *
59025 CA-TTGATGGATCAACATTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGA
1 CACTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
59089 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATTCATCATTTGATGGATCAACA
66 AGAAGTTCATAATGAGAAGAACTTGTTCAA-TTTTTGTTTAAATTCATCATTTGATGGATCAACA
59154 TTGCCAGAGAAAGTTCATGAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
130 TTGCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * *
59219 AAGAATTTGTTCAACCTTTTGTTTGAATTCAT
194 AAGAACTTGTTCAACTTTTTGTTTAAATTCAT
* *** *
59251 CACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
1 CACTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
* **
59316 AGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTGTTT
66 AGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTGTTT
59355 GATACTATCA
Statistics
Matches: 745, Mismatches: 23, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
221 53 0.07
222 27 0.04
223 148 0.20
224 212 0.28
225 204 0.27
226 15 0.02
227 86 0.12
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.29
Consensus pattern (225 bp):
CACTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
AGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTGTTTAAATTCATCATTTGATGGATCAACAT
TGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
GAACTTGTTCAACTTTTTGTTTAAATTCAT
Found at i:59678 original size:3 final size:3
Alignment explanation
Indices: 59670--59735 Score: 104
Period size: 3 Copynumber: 23.3 Consensus size: 3
59660 TTATCCATAT
59670 TTA TTA TTA TTA -TA TTA TTA TTA -TA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59715 TTA TTA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
59736 AATATATATT
Statistics
Matches: 59, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 8 0.14
3 51 0.86
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59687 original size:11 final size:11
Alignment explanation
Indices: 59667--59746 Score: 105
Period size: 11 Copynumber: 7.5 Consensus size: 11
59657 TTTTTATCCA
59667 TATT-TATTAT
1 TATTATATTAT
59677 TATTATATTAT
1 TATTATATTAT
59688 TATTATATTAT
1 TATTATATTAT
59699 TA-T-TATTAT
1 TATTATATTAT
59708 T-TTATTATTAT
1 TATTA-TATTAT
59719 TATTATATTAT
1 TATTATATTAT
*
59730 TATTATAATAT
1 TATTATATTAT
59741 ATATTA
1 -TATTA
59747 AATAAATAAT
Statistics
Matches: 63, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
9 8 0.13
10 5 0.08
11 42 0.67
12 8 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATATTAT
Found at i:59689 original size:14 final size:14
Alignment explanation
Indices: 59670--59746 Score: 111
Period size: 14 Copynumber: 5.4 Consensus size: 14
59660 TTATCCATAT
59670 TTATTATTATTATA
1 TTATTATTATTATA
59684 TTATTATTA-TATTA
1 TTATTATTATTA-TA
*
59698 TTATTATTATTTTA
1 TTATTATTATTATA
59712 TTATTATTATTATA
1 TTATTATTATTATA
*
59726 TTATTATTATAATA
1 TTATTATTATTATA
59740 TATATTA
1 T-TATTA
59747 AATAAATAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
13 2 0.04
14 49 0.86
15 6 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTATTATTATTATA
Found at i:60078 original size:21 final size:21
Alignment explanation
Indices: 60052--60095 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
60042 GCCGTCCACG
*
60052 CCATGGCTACT-CGGTGAGTCA
1 CCATGG-TACTCCGGTGACTCA
*
60073 CCATGGTAGTCCGGTGACTCA
1 CCATGGTACTCCGGTGACTCA
60094 CC
1 CC
60096 GAGAGCCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (21 bp):
CCATGGTACTCCGGTGACTCA
Done.