Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002586.1 Hibiscus syriacus cultivar Beakdansim tig00005233_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: 112978
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:344 original size:18 final size:20
Alignment explanation
Indices: 321--366 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
311 AATGATTTTC
*
321 TTTTGAAA-CAAAAAT-AGA
1 TTTTGAAAGCAAAAATGAAA
*
339 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAGCAAAAATGAAA
359 TTTTGAAA
1 TTTTGAAA
367 AAGGATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 6 0.25
20 10 0.42
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (20 bp):
TTTTGAAAGCAAAAATGAAA
Found at i:1416 original size:21 final size:21
Alignment explanation
Indices: 1390--1466 Score: 95
Period size: 21 Copynumber: 3.6 Consensus size: 21
1380 GGTGTCAAAG
1390 TGCATCCATGCACCCCTGCAA
1 TGCATCCATGCACCCCTGCAA
* *
1411 TGCATCCATGTACCCCTGCAG
1 TGCATCCATGCACCCCTGCAA
1432 TGCATCCATGCA--CCTGCACTA
1 TGCATCCATGCACCCCTGCA--A
1453 GTGCATCCATGCAC
1 -TGCATCCATGCAC
1467 TCCATTTTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.12
21 30 0.62
22 12 0.25
ACGTcount: A:0.22, C:0.39, G:0.17, T:0.22
Consensus pattern (21 bp):
TGCATCCATGCACCCCTGCAA
Found at i:1510 original size:20 final size:20
Alignment explanation
Indices: 1485--1576 Score: 166
Period size: 20 Copynumber: 4.6 Consensus size: 20
1475 GAATGCCTTA
1485 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
1505 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
1525 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
1545 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTGCT
*
1565 GTGCATCCATGC
1 GTGCATCGATGC
1577 CACGAAGGCT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.15, C:0.30, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:1709 original size:21 final size:21
Alignment explanation
Indices: 1680--1719 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1670 TTTTAGTAGA
1680 AAAATCATCCTCAAACGGCTCC
1 AAAATCATCC-CAAACGGCTCC
*
1702 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
1720 ATATACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:1970 original size:34 final size:32
Alignment explanation
Indices: 1931--2000 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1921 TTTTGTAAAG
* * *
1931 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGATTCTAGCTTAGCCCG-G-AAAAACTA
*
1965 GGGAAAGATTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGATTCTAGCTTAGCCCGGAAAAACTA
1997 GGGA
1 GGGA
2001 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGATTCTAGCTTAGCCCGGAAAAACTA
Found at i:9266 original size:8 final size:7
Alignment explanation
Indices: 9252--9324 Score: 60
Period size: 7 Copynumber: 9.9 Consensus size: 7
9242 AATGAAATTA
9252 AATAAAT
1 AATAAAT
9259 ACATAAAT
1 A-ATAAAT
9267 AATAATAT
1 AATAA-AT
9275 AATCAAATAT
1 AAT--AA-AT
9285 AATAAAT
1 AATAAAT
*
9292 -GTAAAAT
1 AAT-AAAT
9299 AATAAAT
1 AATAAAT
9306 -ATAAAT
1 AATAAAT
*
9312 AATATAT
1 AATAAAT
9319 AATAAA
1 AATAAA
9325 AACTATATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
6 7 0.13
7 25 0.45
8 15 0.27
10 8 0.15
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (7 bp):
AATAAAT
Found at i:9282 original size:24 final size:22
Alignment explanation
Indices: 9252--9324 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 22
9242 AATGAAATTA
9252 AATAAATACATAAATAATAATAT
1 AATAAATA-ATAAATAATAATAT
* *
9275 AATCAAATATAATAAAT-GTAAAAT
1 AAT--AA-ATAATAAATAATAATAT
9299 AATAAAT-ATAAATAAT-ATAT
1 AATAAATAATAAATAATAATAT
9319 AATAAA
1 AATAAA
9325 AACTATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
20 15 0.36
21 3 0.07
22 2 0.05
23 3 0.07
24 8 0.19
25 8 0.19
26 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (22 bp):
AATAAATAATAAATAATAATAT
Found at i:9302 original size:14 final size:13
Alignment explanation
Indices: 9253--9315 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
9243 ATGAAATTAA
9253 ATAAATACATAAAT
1 ATAAATA-ATAAAT
*
9267 AATAATATAATCAA-
1 -ATAA-ATAATAAAT
9281 AT--ATAATAAAT
1 ATAAATAATAAAT
*
9292 GTAAAATAATAAAT
1 AT-AAATAATAAAT
9306 ATAAATAATA
1 ATAAATAATA
9316 TATAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
10 7 0.18
11 1 0.03
13 10 0.26
14 10 0.26
15 8 0.21
16 3 0.08
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAAATAATAAAT
Found at i:10485 original size:35 final size:36
Alignment explanation
Indices: 10439--10512 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
10429 AATTCCCCTG
*
10439 AAACCATACCC-AAACCATGTATCAGCAGCGTTACC
1 AAACCATACCCAAAACCATGAATCAGCAGCGTTACC
* * *
10474 AAACCATACCCAAAACCATGAATTAGCAGTGTTGCC
1 AAACCATACCCAAAACCATGAATCAGCAGCGTTACC
10510 AAA
1 AAA
10513 AATTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
35 11 0.32
36 23 0.68
ACGTcount: A:0.41, C:0.30, G:0.12, T:0.18
Consensus pattern (36 bp):
AAACCATACCCAAAACCATGAATCAGCAGCGTTACC
Found at i:18514 original size:17 final size:16
Alignment explanation
Indices: 18489--18522 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
18479 AGTAATTTAG
18489 TAATATTTTTCAATGAT
1 TAATATTTTT-AATGAT
*
18506 TAATTTTTTTAATGAT
1 TAATATTTTTAATGAT
18522 T
1 T
18523 TATTCCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (16 bp):
TAATATTTTTAATGAT
Found at i:18519 original size:16 final size:17
Alignment explanation
Indices: 18489--18522 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
18479 AGTAATTTAG
18489 TAATATTTTTCAATGAT
1 TAATATTTTTCAATGAT
*
18506 TAAT-TTTTTTAATGAT
1 TAATATTTTTCAATGAT
18522 T
1 T
18523 TATTCCATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (17 bp):
TAATATTTTTCAATGAT
Found at i:21262 original size:33 final size:33
Alignment explanation
Indices: 21217--21280 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
21207 TCGCCAGACG
*
21217 CTTGAGCAACTGAAGCAGATTCAGGAACAGGAT
1 CTTGAGCAACTGAAGCAGACTCAGGAACAGGAT
*
21250 CTTGAGCTACTGAAGCAGACTCAGGAACAGG
1 CTTGAGCAACTGAAGCAGACTCAGGAACAGG
21281 GTCAGGCGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.17
Consensus pattern (33 bp):
CTTGAGCAACTGAAGCAGACTCAGGAACAGGAT
Found at i:21988 original size:53 final size:54
Alignment explanation
Indices: 21926--22091 Score: 163
Period size: 53 Copynumber: 2.9 Consensus size: 54
21916 TGTCTTTGGT
21926 ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATCATTTT-AAAA
1 ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATCATTTTAAAAA
* * * * *
21979 ATTTAAAGATTTATATAGTATTTCATTTACAATGTATTAAATTATTCTTCATTTTAAAAA
1 ATTTAAAGATTTATATAGTATTTTA-GT-C--T-TATAAAATT-TACATCATTTTAAAAA
*
22039 ATGAAAATTAAAATATTTATATAGTATTTTAGTCTTATAAAATTTACATCATT
1 AT-----TT-AAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATCATT
22092 ATCACTTTGG
Statistics
Matches: 89, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
53 24 0.27
54 1 0.01
55 1 0.01
57 1 0.01
58 8 0.09
59 9 0.10
60 13 0.15
61 8 0.09
62 1 0.01
64 1 0.01
65 3 0.03
66 19 0.21
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (54 bp):
ATTTAAAGATTTATATAGTATTTTAGTCTTATAAAATTTACATCATTTTAAAAA
Found at i:23364 original size:14 final size:15
Alignment explanation
Indices: 23345--23373 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23335 TACATGATCT
23345 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
23359 GCATAAAACATAAGA
1 GCATAAAACATAAGA
23374 TATAGGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:25753 original size:14 final size:14
Alignment explanation
Indices: 25717--25751 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
25707 AAGACTTTTC
*
25717 CCGCTCCGCATCCA
1 CCGCCCCGCATCCA
25731 CCGCCCCGCATCCA
1 CCGCCCCGCATCCA
25745 CCTGCCC
1 CC-GCCC
25752 GCTAATTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.11, C:0.63, G:0.14, T:0.11
Consensus pattern (14 bp):
CCGCCCCGCATCCA
Found at i:26183 original size:28 final size:28
Alignment explanation
Indices: 26126--26227 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
26116 AAAAGGTTTG
*
26126 AATAGTTTAAGTACCTATTTTGACATAA
1 AATACTTTAAGTACCTATTTTGACATAA
* *
26154 AATACTTTAGGTACCTATTTTGACTAAAA
1 AATACTTTAAGTACCTATTTTGAC-ATAA
* * **
26183 AGATAATTTTAGATATTTATTTTGATCA-AA
1 A-ATACTTTAAG-TACCTATTTTGA-CATAA
26213 TAATACTTTAAGTAC
1 -AATACTTTAAGTAC
26228 TTAAACGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
28 22 0.38
29 6 0.10
30 17 0.29
31 12 0.21
32 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (28 bp):
AATACTTTAAGTACCTATTTTGACATAA
Found at i:39457 original size:13 final size:13
Alignment explanation
Indices: 39439--39464 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39429 CGTACTCCGC
39439 CGCCGGCCACCGT
1 CGCCGGCCACCGT
39452 CGCCGGCCACCGT
1 CGCCGGCCACCGT
39465 AAACGGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:40180 original size:11 final size:11
Alignment explanation
Indices: 40177--40221 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
40167 TAATTATTTA
40177 ATAATAAT-AT
1 ATAATAATAAT
40187 AATAATAATAAT
1 -ATAATAATAAT
40199 ATAATAATAAT
1 ATAATAATAAT
*
40210 ATTTATAATAAT
1 A-TAATAATAAT
40222 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:40181 original size:3 final size:3
Alignment explanation
Indices: 40175--40221 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
40165 AATAATTATT
* *
40175 TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40221 T
1 T
40222 TTTAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:40248 original size:21 final size:22
Alignment explanation
Indices: 40194--40250 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
40184 TATAATAATA
**
40194 ATAAT-ATAATAATAAT-ATTT
1 ATAATAATAATAATTTTAATTT
**
40214 ATAATAATTTTAATTTTAATTT
1 ATAATAATAATAATTTTAATTT
40236 -TAATAATAATAATTT
1 ATAATAATAATAATTT
40251 AAGTAAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAATAATAATTTTAATTT
Found at i:40528 original size:76 final size:76
Alignment explanation
Indices: 40402--40813 Score: 725
Period size: 76 Copynumber: 5.4 Consensus size: 76
40392 GAGGTCTTAA
* * *
40402 AAACATCATGCACTGCAGGATTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40467 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
40478 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40543 AGGCTTTTTGG
66 AGGCTTTTTGG
*
40554 AAACATCATGCACTGAAGGACTTACGGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40619 AGGCTTTTTGG
66 AGGCTTTTTGG
*
40630 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
40695 AGGCTTTTTGG
66 AGGCTTTTTGG
*
40706 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCC
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC--TTTGAAAACATCAAAAAGCTCCC
40771 GAAGGCTTTTTGG
64 GAAGGCTTTTTGG
*
40784 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
40814 TGAGAAATAG
Statistics
Matches: 321, Mismatches: 13, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
76 258 0.80
78 63 0.20
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:41499 original size:22 final size:22
Alignment explanation
Indices: 41474--41528 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
41464 CATAAAGCTT
*
41474 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
41496 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
41518 TCATCTTTGAA
1 TCATCTTTGAA
41529 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:43072 original size:75 final size:75
Alignment explanation
Indices: 42969--43133 Score: 303
Period size: 75 Copynumber: 2.2 Consensus size: 75
42959 GGTTTTCAGC
*
42969 ATGCCCTAATATTTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATCTGTCTGAAG
1 ATGCCCCAATA-TTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATCTGTCTGAAG
*
43034 TGAGCTCTAAA
65 TGAGCTATAAA
43045 ATGCCCCAATATTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATCTGTCTGAAGT
1 ATGCCCCAATATTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATCTGTCTGAAGT
43110 GAGCTATAAA
66 GAGCTATAAA
43120 ATGCCCCAATATTG
1 ATGCCCCAATATTG
43134 GCTGATACAG
Statistics
Matches: 87, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
75 77 0.89
76 10 0.11
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (75 bp):
ATGCCCCAATATTGCTTCTTGTTAATATGAGTCTTCAAAATACACCACATGGATCTGTCTGAAGT
GAGCTATAAA
Found at i:43121 original size:36 final size:35
Alignment explanation
Indices: 42997--43121 Score: 92
Period size: 36 Copynumber: 3.3 Consensus size: 35
42987 CTTGTTAATA
42997 TGAGTCTTCAAAATACACCACATGGATCTGTCTGAAG
1 TGAG-CTT-AAAATACACCACATGGATCTGTCTGAAG
* * * ** *
43034 TGAGCTCTAAAATGCCCCAATATTGCTTCTTGT-T-AATA
1 TGAGCT-TAAAATACACC-ACA-TGGATC-TGTCTGAA-G
43072 TGAGTCTTCAAAATACACCACATGGATCTGTCTGAAG
1 TGAG-CTT-AAAATACACCACATGGATCTGTCTGAAG
43109 TGAGCTATAAAAT
1 TGAGCT-TAAAAT
43122 GCCCCAATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
36 20 0.30
37 19 0.29
38 14 0.21
39 13 0.20
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (35 bp):
TGAGCTTAAAATACACCACATGGATCTGTCTGAAG
Found at i:44347 original size:83 final size:83
Alignment explanation
Indices: 44208--44553 Score: 638
Period size: 83 Copynumber: 4.2 Consensus size: 83
44198 TTTATTTCTC
*
44208 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
44273 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
44291 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
44356 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
44374 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATGACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
44439 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
44457 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCATATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
44522 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
44540 CTATTGAGCACATT
1 CTA-TGAGCACATT
44554 ACATTTGTTC
Statistics
Matches: 257, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 247 0.96
84 10 0.04
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:47176 original size:2 final size:2
Alignment explanation
Indices: 47169--47237 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
47159 ACAACAAAGG
47169 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
47211 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
47238 GGATAATGAA
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:53020 original size:13 final size:13
Alignment explanation
Indices: 53002--53027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52992 CGTACTCCGC
53002 CGCCGGCCACCGT
1 CGCCGGCCACCGT
53015 CGCCGGCCACCGT
1 CGCCGGCCACCGT
53028 AAACGGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:53291 original size:12 final size:12
Alignment explanation
Indices: 53274--53298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53264 GCTCTTGCTT
53274 TGTTTTTTTTTC
1 TGTTTTTTTTTC
53286 TGTTTTTTTTTC
1 TGTTTTTTTTTC
53298 T
1 T
53299 TGTCGTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (12 bp):
TGTTTTTTTTTC
Found at i:53737 original size:11 final size:11
Alignment explanation
Indices: 53734--53778 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
53724 TAATTATTTA
53734 ATAATAAT-AT
1 ATAATAATAAT
53744 AATAATAATAAT
1 -ATAATAATAAT
53756 ATAATAATAAT
1 ATAATAATAAT
*
53767 ATTTATAATAAT
1 A-TAATAATAAT
53779 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:53738 original size:3 final size:3
Alignment explanation
Indices: 53732--53778 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
53722 AATAATTATT
* *
53732 TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
53778 T
1 T
53779 TTTAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:53805 original size:21 final size:22
Alignment explanation
Indices: 53751--53807 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
53741 TATAATAATA
**
53751 ATAAT-ATAATAATAAT-ATTT
1 ATAATAATAATAATTTTAATTT
**
53771 ATAATAATTTTAATTTTAATTT
1 ATAATAATAATAATTTTAATTT
53793 -TAATAATAATAATTT
1 ATAATAATAATAATTT
53808 AAGTAAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAATAATAATTTTAATTT
Found at i:54001 original size:107 final size:107
Alignment explanation
Indices: 53863--54074 Score: 406
Period size: 107 Copynumber: 2.0 Consensus size: 107
53853 CTGAAAAATG
*
53863 ACTCTGTATCCCCTTTTCATGCTTGCAGAAACAAAAGAGAGACACGAAGTTATGTCAAAATCACC
1 ACTCTGTATCCCCTTTTCATGCTTGCAGAAACAAAAGAGAAACACGAAGTTATGTCAAAATCACC
53928 GAGTCATTGGGAGTTGATAAACCATCTGATATACTATTTCCA
66 GAGTCATTGGGAGTTGATAAACCATCTGATATACTATTTCCA
*
53970 ACTCTGTATCCCCTTTTCATGCTTGCAGAAACAAAAGAGAAACACGAAGTTATGTCGAAATCACC
1 ACTCTGTATCCCCTTTTCATGCTTGCAGAAACAAAAGAGAAACACGAAGTTATGTCAAAATCACC
54035 GAGTCATTGGGAGTTGATAAACCATCTGATATACTATTTC
66 GAGTCATTGGGAGTTGATAAACCATCTGATATACTATTTC
54075 TGACCGATGT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 103 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (107 bp):
ACTCTGTATCCCCTTTTCATGCTTGCAGAAACAAAAGAGAAACACGAAGTTATGTCAAAATCACC
GAGTCATTGGGAGTTGATAAACCATCTGATATACTATTTCCA
Found at i:77997 original size:64 final size:64
Alignment explanation
Indices: 77790--77997 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
77780 TTTCAAAGTG
* **
77790 ATGCACCGATGCACCGAT-CCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCAT
1 ATGCATCGATGCA-C-ATACCATGCATCGATGCACTC-TGG-ATATTTTGAAACATCGAATGCAT
*
77852 TTT
62 TTC
* * *
77855 ATGCATCGATGCATATACCATGCATTGATGCACTCAGGAT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACATACCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCATTT
*
77919 G
64 C
* *
77920 ATGCATCGATGCACA-AGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGGATGCATTTC
1 ATGCATCGATGCACATA-CCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATTTC
*
77984 ATGCATCGTTGCAC
1 ATGCATCGATGCAC
77998 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 47 0.39
65 65 0.53
66 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
ATGCATCGATGCACATACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATTTC
Found at i:78879 original size:31 final size:31
Alignment explanation
Indices: 78838--78957 Score: 152
Period size: 31 Copynumber: 3.9 Consensus size: 31
78828 AGTAGAGGGT
*
78838 TTACCAATGTTCTTCGAAACATATGGACTGA
1 TTACCTATGTTCTTCGAAACATATGGACTGA
** * *
78869 TTACCTATGTTCTTCGGGACATATGGATTGT
1 TTACCTATGTTCTTCGAAACATATGGACTGA
*
78900 TTACCTATGTTCTTCGAAACATATGAACTGA
1 TTACCTATGTTCTTCGAAACATATGGACTGA
* *
78931 TTA-CTAATGTTCTTCGGAATATATGGA
1 TTACCT-ATGTTCTTCGAAACATATGGA
78958 TTGGTCCTTC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
30 2 0.03
31 73 0.97
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGAAACATATGGACTGA
Found at i:78910 original size:62 final size:62
Alignment explanation
Indices: 78836--78960 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
78826 AGAGTAGAGG
* *
78836 GTTTACCAATGTTCTTCGAAACATATGGACTGATTACCT-ATGTTCTTCGGGACATATGGATT
1 GTTTACCAATGTTCTTCGAAACATATGAACTGATTA-CTAATGTTCTTCGGAACATATGGATT
* *
78898 GTTTACCTATGTTCTTCGAAACATATGAACTGATTACTAATGTTCTTCGGAATATATGGATT
1 GTTTACCAATGTTCTTCGAAACATATGAACTGATTACTAATGTTCTTCGGAACATATGGATT
78960 G
1 G
78961 GTCCTTCAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 2 0.03
62 56 0.97
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.38
Consensus pattern (62 bp):
GTTTACCAATGTTCTTCGAAACATATGAACTGATTACTAATGTTCTTCGGAACATATGGATT
Found at i:79600 original size:20 final size:19
Alignment explanation
Indices: 79575--79621 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
79565 ACTGTTCACG
* *
79575 GTACTATTTGCACAGTATTA
1 GTACTATTTACACAATA-TA
*
79595 GTACTATTTATACAATATA
1 GTACTATTTACACAATATA
79614 GTACTATT
1 GTACTATT
79622 CATAAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.43
Consensus pattern (19 bp):
GTACTATTTACACAATATA
Found at i:97887 original size:44 final size:45
Alignment explanation
Indices: 97778--97899 Score: 183
Period size: 44 Copynumber: 2.7 Consensus size: 45
97768 GGTAAGCATA
97778 TAAAATAAGCTTACGAGCTTATGGGAATAAATGATAAGTATATTGG
1 TAAAATAAGCTTACGAGCTTAT-GGAATAAATGATAAGTATATTGG
* * *
97824 TAAAATAAGCTTGCGAGCTTATAGAATAAATGATAAGTAT-TTGT
1 TAAAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGG
* *
97868 TAAAATAAGCTTACAAGCTTATGGGATAAATG
1 TAAAATAAGCTTACGAGCTTATGGAATAAATG
97900 GTGAGAAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 31 0.45
45 17 0.25
46 21 0.30
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (45 bp):
TAAAATAAGCTTACGAGCTTATGGAATAAATGATAAGTATATTGG
Found at i:99045 original size:23 final size:23
Alignment explanation
Indices: 99011--99054 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
99001 GAATAATTTG
**
99011 ATTTATGCTATATTTATATATAT
1 ATTTATGCTATACATATATATAT
99034 ATTTATAG-TATACATATATAT
1 ATTTAT-GCTATACATATATAT
99055 TTAATCTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.94
24 1 0.06
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.52
Consensus pattern (23 bp):
ATTTATGCTATACATATATATAT
Found at i:104017 original size:21 final size:21
Alignment explanation
Indices: 103993--104043 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
103983 GACGAGTTTG
* *
103993 TTGATGATGAAGATGTCGAGT
1 TTGATGATGAAGATGACGACT
* *
104014 TTGATGCTAAAGATGACGACT
1 TTGATGATGAAGATGACGACT
*
104035 GTGATGATG
1 TTGATGATG
104044 GTGGTGATGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGATGATGAAGATGACGACT
Found at i:104193 original size:4 final size:4
Alignment explanation
Indices: 104184--104209 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
104174 GAAATTTCAT
104184 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
104210 CTAACTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:107125 original size:19 final size:19
Alignment explanation
Indices: 107101--107143 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
107091 GTCCCACTCA
107101 ACCCGAACTGTTTGACCCG
1 ACCCGAACTGTTTGACCCG
*
107120 ACCCGAACTGTTTGACTCG
1 ACCCGAACTGTTTGACCCG
107139 ACCCG
1 ACCCG
107144 TTGACTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.37, G:0.21, T:0.21
Consensus pattern (19 bp):
ACCCGAACTGTTTGACCCG
Found at i:108386 original size:20 final size:20
Alignment explanation
Indices: 108356--108393 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
108346 TAATATATAA
108356 AATATTTTCGGGTTCGGGTAT
1 AATATTTTCGGG-TCGGGTAT
108377 AATA-TTTCGGGTCGGGT
1 AATATTTTCGGGTCGGGT
108394 TCGGGGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.39
Consensus pattern (20 bp):
AATATTTTCGGGTCGGGTAT
Found at i:111497 original size:21 final size:21
Alignment explanation
Indices: 111471--111524 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
111461 AAAAGAAATC
111471 CGATAACAAGTTAGTGCCGGT
1 CGATAACAAGTTAGTGCCGGT
111492 CGATAACAAGTTAGTGCCGGT
1 CGATAACAAGTTAGTGCCGGT
111513 CGATAACAAGTT
1 CGATAACAAGTT
111525 TAATTTTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (21 bp):
CGATAACAAGTTAGTGCCGGT
Done.