Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002635.1 Hibiscus syriacus cultivar Beakdansim tig00005369_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: 56682
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1168 original size:12 final size:11
Alignment explanation
Indices: 1148--1183 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
1138 GCTTAATCGG
1148 AAAAAAAAAAT
1 AAAAAAAAAAT
*
1159 AAAGAAAAAAT
1 AAAAAAAAAAT
1170 AAAAATAAAAAT
1 AAAAA-AAAAAT
1182 AA
1 AA
1184 CGGAATTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:12478 original size:15 final size:15
Alignment explanation
Indices: 12458--12489 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12448 TCAAATATTT
*
12458 AAAAAAATAAATATA
1 AAAAAAATAAACATA
12473 AAAAAAATAAACATA
1 AAAAAAATAAACATA
12488 AA
1 AA
12490 CATTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAAAATAAACATA
Found at i:12672 original size:25 final size:25
Alignment explanation
Indices: 12639--12704 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
12629 ATTTTACTAG
*
12639 ATTAATTGAGATTTACAAAATTTAA
1 ATTAGTTGAGATTTACAAAATTTAA
* * * *
12664 ATTAGTTGAGACTTATAAATTTTAG
1 ATTAGTTGAGATTTACAAAATTTAA
* *
12689 ATTAGTCGAAATTTAC
1 ATTAGTTGAGATTTAC
12705 TATGTATTCT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (25 bp):
ATTAGTTGAGATTTACAAAATTTAA
Found at i:12959 original size:2 final size:2
Alignment explanation
Indices: 12888--12943 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
12878 AGTGTTGATA
12888 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
12930 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
12944 GTTACATGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13111 original size:14 final size:15
Alignment explanation
Indices: 13094--13126 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
13084 TTAATAATTC
13094 ATTTTTAT-TTTATT
1 ATTTTTATATTTATT
13108 ATTTTTATATTTATT
1 ATTTTTATATTTATT
13123 -TTTT
1 ATTTT
13127 AACTATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTATATTTATT
Found at i:15712 original size:41 final size:42
Alignment explanation
Indices: 15665--15750 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 42
15655 AACATTTTGT
* * * *
15665 CTAGTCTAAGTTGGTTATTTGAGACGATAAT-TTTTTTGTCA
1 CTAGTCTAAGTTGGTGATTTGAGACGACAATAGTTTTTATCA
* *
15706 CTAGTCTTAGTTGGTGATTTGTGACGACAATAGTTTTTATCA
1 CTAGTCTAAGTTGGTGATTTGAGACGACAATAGTTTTTATCA
15748 CTA
1 CTA
15751 TTGAAGTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
41 27 0.71
42 11 0.29
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (42 bp):
CTAGTCTAAGTTGGTGATTTGAGACGACAATAGTTTTTATCA
Found at i:16619 original size:12 final size:12
Alignment explanation
Indices: 16590--16633 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
16580 TAAGAAAGAA
*
16590 AAAAAAAAGATT
1 AAAAAGAAGATT
**
16602 TCAAAGAAGATT
1 AAAAAGAAGATT
*
16614 AAAAAGAAGTTT
1 AAAAAGAAGATT
16626 AAAAAGAA
1 AAAAAGAA
16634 AGTTCAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.66, C:0.02, G:0.14, T:0.18
Consensus pattern (12 bp):
AAAAAGAAGATT
Found at i:18225 original size:10 final size:10
Alignment explanation
Indices: 18210--18243 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
18200 AACAGTGGAC
18210 TTTTTCTTTT
1 TTTTTCTTTT
18220 TTTTTCTTTTT
1 TTTTTC-TTTT
18231 TTTTTCTTTT
1 TTTTTCTTTT
18241 TTT
1 TTT
18244 CTCCAACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:18230 original size:11 final size:11
Alignment explanation
Indices: 18210--18243 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
18200 AACAGTGGAC
18210 TTTTTC-TTTT
1 TTTTTCTTTTT
18220 TTTTTCTTTTT
1 TTTTTCTTTTT
18231 TTTTTCTTTTT
1 TTTTTCTTTTT
18242 TT
1 TT
18244 CTCCAACAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:19639 original size:10 final size:10
Alignment explanation
Indices: 19620--19649 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
19610 AAATTCAAAG
19620 AAAAAT-AAA
1 AAAAATAAAA
19629 AAAAATAAAA
1 AAAAATAAAA
19639 AAAAATAAAA
1 AAAAATAAAA
19649 A
1 A
19650 TTGACAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.30
10 14 0.70
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:19642 original size:19 final size:19
Alignment explanation
Indices: 19620--19684 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
19610 AAATTCAAAG
19620 AAAAATAAAAAAAATAAAA
1 AAAAATAAAAAAAATAAAA
19639 AAAAATAAAAATTGACAATAAAA
1 AAAAATAAAAA---A-AATAAAA
* * *
19662 AAAATTGAACAAAATAAAA
1 AAAAATAAAAAAAATAAAA
19681 AAAA
1 AAAA
19685 GGGTTGCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 22 0.56
20 1 0.03
22 1 0.03
23 15 0.38
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (19 bp):
AAAAATAAAAAAAATAAAA
Found at i:20132 original size:13 final size:12
Alignment explanation
Indices: 20096--20130 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
20086 TCAAAGAAGA
20096 TTAAAAGGAAATT
1 TTAAAA-GAAATT
*
20109 TAAAAAGAAATT
1 TTAAAAGAAATT
20121 TTAAAAGAAA
1 TTAAAAGAAA
20131 ATGCAATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (12 bp):
TTAAAAGAAATT
Found at i:20887 original size:14 final size:14
Alignment explanation
Indices: 20868--20900 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
20858 CATTCATTTT
*
20868 CTGGACGCTGCTGA
1 CTGGACGCTGCTAA
20882 CTGGACGCTGCTAA
1 CTGGACGCTGCTAA
20896 CTGGA
1 CTGGA
20901 TCTTCTAGAA
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:0.18, C:0.27, G:0.33, T:0.21
Consensus pattern (14 bp):
CTGGACGCTGCTAA
Found at i:21428 original size:104 final size:102
Alignment explanation
Indices: 21306--21524 Score: 276
Period size: 104 Copynumber: 2.1 Consensus size: 102
21296 GAGTTATTCC
* *
21306 TAATAGTGTCGAACATTTGGTCACTAAAAACACTTAGTGTGACAAGATTGGTCGCCACAAAATAT
1 TAATAGTGTCGAACATTTGGTCACTAAAAACACTTAATGTGACAAGATTGATCGCCACAAAATAT
* *
21371 ATGTTCACTGTCAAATAAATTTATCACAATTTCTATTGA
66 ATGTTCACTG-CAAA-AAATTCATCACAATTTATATTGA
* * * * * * *
21410 TAATAGTATCGAACATTTGGTCACTAAAAATACTTAATGTGATAATATTGATGGTCACAAAGTAT
1 TAATAGTGTCGAACATTTGGTCACTAAAAACACTTAATGTGACAAGATTGATCGCCACAAAATAT
* * * *
21475 ATTTTTAGTGCCAAAAATTCATCACAATTTATATTGA
66 ATGTTCACTGCAAAAAATTCATCACAATTTATATTGA
*
21512 TAATTGTGTCGAA
1 TAATAGTGTCGAA
21525 TAGAATGTCA
Statistics
Matches: 98, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
102 32 0.33
103 3 0.03
104 63 0.64
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (102 bp):
TAATAGTGTCGAACATTTGGTCACTAAAAACACTTAATGTGACAAGATTGATCGCCACAAAATAT
ATGTTCACTGCAAAAAATTCATCACAATTTATATTGA
Found at i:27368 original size:30 final size:30
Alignment explanation
Indices: 27332--27405 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
27322 AATGTTGTTT
*
27332 GGACCAATTTGAAAGCATGGAAAGGTTAAG
1 GGACCAATTTGAAAGCATAGAAAGGTTAAG
27362 GGACCAATTTGAAAGCATAGAAAGGTTAAG
1 GGACCAATTTGAAAGCATAGAAAGGTTAAG
27392 GGACCAATTTGAAA
1 GGACCAATTTGAAA
27406 TATGTAGGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.42, C:0.11, G:0.27, T:0.20
Consensus pattern (30 bp):
GGACCAATTTGAAAGCATAGAAAGGTTAAG
Found at i:29365 original size:22 final size:22
Alignment explanation
Indices: 29340--29393 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
29330 TAGATATAAT
* * *
29340 GCACTTTCGTATCAGTGCTGAG
1 GCACTTTAGTACCAGTGATGAG
*
29362 GCACTTTAGTACCAGTGATGTG
1 GCACTTTAGTACCAGTGATGAG
29384 GCACTTTAGT
1 GCACTTTAGT
29394 TATTTGATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.33
Consensus pattern (22 bp):
GCACTTTAGTACCAGTGATGAG
Found at i:29751 original size:21 final size:22
Alignment explanation
Indices: 29727--29767 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
29717 AACTCTTTTG
29727 TTAAACT-T-AAATGTTTATGTT
1 TTAAACTATGAAAT-TTTATGTT
29748 TTAAACTATGAAATTTTATG
1 TTAAACTATGAAATTTTATG
29768 GATGATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (22 bp):
TTAAACTATGAAATTTTATGTT
Found at i:37019 original size:37 final size:37
Alignment explanation
Indices: 36969--37043 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
36959 GGAGCAAGTA
36969 GCAGCAATATAGTCATCCCGAAGAAAGAATTATCGTG
1 GCAGCAATATAGTCATCCCGAAGAAAGAATTATCGTG
*
37006 GCAGCAATATAGTCATCCTGAAGAAAGAATTATCGTG
1 GCAGCAATATAGTCATCCCGAAGAAAGAATTATCGTG
37043 G
1 G
37044 AGAGAAAGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (37 bp):
GCAGCAATATAGTCATCCCGAAGAAAGAATTATCGTG
Found at i:39922 original size:64 final size:63
Alignment explanation
Indices: 39852--40007 Score: 219
Period size: 64 Copynumber: 2.5 Consensus size: 63
39842 GTACACTAAG
39852 AGTGCATTGATGCATAAAATGCTTTCGATGTTTT-A-AACAAGCCTGAGTGCATCGATGCATGGT
1 AGTGCATTGATGCATAAAATGCTTTCGATGTTTTCATAA-AA-CCTGAGTGCATCGATGCATGG-
39915 T
63 T
* * *
39916 TGTGCATCGATTCATAAAATGCATTT-GATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
1 AGTGCATTGATGCATAAAATGC-TTTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
*
39979 AGTGCATTGATGCATAAAATGCATTCGAT
1 AGTGCATTGATGCATAAAATGCTTTCGAT
40008 ATGGTGAGTG
Statistics
Matches: 81, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
62 2 0.02
63 23 0.28
64 48 0.59
65 6 0.07
66 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (63 bp):
AGTGCATTGATGCATAAAATGCTTTCGATGTTTTCATAAAACCTGAGTGCATCGATGCATGGT
Found at i:40402 original size:21 final size:23
Alignment explanation
Indices: 40364--40407 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
40354 TTTGAAATCA
40364 ACTTTGAAAAATTACTCCCCCTT
1 ACTTTGAAAAATTACTCCCCCTT
*
40387 ACTTT-AAAACTT-CTCCCCCTT
1 ACTTTGAAAAATTACTCCCCCTT
40408 TTTGTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.36
Consensus pattern (23 bp):
ACTTTGAAAAATTACTCCCCCTT
Found at i:40700 original size:16 final size:18
Alignment explanation
Indices: 40664--40702 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
40654 CCAAAACATA
40664 AATCC-AAATAAATAATC
1 AATCCAAAATAAATAATC
40681 -ATCCAAAATAAA-AA-C
1 AATCCAAAATAAATAATC
40696 AATCCAA
1 AATCCAA
40703 GAACAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.05
16 12 0.60
17 7 0.35
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (18 bp):
AATCCAAAATAAATAATC
Found at i:42680 original size:21 final size:21
Alignment explanation
Indices: 42662--42725 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 21
42652 TCGGTGCATC
42662 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* *
42683 TTCAAATGGATATATCGATGCACT
1 TTC--AT-GATGTATCGATGCACA
42707 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
42726 TTATGCATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 2 0.06
23 2 0.06
24 17 0.47
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:48558 original size:10 final size:10
Alignment explanation
Indices: 48545--48569 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48535 TTTATAAAGG
48545 TTGATTGAAT
1 TTGATTGAAT
48555 TTGATTGAAT
1 TTGATTGAAT
48565 TTGAT
1 TTGAT
48570 GTTGTGATTA
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:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (10 bp):
TTGATTGAAT
Found at i:50229 original size:6 final size:6
Alignment explanation
Indices: 50220--50288 Score: 66
Period size: 6 Copynumber: 11.0 Consensus size: 6
50210 ACATTGGGCT
* * * * *
50220 ATGAAA ATGAAA TGTGAAA ATGAAT ATGAAT ATGAAA GTAAAAA ATGAAA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA AT-GAAA ATGAAA
50270 ATGAAA ATGAAA TATGAAA
1 ATGAAA ATGAAA -ATGAAA
50289 GTTTTTGAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
6 37 0.71
7 15 0.29
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (6 bp):
ATGAAA
Found at i:50248 original size:19 final size:19
Alignment explanation
Indices: 50220--50288 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
50210 ACATTGGGCT
*
50220 ATGAAAATGAAATGTGAAA
1 ATGAAAATGAAATATGAAA
*
50239 ATGAATATG-AATATGAAA
1 ATGAAAATGAAATATGAAA
* *
50257 GTAAAAAATGAAA-ATGAAA
1 AT-GAAAATGAAATATGAAA
50276 ATGAAATATGAAA
1 ATGAAA-ATGAAA
50289 GTTTTTGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
18 12 0.30
19 26 0.65
20 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (19 bp):
ATGAAAATGAAATATGAAA
Found at i:50254 original size:12 final size:12
Alignment explanation
Indices: 50219--50288 Score: 61
Period size: 13 Copynumber: 5.6 Consensus size: 12
50209 TACATTGGGC
50219 TATGAAAATGAAA
1 TATGAAAATG-AA
*
50232 TGTGAAAATGAA
1 TATGAAAATGAA
*
50244 TATGAATATGAA
1 TATGAAAATGAA
*
50256 -AGTAAAAAATGAA
1 TA-T-GAAAATGAA
*
50269 AATGAAAATGAAA
1 TATGAAAATG-AA
50282 TATGAAA
1 TATGAAA
50289 GTTTTTGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
11 1 0.02
12 19 0.41
13 25 0.54
14 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (12 bp):
TATGAAAATGAA
Found at i:50254 original size:25 final size:25
Alignment explanation
Indices: 50219--50288 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
50209 TACATTGGGC
50219 TATGAAAATGAAATGTGAAAATGAA
1 TATGAAAATGAAATGTGAAAATGAA
* *
50244 TATGAATATGAAA-GTAAAAAATGAA
1 TATGAAAATGAAATGT-GAAAATGAA
* *
50269 AATGAAAATGAAATATGAAA
1 TATGAAAATGAAATGTGAAA
50289 GTTTTTGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 2 0.05
25 34 0.92
26 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (25 bp):
TATGAAAATGAAATGTGAAAATGAA
Found at i:51355 original size:2 final size:2
Alignment explanation
Indices: 51348--51402 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
51338 TAAAGCATAG
51348 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
51390 TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA
51403 AATAGAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:51649 original size:14 final size:14
Alignment explanation
Indices: 51625--51651 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
51615 AATATAATGT
51625 ATATAATATATTTC
1 ATATAATATATTTC
51639 ATATAATATATTT
1 ATATAATATATTT
51652 TTATACGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATAATATATTTC
Found at i:51670 original size:26 final size:28
Alignment explanation
Indices: 51633--51684 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
51623 GTATATAATA
51633 TATTTCATAT-AATAT-ATTTTTATACG
1 TATTTCATATAAATATGATTTTTATACG
*
51659 TATTT-ATAATAAATATGCTTTTTATA
1 TATTTCAT-ATAAATATGATTTTTATA
51685 TATTATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.09
26 7 0.32
27 5 0.23
28 8 0.36
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (28 bp):
TATTTCATATAAATATGATTTTTATACG
Found at i:51749 original size:23 final size:23
Alignment explanation
Indices: 51715--51798 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
51705 ATTTCTATAG
* *
51715 AATAAATCATATAAATATATTAT
1 AATAAATTATATCAATATATTAT
51738 AATAAATTATATCAATATA-TAT
1 AATAAATTATATCAATATATTAT
51760 AATATAA-TATAT---TATATTAT
1 AATA-AATTATATCAATATATTAT
*
51780 AAT-AATAATATCAATATAT
1 AATAAATTATATCAATATAT
51799 AATATATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
18 2 0.04
19 8 0.15
20 6 0.12
22 17 0.33
23 19 0.37
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAATTATATCAATATATTAT
Found at i:51765 original size:27 final size:28
Alignment explanation
Indices: 51720--51776 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
51710 TATAGAATAA
*
51720 ATCATATAAATATATTATAATAAATTAT
1 ATCATATAAATATAATATAATAAATTAT
* *
51748 ATCA-ATATATATAATATAATATATTAT
1 ATCATATAAATATAATATAATAAATTAT
51775 AT
1 AT
51777 TATAATAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (28 bp):
ATCATATAAATATAATATAATAAATTAT
Found at i:51765 original size:32 final size:32
Alignment explanation
Indices: 51723--51798 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
51713 AGAATAAATC
51723 ATATA-AATATATTATAATAAATTAT-ATCAAT
1 ATATATAATATATTATAATAAATTATAAT-AAT
* * *
51754 ATATATAATATAATATATTATATTATAATAAT
1 ATATATAATATATTATAATAAATTATAATAAT
51786 A-ATATCAATATAT
1 ATATAT-AATATAT
51799 AATATATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
31 9 0.24
32 27 0.71
33 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (32 bp):
ATATATAATATATTATAATAAATTATAATAAT
Found at i:53016 original size:37 final size:37
Alignment explanation
Indices: 52961--53103 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
52951 AAACAAACGT
* *
52961 TAGAGTTTTAGTAGGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
*
52998 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
53035 TAGAG-TTTACTATGATTCAAACTCCT-AAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
53070 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
53104 GGTTCCACAA
Statistics
Matches: 100, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
35 13 0.13
36 42 0.42
37 45 0.45
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
Found at i:53080 original size:72 final size:74
Alignment explanation
Indices: 52961--53105 Score: 258
Period size: 72 Copynumber: 2.0 Consensus size: 74
52951 AAACAAACGT
*
52961 TAGAGTTTTAGTAGGATTCAAACTCCTAAAAATATGATAGAGTTTTACTATGATTCAAACTCCTA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGATAGAGTTTTACTATGATTCAAACTCCTA
53026 AAAATAGGA
66 AAAATAGGA
*
53035 TAGAG-TTTACTATGATTCAAACTCCT-AAAATATGATAGAGTTTTACTATGATTCAAACTCCTA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGATAGAGTTTTACTATGATTCAAACTCCTA
53098 AAAATAGG
66 AAAATAGG
53106 TTCCACAAGC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
72 45 0.65
73 19 0.28
74 5 0.07
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (74 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATATGATAGAGTTTTACTATGATTCAAACTCCTA
AAAATAGGA
Found at i:53816 original size:73 final size:77
Alignment explanation
Indices: 53667--53819 Score: 176
Period size: 73 Copynumber: 2.0 Consensus size: 77
53657 TATTATCCGT
53667 TTTATTAATTTTATATATATTTTACTGTTTTTTATGTTTTTTTTTTTATATATATATATATATTA
1 TTTATTAATTTTATATATATTTTACTGTTTTTTATGTTTTTTTTTTTATATATATATATATATTA
**
53732 TTTTTACTTTTA
66 TTACTACTTTTA
* * * *
53744 TTTATT-A-TTTATATATA-TTTA-TTTTTTTTCT-TTTTCTTTTTTTATATAT-TGTTTTATAT
1 TTTATTAATTTTATATATATTTTACTGTTTTTTATGTTTT-TTTTTTTATATATAT-ATATATAT
53803 TACTTACTA-TTTTA
64 TA-TTACTACTTTTA
53817 TTT
1 TTT
53820 TTTTATCTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
72 5 0.07
73 37 0.55
74 8 0.12
75 10 0.15
76 1 0.01
77 6 0.09
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (77 bp):
TTTATTAATTTTATATATATTTTACTGTTTTTTATGTTTTTTTTTTTATATATATATATATATTA
TTACTACTTTTA
Found at i:53838 original size:25 final size:25
Alignment explanation
Indices: 53761--53849 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 25
53751 TTTATATATA
*
53761 TTTATTTTTTT-TCTTTTTCTTTT-T
1 TTTATTTTTTTATC-TTATCTTTTAT
* *
53785 TTATATATTGTTTTATATTA-CTTACTAT
1 TT-TAT-TT-TTTTATCTTATCTT-TTAT
53813 TTTATTTTTTTATCTTATCTTTTAT
1 TTTATTTTTTTATCTTATCTTTTAT
*
53838 TTAATTGTTTTT
1 TTTATT-TTTTT
53850 TATTCATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
24 2 0.04
25 20 0.39
26 15 0.29
27 10 0.20
28 4 0.08
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (25 bp):
TTTATTTTTTTATCTTATCTTTTAT
Found at i:56565 original size:16 final size:16
Alignment explanation
Indices: 56524--56557 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
56514 AGAATTCACT
56524 TGAAATAATTCTATCA
1 TGAAATAATTCTATCA
56540 TGAAATAATTCTATCA
1 TGAAATAATTCTATCA
56556 TG
1 TG
56558 CATTAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (16 bp):
TGAAATAATTCTATCA
Done.