Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001649.1 Hibiscus syriacus cultivar Beakdansim tig00003300_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: 67137
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1103 original size:207 final size:210
Alignment explanation
Indices: 729--1206 Score: 707
Period size: 207 Copynumber: 2.3 Consensus size: 210
719 ATTCGAAACC
** * ** * *
729 CTTAAGACACCTAACGACTCATTCCGCTACACCGATTACAAGAG--CTAACTTTTACAAAAAACT
1 CTTAAGACACCTAACGACTCATTCCGCTACACTAATTATAAGAGAACTATTTTTTA-ACACAACT
* *
792 GTTCATGTTATAAAGCCTATTTATGAGTAATCTAGAGCGAATTCTGCAGAGTTCCATTACACGAA
65 GTTCATGTGATAAAGCCTATTTATGAGTAATCTAGAGCGAATACTGCAGAGTTCCATTACACGAA
857 CGAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCTCGA-TATTTTCTCCATAAGAT
130 CGAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCTC-ATTATTTTCTCCATAAGAT
*
921 TCGGAGCTCTAACCTTG
194 TCGGAGCTCTAACCTTA
*
938 CTTAAGACACCTAACGACTCATTCCACTACACTAATTATAAGAGAACTATTTTTTAACACAACTG
1 CTTAAGACACCTAACGACTCATTCCGCTACACTAATTATAAGAGAACTATTTTTTAACACAACTG
* * * *
1003 TTCATGTGA-AAA-CCTATTTCTGTGTAATCTAGAGCGAATACTGCAGAGTTCCGTTACATGAAC
66 TTCATGTGATAAAGCCTATTTATGAGTAATCTAGAGCGAATACTGCAGAGTTCCATTACACGAAC
* * * *
1066 G-ACCTCTTCGTCCAGTTTTCTATGTTTAAAACGCTAGAATTTCATTGTTTTCTCCATAAGATTC
131 GAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCTCATTATTTTCTCCATAAGATTC
1130 GGAGCTCTAACCTTA
196 GGAGCTCTAACCTTA
* *
1145 CTTAAGACACCTAAGGACTCATTCCGCTACACTAAATATAAGAGAACTATTTTTTAACACAA
1 CTTAAGACACCTAACGACTCATTCCGCTACACTAATTATAAGAGAACTATTTTTTAACACAA
1207 AATTGTTTAT
Statistics
Matches: 244, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
206 1 0.00
207 130 0.53
208 47 0.19
209 43 0.18
210 15 0.06
211 8 0.03
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (210 bp):
CTTAAGACACCTAACGACTCATTCCGCTACACTAATTATAAGAGAACTATTTTTTAACACAACTG
TTCATGTGATAAAGCCTATTTATGAGTAATCTAGAGCGAATACTGCAGAGTTCCATTACACGAAC
GAACCTCTTCATCCAGTTTTCTAAGTTTAAAACGCTAGAATCTCATTATTTTCTCCATAAGATTC
GGAGCTCTAACCTTA
Found at i:11409 original size:2 final size:2
Alignment explanation
Indices: 11404--11431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11394 TATATTGTTA
11404 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
11432 TCATTCTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12609 original size:22 final size:22
Alignment explanation
Indices: 12584--12665 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 22
12574 TATATCACGG
*
12584 AAGTGCCTTAGCACTAATACTA
1 AAGTGCCTTAGCACTGATACTA
12606 AAGTGCCTTAGCACTGATAC-A
1 AAGTGCCTTAGCACTGATACTA
*
12627 GAAGTG-CATACGCACTGATACTA
1 -AAGTGCCTTA-GCACTGATACTA
* *
12650 AAGTGGCTTAGTACTG
1 AAGTGCCTTAGCACTG
12666 GGAGAGAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
21 4 0.08
22 44 0.85
23 4 0.08
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATACTA
Found at i:15155 original size:3 final size:3
Alignment explanation
Indices: 15147--15175 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15137 GAAGGCGGAG
15147 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
15176 GACGAGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:15650 original size:2 final size:2
Alignment explanation
Indices: 15643--15696 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
15633 ACTATTTAAC
15643 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
15685 AT AT AT AT AT AT
1 AT AT AT AT AT AT
15697 TAGTTTTGTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16083 original size:16 final size:16
Alignment explanation
Indices: 16058--16115 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
16048 TTTATCCTAA
16058 TTTTAATTATTTCATT
1 TTTTAATTATTTCATT
* **
16074 TTTTAGTTATTTCAAC
1 TTTTAATTATTTCATT
16090 TTTTAA-TATTTCATT
1 TTTTAATTATTTCATT
16105 CTTTTAATTAT
1 -TTTTAATTAT
16116 CAAAGTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
15 7 0.21
16 24 0.71
17 3 0.09
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.64
Consensus pattern (16 bp):
TTTTAATTATTTCATT
Found at i:16331 original size:18 final size:18
Alignment explanation
Indices: 16300--16334 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16290 TAGTTTTCAA
*
16300 ATAAAAATTTATTTGATT
1 ATAAAAATTCATTTGATT
*
16318 ATAAATATTCATTTGAT
1 ATAAAAATTCATTTGAT
16335 CATGATTGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (18 bp):
ATAAAAATTCATTTGATT
Found at i:21241 original size:15 final size:15
Alignment explanation
Indices: 21212--21253 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
21202 GATTTAACTT
* *
21212 TTTTATTTTTTTTAA
1 TTTTATTTCTCTTAA
21227 TTTTATTTCTCTTAA
1 TTTTATTTCTCTTAA
21242 TATTT-TTTCTCT
1 T-TTTATTTCTCT
21254 CTCTTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 21 0.88
16 3 0.12
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATTTCTCTTAA
Found at i:24080 original size:2 final size:2
Alignment explanation
Indices: 24073--24099 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24063 TCTTTTTAAA
24073 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
24100 CCCCCATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24285 original size:24 final size:24
Alignment explanation
Indices: 24258--24364 Score: 88
Period size: 24 Copynumber: 4.5 Consensus size: 24
24248 AAACGGAGAT
* *
24258 ATCAAAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
24282 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
24306 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
24330 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
24354 ATCAAAAATCA
1 ATCAGAAATCA
24365 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:24364 original size:48 final size:48
Alignment explanation
Indices: 24258--24366 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
24248 AAACGGAGAT
* * * *
24258 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAAAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * ** * * *
24306 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAAAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
24354 ATCAAAAATCAGA
1 ATCAAAAATCAGA
24367 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAAAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:26865 original size:7 final size:7
Alignment explanation
Indices: 26853--26893 Score: 64
Period size: 7 Copynumber: 5.6 Consensus size: 7
26843 TGGTCAACTC
26853 CGGTCAA
1 CGGTCAA
26860 CGGTCAA
1 CGGTCAA
26867 CGGGTCAA
1 C-GGTCAA
26875 CGGTCAA
1 CGGTCAA
26882 CGGGTCAA
1 C-GGTCAA
26890 CGGT
1 CGGT
26894 TCGGGTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 18 0.56
8 14 0.44
ACGTcount: A:0.24, C:0.27, G:0.34, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:26874 original size:8 final size:8
Alignment explanation
Indices: 26854--26939 Score: 71
Period size: 8 Copynumber: 11.5 Consensus size: 8
26844 GGTCAACTCC
26854 GGTCAAC-
1 GGTCAACG
26861 GGTCAACG
1 GGTCAACG
26869 GGTCAAC-
1 GGTCAACG
26876 GGTCAACG
1 GGTCAACG
26884 GGTCAAC-
1 GGTCAACG
*
26891 GGT--TCG
1 GGTCAACG
26897 GGTCAACG
1 GGTCAACG
**
26905 GGTCGGGTCG
1 GGTC--AACG
26915 GGTCAACG
1 GGTCAACG
26923 GGT---CG
1 GGTCAACG
26928 GGTCAACG
1 GGTCAACG
26936 GGTC
1 GGTC
26940 GGGTTGTGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 19
0.72 0.07 0.22
Matches are distributed among these distances:
5 6 0.10
6 3 0.05
7 17 0.27
8 31 0.49
10 6 0.10
ACGTcount: A:0.19, C:0.24, G:0.41, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:26874 original size:15 final size:15
Alignment explanation
Indices: 26854--26905 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
26844 GGTCAACTCC
26854 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
26869 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
26884 GGTCAACGGT--TCG
1 GGTCAACGGTCAACG
26897 GGTCAACGG
1 GGTCAACGG
26906 GTCGGGTCGG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
13 11 0.31
15 25 0.69
ACGTcount: A:0.23, C:0.25, G:0.37, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:26900 original size:13 final size:13
Alignment explanation
Indices: 26867--26943 Score: 64
Period size: 13 Copynumber: 5.4 Consensus size: 13
26857 CAACGGTCAA
*
26867 CGGGTCAACGGTCAA
1 CGGGTCAACGGT--T
26882 CGGGTCAACGGTT
1 CGGGTCAACGGTT
26895 CGGGTCAACGGGTCGGGT
1 CGGGTCAAC-GGT----T
*
26913 CGGGTCAACGGGT
1 CGGGTCAACGGTT
*
26926 CGGGTCAACGGGT
1 CGGGTCAACGGTT
26939 CGGGT
1 CGGGT
26944 TGTGACCGGT
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
13 28 0.51
14 3 0.05
15 12 0.22
17 2 0.04
18 10 0.18
ACGTcount: A:0.16, C:0.23, G:0.44, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGTT
Found at i:26920 original size:31 final size:31
Alignment explanation
Indices: 26882--26943 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
26872 CAACGGTCAA
*
26882 CGGGTCAACGGTTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
26913 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
26944 TGTGACCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.13, C:0.23, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:26943 original size:18 final size:18
Alignment explanation
Indices: 26894--26931 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
26884 GGTCAACGGT
26894 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACGGGTCGGG
26912 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACGGGTCGGG
26930 TC
1 TC
26932 AACGGGTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.47, T:0.18
Consensus pattern (18 bp):
TCGGGTCAACGGGTCGGG
Found at i:27990 original size:15 final size:15
Alignment explanation
Indices: 27970--28007 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
27960 CATAATATAT
27970 TTCATGACCATCTTC
1 TTCATGACCATCTTC
27985 TTCATGACCATCTTC
1 TTCATGACCATCTTC
28000 TTCATGAC
1 TTCATGAC
28008 AAGGTTGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.32, G:0.08, T:0.39
Consensus pattern (15 bp):
TTCATGACCATCTTC
Found at i:32524 original size:64 final size:63
Alignment explanation
Indices: 32442--32598 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 63
32432 TTAAGTGTGT
* * * *
32442 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACGTCAAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCATT-AAAATGAAAACATCAAAGGCAATTAGTGC
* * ** * *
32506 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCAAAGGCAATTAGTGC
* *
32570 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
32599 TTCAAGGGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCAAAGGCAATTAGTGC
Found at i:33027 original size:20 final size:20
Alignment explanation
Indices: 32991--33052 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
32981 CTATGTTATG
*
32991 ATGATAA-AAACTATATGAT
1 ATGATAAGAAATTATATGAT
33010 ATGATAAGAAATTATATGAAT
1 ATGATAAGAAATTATATG-AT
*
33031 AT-AAAAGAGAAGTTATATGAT
1 ATGATAAGA-AA-TTATATGAT
33052 A
1 A
33053 AGACACAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 7 0.19
20 14 0.38
21 9 0.24
22 7 0.19
ACGTcount: A:0.53, C:0.02, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGATAAGAAATTATATGAT
Found at i:33488 original size:24 final size:24
Alignment explanation
Indices: 33456--33517 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
33446 TTCGGTGCAT
33456 TTCTACGCGGCACTACAGTGCAAA
1 TTCTACGCGGCACTACAGTGCAAA
* *
33480 TTCTACGCGACACTACGGTGCAAA
1 TTCTACGCGGCACTACAGTGCAAA
*
33504 TTCTACGTGGCACT
1 TTCTACGCGGCACT
33518 TCGATGCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (24 bp):
TTCTACGCGGCACTACAGTGCAAA
Found at i:33525 original size:24 final size:24
Alignment explanation
Indices: 33456--33525 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
33446 TTCGGTGCAT
33456 TTCTACGCGGCACTAC-AGTGCAAA
1 TTCTACGCGGCACTACGA-TGCAAA
* *
33480 TTCTACGCGACACTACGGTGCAAA
1 TTCTACGCGGCACTACGATGCAAA
* *
33504 TTCTACGTGGCACTTCGATGCA
1 TTCTACGCGGCACTACGATGCA
33526 TTTATACGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (24 bp):
TTCTACGCGGCACTACGATGCAAA
Found at i:33722 original size:28 final size:28
Alignment explanation
Indices: 33669--33722 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
33659 TATGAATGGT
* * *
33669 ATTATATGATTTATATGATGATATGTGG
1 ATTATATGATTTAAATGATCAAATGTGG
33697 ATTATATGA-TTAAATGAGTCAAATGT
1 ATTATATGATTTAAATGA-TCAAATGT
33723 TGGTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
28 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.43
Consensus pattern (28 bp):
ATTATATGATTTAAATGATCAAATGTGG
Found at i:37031 original size:64 final size:63
Alignment explanation
Indices: 36944--37100 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 63
36934 TTCAGTGTGT
* * * *
36944 ATCGATGCACAGGAAGTGTATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGGCAATTAGTGC
* * ** * *
37008 ATCGATGCATAAGG-AGTGCATCGATCCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
* *
37072 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
37101 TTCAAGGGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
63 3 0.04
64 67 0.86
65 8 0.10
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTAGTGC
Found at i:37532 original size:21 final size:21
Alignment explanation
Indices: 37506--37557 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
37496 TGATATAAAC
*
37506 TATATGATATGATAAGA-AAAT
1 TATATGATAT-AAAAGAGAAAT
*
37527 TATATGAATATAAAAGAGAAGT
1 TATATG-ATATAAAAGAGAAAT
37549 TATATGATA
1 TATATGATA
37558 AGACACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.52
22 13 0.48
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (21 bp):
TATATGATATAAAAGAGAAAT
Found at i:38005 original size:24 final size:24
Alignment explanation
Indices: 37945--38006 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
37935 TAACTTTATA
* *
37945 TGGCACTTCCGTGC-ATTTCTACG
1 TGGCACTTCAGTGCAAATTCTACG
* * *
37968 CGGTACTACAGTGCAAATTCTACG
1 TGGCACTTCAGTGCAAATTCTACG
*
37992 TGGCACTTCGGTGCA
1 TGGCACTTCAGTGCA
38007 TTTATACGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.29
Consensus pattern (24 bp):
TGGCACTTCAGTGCAAATTCTACG
Found at i:49714 original size:110 final size:110
Alignment explanation
Indices: 49520--49736 Score: 337
Period size: 110 Copynumber: 2.0 Consensus size: 110
49510 GATCAAAAAG
* * *
49520 GTCAACGATCTCGTATAATTAAATCTCTTTTGTGACAGTTTATTTGATGCATTCAAAACCGCTCA
1 GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTCA
* *
49585 TAAAATAATCTGTCAAATTGATTTTATCAATCGTCAAGCCTTCTA
66 TAAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTTCTA
49630 GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTC-
1 GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTCA
* * * *
49694 TCAAAACAATATGTCGAATTGATTTTATCTATCTTCAGGCCTT
66 T-AAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTT
49737 TTTATTTATT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 1 0.01
110 96 0.99
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (110 bp):
GTCAACGATCTCATATAATTAAATCTCTTTTGTGACAATTTATTTGATCCATTCAAAACCGCTCA
TAAAACAATATGTCAAATTGATTTTATCAATCGTCAAGCCTTCTA
Found at i:50997 original size:3 final size:3
Alignment explanation
Indices: 50989--51023 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
50979 AATAGAGAAG
50989 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
51024 ACCTAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:51243 original size:15 final size:15
Alignment explanation
Indices: 51223--51257 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
51213 CCGTGCCTAT
51223 CGACACACACATATC
1 CGACACACACATATC
51238 CG--ACACACATATC
1 CGACACACACATATC
51251 CGACACA
1 CGACACA
51258 TTTTCGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
13 13 0.72
15 5 0.28
ACGTcount: A:0.40, C:0.40, G:0.09, T:0.11
Consensus pattern (15 bp):
CGACACACACATATC
Found at i:51245 original size:13 final size:13
Alignment explanation
Indices: 51227--51257 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
51217 GCCTATCGAC
51227 ACACACATATCCG
1 ACACACATATCCG
51240 ACACACATATCCG
1 ACACACATATCCG
51253 ACACA
1 ACACA
51258 TTTTCGGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.39, G:0.06, T:0.13
Consensus pattern (13 bp):
ACACACATATCCG
Found at i:52947 original size:12 final size:12
Alignment explanation
Indices: 52927--52956 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52917 AAAAAAAGGG
*
52927 AAAATAATATAT
1 AAAAAAATATAT
52939 AAAAAAATATAT
1 AAAAAAATATAT
52951 AAAAAA
1 AAAAAA
52957 TGTTATTAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAAAATATAT
Found at i:54268 original size:16 final size:15
Alignment explanation
Indices: 54244--54285 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
54234 AAAAAAGAGA
54244 AAAAT-AATAATAAAT
1 AAAATAAATAAT-AAT
54259 AAAATAAATAATAAT
1 AAAATAAATAATAAT
*
54274 AATGATAAATAA
1 AA-AATAAATAA
54286 CAAAATAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAATAAATAATAAT
Found at i:54274 original size:25 final size:24
Alignment explanation
Indices: 54246--54293 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
54236 AAAAGAGAAA
54246 AATAATAATAAATAAAATAAATAAT
1 AATAATAATAAATAAAA-AAATAAT
* *
54271 AATAATGATAAATAACAAAATAA
1 AATAATAATAAATAAAAAAATAA
54294 CAAAAGGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (24 bp):
AATAATAATAAATAAAAAAATAAT
Found at i:54364 original size:39 final size:38
Alignment explanation
Indices: 54318--54417 Score: 118
Period size: 38 Copynumber: 2.6 Consensus size: 38
54308 ATTAAAATAA
54318 AAAAATATTTTTCAAAAATCTATATAATATATA-TTTTAT
1 AAAAATA-TTTTCAAAAAT-TATATAATATATACTTTTAT
*
54357 AAAAATATTTT--AAAATTATATATTATATATACTTTTTT
1 AAAAATATTTTCAAAAATTATATA--ATATATACTTTTAT
*
54395 AAAAATGTTTTC-AAAATTATATA
1 AAAAATATTTTCAAAAATTATATA
54418 GTTTTCAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
35 6 0.11
36 5 0.09
37 7 0.13
38 19 0.35
39 18 0.33
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (38 bp):
AAAAATATTTTCAAAAATTATATAATATATACTTTTAT
Found at i:54438 original size:16 final size:16
Alignment explanation
Indices: 54402--54458 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
54392 TTTAAAAATG
**
54402 TTTTCAAAATTATATA
1 TTTTCAAAACAATATA
*
54418 GTTTTCAAAA-AATATT
1 -TTTTCAAAACAATATA
*
54434 TTTTTAAAACAATATA
1 TTTTCAAAACAATATA
54450 TTTTCAAAA
1 TTTTCAAAA
54459 TGTTTTTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 8 0.24
16 17 0.50
17 9 0.26
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (16 bp):
TTTTCAAAACAATATA
Found at i:55139 original size:20 final size:21
Alignment explanation
Indices: 55119--55158 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55109 CAAAATATTT
*
55119 GAAAAATGATCAATCCCTTTG
1 GAAAAAGGATCAATCCCTTTG
* *
55140 GTAAAAGGATCGATCCCTT
1 GAAAAAGGATCAATCCCTT
55159 GTGCCTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
GAAAAAGGATCAATCCCTTTG
Found at i:57857 original size:21 final size:21
Alignment explanation
Indices: 57818--57883 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
57808 TTAATTATCG
* * *
57818 TAAACTATCATGTTAATATTA
1 TAAATTATCATATCAATATTA
* * *
57839 TAGATTATTATATCAATATCA
1 TAAATTATCATATCAATATTA
* *
57860 TAAATTATCATGTCAACATTA
1 TAAATTATCATATCAATATTA
57881 TAA
1 TAA
57884 TAATCAATTA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAATTATCATATCAATATTA
Found at i:57872 original size:42 final size:41
Alignment explanation
Indices: 57801--57882 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 41
57791 CATATCATTA
* * *
57801 ATTATTATTAATTATCGTAAACTATCATGTTAATATTATAG
1 ATTATTATTAATTATCATAAACTATCATGTCAACATTATAG
*
57842 ATTATTATATCAA-TATCATAAATTATCATGTCAACATTATA
1 ATTATTAT-T-AATTATCATAAACTATCATGTCAACATTATA
57883 ATAATCAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 8 0.23
42 25 0.71
43 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (41 bp):
ATTATTATTAATTATCATAAACTATCATGTCAACATTATAG
Found at i:62767 original size:29 final size:30
Alignment explanation
Indices: 62724--62782 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
62714 CTATACTCTC
62724 TTCTATTTTCCTCACCTG-ACTTT-CAATTT
1 TTCTATTTTCCTCA-CTGAACTTTACAATTT
**
62753 TTCTATTTTGTTCACTGAACTTTACAATTT
1 TTCTATTTTCCTCACTGAACTTTACAATTT
62783 GAATCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.65
30 6 0.23
ACGTcount: A:0.20, C:0.22, G:0.05, T:0.53
Consensus pattern (30 bp):
TTCTATTTTCCTCACTGAACTTTACAATTT
Found at i:64685 original size:23 final size:23
Alignment explanation
Indices: 64659--64724 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
64649 TTGTGATTTA
* * *
64659 TGTTCATTTATATTCTTTTGTTT
1 TGTTCATTTATATTCGTTTATTG
* *
64682 TGTTCATCTATGTTCGTTTATTG
1 TGTTCATTTATATTCGTTTATTG
* *
64705 TGTTCTTTTATGTTCGTTTA
1 TGTTCATTTATATTCGTTTA
64725 CATCCGTGTG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.64
Consensus pattern (23 bp):
TGTTCATTTATATTCGTTTATTG
Done.