Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002198.1 Hibiscus syriacus cultivar Beakdansim tig00004479_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: 121885
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5471 original size:12 final size:12
Alignment explanation
Indices: 5446--5538 Score: 64
Period size: 12 Copynumber: 7.8 Consensus size: 12
5436 ACGGAGATAT
* *
5446 CAGAAATCAAAA
1 CAGAATTCAGAA
5458 CAGAATTCAGAA
1 CAGAATTCAGAA
5470 CAGATATT-AGAA
1 CAGA-ATTCAGAA
* * * *
5482 CATAATCCATAT
1 CAGAATTCAGAA
*
5494 CAGAAATCAGAA
1 CAGAATTCAGAA
**
5506 CAGAATTCAGGT
1 CAGAATTCAGAA
*
5518 CATGTA-TCAGAA
1 CA-GAATTCAGAA
5530 CAGAATTCA
1 CAGAATTCA
5539 AGTCGAAAAT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
11 4 0.07
12 50 0.85
13 5 0.08
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:5473 original size:24 final size:24
Alignment explanation
Indices: 5446--5538 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
5436 ACGGAGATAT
*
5446 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAGAACAGAATTCAGAA
* * * * * *
5470 CAGATATTAGAACATAATCCATAT
1 CAGAAATCAGAACAGAATTCAGAA
**
5494 CAGAAATCAGAACAGAATTCAGGT
1 CAGAAATCAGAACAGAATTCAGAA
*
5518 CATG-TATCAGAACAGAATTCA
1 CA-GAAATCAGAACAGAATTCA
5539 AGTCGAAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
24 53 0.98
25 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.20
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTCAGAA
Found at i:5550 original size:24 final size:24
Alignment explanation
Indices: 5497--5552 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
5487 TCCATATCAG
*
5497 AAATCAGAACAGAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAT
**
5521 GTATCAGAACAGAATTCAAGTCGA-
1 AAATCAGAACAGAATTCAAGTC-AT
5545 AAATCAGA
1 AAATCAGA
5553 TAAAATAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAT
Found at i:6714 original size:18 final size:18
Alignment explanation
Indices: 6693--6728 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6683 CTTCCATCCG
*
6693 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
6711 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
6729 GTCCTTTCGA
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:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:8068 original size:13 final size:13
Alignment explanation
Indices: 8050--8078 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8040 AAGGGTCAAC
8050 GGTCAACGGGTCG
1 GGTCAACGGGTCG
8063 GGTCAACGGGTCG
1 GGTCAACGGGTCG
8076 GGT
1 GGT
8079 TGTGACCGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:14047 original size:14 final size:13
Alignment explanation
Indices: 14016--14040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14006 GTAAATAATT
14016 AATAAAAATTATA
1 AATAAAAATTATA
14029 AATAAAAATTAT
1 AATAAAAATTAT
14041 TTTATAATTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAAAAATTATA
Found at i:18531 original size:15 final size:15
Alignment explanation
Indices: 18511--18543 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18501 GCGGCGACAT
*
18511 CTTTAGAGACTTTGA
1 CTTTAGAGAATTTGA
18526 CTTTAGAGAATTTGA
1 CTTTAGAGAATTTGA
18541 CTT
1 CTT
18544 CCTTTGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.42
Consensus pattern (15 bp):
CTTTAGAGAATTTGA
Found at i:25935 original size:2 final size:2
Alignment explanation
Indices: 25930--25972 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
25920 AATATATGTT
25930 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25972 A
1 A
25973 CATACTGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26510 original size:34 final size:31
Alignment explanation
Indices: 26430--26518 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
26420 GTTAGTATTT
* * *
26430 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
26462 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
26496 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
26519 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:26680 original size:17 final size:17
Alignment explanation
Indices: 26658--26711 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
26648 AATGTTAATA
26658 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
26675 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
26692 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
26709 TTT
1 TTT
26712 TTTATAATGT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:27348 original size:34 final size:34
Alignment explanation
Indices: 27243--27349 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
27233 ATAAATGTTT
* *
27243 TTAAAATACAAATTATATTATTCAAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* *
27277 TAAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
* * *
27311 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAAA
27345 TTAAA
1 TTAAA
27350 TTTCAACTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (34 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAAA
Found at i:27646 original size:33 final size:32
Alignment explanation
Indices: 27577--27647 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
27567 CACTTCACAT
* *
27577 TTATTCAATTTATCCATAACATTTTATCTAAT
1 TTATTCAAATTATCCATAACATTTTATCTAAG
* *
27609 TTATTCAAATT-TCACATAACGTTTTAATTTAAG
1 TTATTCAAATTATC-CATAACATTTT-ATCTAAG
27642 TTATTC
1 TTATTC
27648 TTAACTTGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.06
32 20 0.61
33 11 0.33
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (32 bp):
TTATTCAAATTATCCATAACATTTTATCTAAG
Found at i:27854 original size:128 final size:128
Alignment explanation
Indices: 27702--28031 Score: 633
Period size: 128 Copynumber: 2.6 Consensus size: 128
27692 TTACCTGATT
27702 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
27767 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
*
27830 TACTGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
27895 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
*
27958 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATTATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
28023 TGACAAAAT
66 TGACAAAAT
28032 GTGAAGCAAC
Statistics
Matches: 198, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 198 1.00
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
Found at i:35548 original size:17 final size:17
Alignment explanation
Indices: 35522--35559 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35512 TTGTGATGGT
*
35522 AATTAACCATAGTTTTG
1 AATTAACCATAATTTTG
*
35539 AATTAGCCATAATTTTG
1 AATTAACCATAATTTTG
35556 AATT
1 AATT
35560 TATTTGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (17 bp):
AATTAACCATAATTTTG
Found at i:39296 original size:31 final size:30
Alignment explanation
Indices: 39261--39335 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
39251 GGGGTCGTGG
*
39261 GGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
39292 GGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGCCTACCTAAGAAACATCTCAGGGCCACA
39322 GAGCCTACCTAAGA
1 G-GCCTACCTAAGA
39336 GTCACATTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.15
Consensus pattern (30 bp):
GGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:43087 original size:2 final size:2
Alignment explanation
Indices: 43080--43117 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43070 CATTATCTTT
43080 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
43118 AACAAATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47631 original size:23 final size:25
Alignment explanation
Indices: 47607--47653 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
47597 ATCTTTTAAA
47607 TTTTATAAAAAAAT-TATATATAAT
1 TTTTATAAAAAAATATATATATAAT
* *
47631 TTTTATTAAAAAGTATATATATA
1 TTTTATAAAAAAATATATATATA
47654 TATATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTTATAAAAAAATATATATATAAT
Found at i:47649 original size:25 final size:23
Alignment explanation
Indices: 47607--47666 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
47597 ATCTTTTAAA
*
47607 TTTTATAAAAAAATTATATATAAT
1 TTTTATTAAAAAATTATATAT-AT
*
47631 TTTTATTAAAAAGTATATATATAT
1 TTTTATTAAAAAAT-TATATATAT
* *
47655 ATATATTAAAAA
1 TTTTATTAAAAA
47667 TAATAAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TTTTATTAAAAAATTATATATAT
Found at i:47665 original size:23 final size:23
Alignment explanation
Indices: 47615--47666 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
47605 AATTTTATAA
* * *
47615 AAAAATTATATATAATTTTTATT
1 AAAAAGTATATATAATATATATT
47638 AAAAAGTATATATATATATATATT
1 AAAAAGTATATATA-ATATATATT
47662 AAAAA
1 AAAAA
47667 TAATAAAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAAAGTATATATAATATATATT
Found at i:48439 original size:26 final size:25
Alignment explanation
Indices: 48391--48438 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
48381 TTAAATACTC
48391 ATGTATTTGTTTTTAATGAAAAATT
1 ATGTATTTGTTTTTAATGAAAAATT
48416 ATGTATTTGTTTTTAATGAAAAA
1 ATGTATTTGTTTTTAATGAAAAA
48439 ACTTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (25 bp):
ATGTATTTGTTTTTAATGAAAAATT
Found at i:49688 original size:28 final size:28
Alignment explanation
Indices: 49656--49715 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
49646 CTATCCGTTT
* *
49656 ACATTATGACGTTGAGTCATTGCATGAA
1 ACATTATGACGTCGAGTCAATGCATGAA
* *
49684 ACATTATGTCGTCGAGTCAATGCTTGAA
1 ACATTATGACGTCGAGTCAATGCATGAA
49712 ACAT
1 ACAT
49716 ATACCGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (28 bp):
ACATTATGACGTCGAGTCAATGCATGAA
Found at i:55685 original size:21 final size:22
Alignment explanation
Indices: 55634--55683 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 22
55624 TCAAATGTAA
55634 AATAATTAAATTCTTTTTTATT
1 AATAATTAAATTCTTTTTTATT
55656 AAATAATTAAATTCTTTTTGTATCT
1 -AATAATTAAATTCTTTTT-TAT-T
55681 AAT
1 AAT
55684 TACCTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 18 0.72
24 6 0.24
25 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (22 bp):
AATAATTAAATTCTTTTTTATT
Found at i:63111 original size:24 final size:24
Alignment explanation
Indices: 63067--63116 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
63057 ATAAAGAACC
*
63067 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
63091 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
63115 AA
1 AA
63117 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:66484 original size:20 final size:21
Alignment explanation
Indices: 66450--66504 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
66440 GAATGAAGGA
* * *
66450 AAAGAAAAAGTAAAAGTTAA-
1 AAAGAAAGAGAAAAAATTAAT
*
66470 AATGAAAGAGAAAAAATTAAT
1 AAAGAAAGAGAAAAAATTAAT
66491 AAAGAAAGAGAAAA
1 AAAGAAAGAGAAAA
66505 GAAAAAGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (21 bp):
AAAGAAAGAGAAAAAATTAAT
Found at i:66525 original size:26 final size:25
Alignment explanation
Indices: 66448--66526 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 25
66438 ATGAATGAAG
* *
66448 GAAAAGAAAAAG-TAAAAGTTAAAA
1 GAAAAGAAAAAGTTAAAAATTAAGA
* **
66472 TGAAAGAGAAAAAATTAATAAAGAAAGA
1 -GAAA-AGAAAAAGTTAA-AAATTAAGA
66500 GAAAAGAAAAAGTTAAAAATTTAAGA
1 GAAAAGAAAAAGTTAAAAA-TTAAGA
66526 G
1 G
66527 GGAAAATGTG
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
25 7 0.17
26 23 0.55
27 7 0.17
28 5 0.12
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (25 bp):
GAAAAGAAAAAGTTAAAAATTAAGA
Found at i:73285 original size:24 final size:24
Alignment explanation
Indices: 73241--73290 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
73231 ATAAAGAACC
*
73241 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
73265 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
73289 AA
1 AA
73291 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:74419 original size:24 final size:24
Alignment explanation
Indices: 74389--74465 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
74379 GCATAGATAG
74389 TGCATCGATGCACCCGTCAAGGGA
1 TGCATCGATGCACCCGTCAAGGGA
* ** **
74413 TGCATCGATACA-TAGTGTA--G-
1 TGCATCGATGCACCCGTCAAGGGA
74433 TGCATCGATGCACCCGTCAAGGGA
1 TGCATCGATGCACCCGTCAAGGGA
74457 TGCATCGAT
1 TGCATCGAT
74466 ACATAGTGTA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
20 11 0.28
21 4 0.10
23 4 0.10
24 20 0.51
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (24 bp):
TGCATCGATGCACCCGTCAAGGGA
Found at i:74438 original size:20 final size:20
Alignment explanation
Indices: 74413--74490 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
74403 CGTCAAGGGA
74413 TGCATCGATACATAGTGTAG
1 TGCATCGATACATAGTGTAG
* ** **
74433 TGCATCGATGCACCCGTCAAGGG
1 TGCATCGATACA-TAGTGTA--G
74456 ATGCATCGATACATAGTGTAG
1 -TGCATCGATACATAGTGTAG
*
74477 TGCATCGATGCATA
1 TGCATCGATACATA
74491 CCTCTATTAA
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
20 24 0.56
21 4 0.09
23 4 0.09
24 11 0.26
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
TGCATCGATACATAGTGTAG
Found at i:74439 original size:44 final size:44
Alignment explanation
Indices: 74369--74488 Score: 206
Period size: 44 Copynumber: 2.8 Consensus size: 44
74359 AATGGGATTT
* * *
74369 ATGCACCGATGCATAG-ATAGTGCATCGATGCACCCGTCAAGGG
1 ATGCATCGATACATAGTGTAGTGCATCGATGCACCCGTCAAGGG
74412 ATGCATCGATACATAGTGTAGTGCATCGATGCACCCGTCAAGGG
1 ATGCATCGATACATAGTGTAGTGCATCGATGCACCCGTCAAGGG
74456 ATGCATCGATACATAGTGTAGTGCATCGATGCA
1 ATGCATCGATACATAGTGTAGTGCATCGATGCA
74489 TACCTCTATT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 14 0.19
44 59 0.81
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (44 bp):
ATGCATCGATACATAGTGTAGTGCATCGATGCACCCGTCAAGGG
Found at i:75122 original size:23 final size:23
Alignment explanation
Indices: 75095--75147 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
75085 TATGGAACTA
*
75095 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGTGACACTT
* *
75118 TGGTGCAATTCTTCGTGACACTT
1 CGGTGCAATTCTACGTGACACTT
75141 CGGTGCA
1 CGGTGCA
75148 TTTATAAGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (23 bp):
CGGTGCAATTCTACGTGACACTT
Found at i:78121 original size:31 final size:31
Alignment explanation
Indices: 78078--78246 Score: 115
Period size: 31 Copynumber: 5.5 Consensus size: 31
78068 TAAATTATAT
*
78078 TTTTAGTATCTAAACTATCACTTTTGTTTCA
1 TTTTAATATCTAAACTATCACTTTTGTTTCA
*
78109 TTTTAATGTCTAAACT-T---TTTT-TTTCA
1 TTTTAATATCTAAACTATCACTTTTGTTTCA
* *
78135 ---TAATCATGCTTAAAGT-TTACTTTTTGTTTCA
1 TTTTAAT-AT-C-TAAACTATCAC-TTTTGTTTCA
**
78166 TTTTAGTAGTATCTAAACTATCACTTTTGTTTTG
1 TTTTA--A-TATCTAAACTATCACTTTTGTTTCA
* * *
78200 TTTTAATATCTAAACTATCACTTTTCTCTCG
1 TTTTAATATCTAAACTATCACTTTTGTTTCA
78231 TTTTAATA-CATAAACT
1 TTTTAATATC-TAAACT
78247 TTTTCTTTTT
Statistics
Matches: 111, Mismatches: 11, Indels: 32
0.72 0.07 0.21
Matches are distributed among these distances:
23 4 0.04
24 1 0.01
25 1 0.01
26 11 0.10
27 4 0.04
30 6 0.05
31 55 0.50
32 1 0.01
34 20 0.18
35 4 0.04
36 3 0.03
37 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (31 bp):
TTTTAATATCTAAACTATCACTTTTGTTTCA
Found at i:84502 original size:23 final size:23
Alignment explanation
Indices: 84476--84520 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
84466 AAGTTCTCTC
84476 TTCCTCTTGTATTCTTCATTCTA
1 TTCCTCTTGTATTCTTCATTCTA
84499 TTCCTCTTGTATTCTTCATTCT
1 TTCCTCTTGTATTCTTCATTCT
84521 CCCACTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.11, C:0.27, G:0.04, T:0.58
Consensus pattern (23 bp):
TTCCTCTTGTATTCTTCATTCTA
Found at i:87737 original size:21 final size:21
Alignment explanation
Indices: 87695--87737 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
87685 TTTCTGGGCT
*
87695 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
87716 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
87737 A
1 A
87738 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:88560 original size:103 final size:102
Alignment explanation
Indices: 88283--88598 Score: 553
Period size: 103 Copynumber: 3.1 Consensus size: 102
88273 GTAGAGGGTC
*
88283 TATGTGGTCCTTCAGGACACATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACA-ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
88348 TGGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
88386 TATGTGGTCCTTCGGGAC-ATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
*
88450 TGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
88487 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACGCATAC
1 TATGTGGTCCTTCGGGACA-ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
88552 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
88590 TATGTGGTC
1 TATGTGGTC
88599 TTTATGGACA
Statistics
Matches: 203, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
101 98 0.48
103 105 0.52
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACT
TGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:88651 original size:23 final size:23
Alignment explanation
Indices: 88620--88680 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
88610 TATTATATGT
88620 CACTACGGTGCAATTCTACGCGG
1 CACTACGGTGCAATTCTACGCGG
* *
88643 CACTCCGGTGCAATTCTACGTGG
1 CACTACGGTGCAATTCTACGCGG
88666 CACTTA-GGTGCAATT
1 CAC-TACGGTGCAATT
88681 ATATGAGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 33 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
CACTACGGTGCAATTCTACGCGG
Found at i:94774 original size:21 final size:21
Alignment explanation
Indices: 94732--94774 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
94722 TTTCTGGGCT
* *
94732 AGGGGGATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
94753 AGGGGAATCGATCCCCCCTCA
1 AGGGGAATCGATACCCACTCA
94774 A
1 A
94775 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:94827 original size:20 final size:20
Alignment explanation
Indices: 94802--94839 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
94792 GAATGCTAGA
*
94802 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
94822 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
94840 TAATGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:95646 original size:103 final size:103
Alignment explanation
Indices: 95318--95638 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
95308 GTAGAGGGTC
95318 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
95383 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
95421 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
**
95486 TTGATCCTTGATATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
95524 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
95589 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
95627 TATGTGGTCCTT
1 TATGTGGTCCTT
95639 ATGGACATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:95688 original size:23 final size:23
Alignment explanation
Indices: 95655--95717 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
95645 ATTATTATAT
95655 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* **
95678 GGCACTCCGGTGCAATTCTACTT
1 GGCACTACGGTGCAATTCTACGC
95701 GGCACTTA-GGTGCAATT
1 GGCAC-TACGGTGCAATT
95718 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 34 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:108886 original size:28 final size:28
Alignment explanation
Indices: 108845--108930 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 28
108835 TATATAAAAA
*
108845 GAGATGTTTAAGGTTTATGGTTTAAGATTT
1 GAGA-GTTTGAGGTTTA-GGTTTAAGATTT
*
108875 GAG-GTTTGAGG-TTAGGTTTTAGAGTTT
1 GAGAGTTTGAGGTTTAGGTTTAAGA-TTT
* * *
108902 GAGATTTTGAGGTTTGGGTTTGAGATTT
1 GAGAGTTTGAGGTTTAGGTTTAAGATTT
108930 G
1 G
108931 TGATTTGTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 8 0.17
27 9 0.19
28 18 0.38
29 10 0.21
30 3 0.06
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (28 bp):
GAGAGTTTGAGGTTTAGGTTTAAGATTT
Found at i:108923 original size:6 final size:7
Alignment explanation
Indices: 108850--108930 Score: 53
Period size: 7 Copynumber: 11.7 Consensus size: 7
108840 AAAAAGAGAT
*
108850 GTTTAAG
1 GTTTGAG
108857 GTTT-ATG
1 GTTTGA-G
*
108864 GTTTAAG
1 GTTTGAG
*
108871 ATTTGAG
1 GTTTGAG
108878 GTTTGAG
1 GTTTGAG
108885 G-TT-AG
1 GTTTGAG
*
108890 GTTTTAG
1 GTTTGAG
108897 AGTTTGAG
1 -GTTTGAG
*
108905 ATTTTGAG
1 -GTTTGAG
108913 GTTTG-G
1 GTTTGAG
108919 GTTTGAG
1 GTTTGAG
*
108926 ATTTG
1 GTTTG
108931 TGATTTGTGA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
5 3 0.05
6 11 0.18
7 33 0.54
8 14 0.23
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (7 bp):
GTTTGAG
Found at i:109104 original size:2 final size:2
Alignment explanation
Indices: 109097--109132 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
109087 ATTATGCTCC
109097 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
109133 TCTCAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111273 original size:13 final size:13
Alignment explanation
Indices: 111257--111282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
111247 GTTATTTATG
111257 TAAAATTTTTAAT
1 TAAAATTTTTAAT
111270 TAAAATTTTTAAT
1 TAAAATTTTTAAT
111283 GTTGAGATTT
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TAAAATTTTTAAT
Found at i:114470 original size:2 final size:2
Alignment explanation
Indices: 114463--114488 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
114453 TTCAAACTGA
114463 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
114489 GTGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.