Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005346.1 Hibiscus syriacus cultivar Beakdansim tig00012112_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: 89141
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:594 original size:2 final size:2
Alignment explanation
Indices: 587--632 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
577 TAAATACTAA
587 AT AT AT AT AT AT A- AT AT AT A- AT A- AT AT ACT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
626 AT AT AT A
1 AT AT AT A
633 CTCGGTAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.10
2 33 0.85
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:7206 original size:64 final size:63
Alignment explanation
Indices: 7136--7316 Score: 209
Period size: 64 Copynumber: 2.8 Consensus size: 63
7126 TTGGAACACT
* ***
7136 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
7200 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * * *
7264 AGAGTGCATTGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
7317 CAATTAATTC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
64 54 0.55
65 44 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:7288 original size:19 final size:19
Alignment explanation
Indices: 7264--7314 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
7254 GAAAATATTC
7264 AGAGTGCATTGATGCATGG
1 AGAGTGCATTGATGCATGG
* *
7283 AGAGTGCATCGGTGCATGG
1 AGAGTGCATTGATGCATGG
7302 A-A-TGCATTCGATG
1 AGAGTGCATT-GATG
7315 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.19
18 4 0.15
19 18 0.67
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.25
Consensus pattern (19 bp):
AGAGTGCATTGATGCATGG
Found at i:7290 original size:65 final size:65
Alignment explanation
Indices: 7157--7316 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 65
7147 TGCACCAAGT
* ***
7157 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* ** *
7221 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATTGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
7285 A
65 A
* *
7286 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
7317 CAATTAATTC
Statistics
Matches: 83, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:13803 original size:22 final size:21
Alignment explanation
Indices: 13761--13800 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13751 GAGTTTGTTT
*
13761 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
13782 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
13801 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:15796 original size:64 final size:63
Alignment explanation
Indices: 15728--15908 Score: 218
Period size: 64 Copynumber: 2.8 Consensus size: 63
15718 TTGGAACACT
* ***
15728 TGATGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCC
** * **
15792 TGATGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTC
1 TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCC
* * * *
15856 AGAGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGA-TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTT
15909 CAATTAATTC
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
64 54 0.55
65 45 0.45
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (63 bp):
TGATGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCC
Found at i:15880 original size:19 final size:19
Alignment explanation
Indices: 15856--15906 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
15846 GAAAATATTC
15856 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
15875 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
15894 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
15907 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:15882 original size:65 final size:65
Alignment explanation
Indices: 15749--15908 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 65
15739 TGCACCAAGT
* ***
15749 GTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
* **
15813 GTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATGGAG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGA-TGCATCGATGCATGGAG
15877 A
65 A
* *
15878 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
15909 CAATTAATTC
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:15948 original size:65 final size:63
Alignment explanation
Indices: 15750--15957 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 63
15740 GCACCAAGTG
* * *
15750 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGATGCATCGATGCATGGCTTG-
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGAC-TGA
*
15814 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCAT-GACT
15876 GA
62 GA
* * * *
15878 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGTACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATG-ACT
15942 GA
62 GA
*
15944 TGCATCGGTGCATG
1 TGCATCGATGCATG
15958 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
63 11 0.09
64 44 0.36
65 63 0.51
66 5 0.04
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGACTGA
Found at i:33440 original size:80 final size:80
Alignment explanation
Indices: 33342--33547 Score: 324
Period size: 80 Copynumber: 2.6 Consensus size: 80
33332 ATTCTTCGTA
**
33342 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAAAT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG-AAAT
33407 -GTTATGAAGAATGAC
65 GGTTATGAAGAATGAC
*
33422 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCGAAATG
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
33487 GTTATGAAGAATGAC
66 GTTATGAAGAATGAC
* * * * *
33502 ACATTTTAAGTTGCAATCGAAAATGTTATGAAGAATGTCACATTTT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTT
33548 AGGTTGTGTC
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 4 0.03
80 112 0.97
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (80 bp):
ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
GTTATGAAGAATGAC
Found at i:33486 original size:40 final size:40
Alignment explanation
Indices: 33362--33486 Score: 137
Period size: 41 Copynumber: 3.1 Consensus size: 40
33352 TTGCAATCTA
33362 AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
1 AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
* * * * * ** *
33402 AAAATGTTATGAAGAATGACAC-ATTTTAAGTTG-CAATCTA
1 -AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATC-G
*
33442 AAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCG
1 AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
33482 AAATG
1 AAATG
33487 GTTATGAAGA
Statistics
Matches: 64, Mismatches: 17, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
39 21 0.33
40 21 0.33
41 22 0.34
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (40 bp):
AAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG
Found at i:33548 original size:39 final size:39
Alignment explanation
Indices: 33342--33553 Score: 201
Period size: 39 Copynumber: 5.3 Consensus size: 39
33332 ATTCTTCGTA
** * * * *
33342 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTC
1 ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
* * *
33381 ACTTTTTTCGGTTGCCAATCGAAAATGTTATGAAGAATGAC
1 AC-ATTTTAGGTTG-CAATCGAAAATGTTATGAAGAATGTC
* * * * * *
33422 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTC
1 ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
* * *
33461 ACTTTTTTCGGTTGCCAATCG-AAATGGTTATGAAGAATGAC
1 AC-ATTTTAGGTTG-CAATCGAAAAT-GTTATGAAGAATGTC
*
33502 ACATTTTAAGTTGCAATCGAAAATGTTATGAAGAATGTC
1 ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
33541 ACATTTTAGGTTG
1 ACATTTTAGGTTG
33554 TGTCCAACCT
Statistics
Matches: 136, Mismatches: 31, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
39 56 0.41
40 40 0.29
41 40 0.29
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (39 bp):
ACATTTTAGGTTGCAATCGAAAATGTTATGAAGAATGTC
Found at i:33835 original size:41 final size:40
Alignment explanation
Indices: 33780--33913 Score: 153
Period size: 41 Copynumber: 3.3 Consensus size: 40
33770 AACATTTTTT
*
33780 GTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCG
1 GTTGCAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
* * * * * **
33820 GTTGTCAATCGAAAATGTTATGAAGAATGACAC-ATTTTAA
1 GTTG-CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
* *
33860 GTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCG
1 GTTGCAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
33900 GTTGCCAATCGAAA
1 GTTG-CAATCGAAA
33914 TGGTTATGAA
Statistics
Matches: 73, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
39 22 0.30
40 20 0.27
41 31 0.42
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (40 bp):
GTTGCAATCGAAAATGTAACGAAAAATGTCACTTTTTTCG
Found at i:33865 original size:80 final size:80
Alignment explanation
Indices: 33771--33984 Score: 306
Period size: 80 Copynumber: 2.7 Consensus size: 80
33761 CTTCTTCGTA
**
33771 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCGAAAAT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCG-AAAT
33836 -GTTATGAAGAATGAC
65 GGTTATGAAGAATGAC
* *
33851 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCGAAATG
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCGAAATG
33916 GTTATGAAGAATGAC
66 GTTATGAAGAATGAC
* * * * * * *
33931 ACATTTTAAGTTACAATCGAAAATGTTATGAAGAATGTCAC-ATTTTAGGTTGTC
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTC
33985 CAACCTAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
79 14 0.12
80 106 0.88
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (80 bp):
ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGTCAATCGAAATG
GTTATGAAGAATGAC
Found at i:33948 original size:39 final size:39
Alignment explanation
Indices: 33825--33977 Score: 164
Period size: 39 Copynumber: 3.9 Consensus size: 39
33815 TTTCGGTTGT
*
33825 CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTG
1 CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTA
* * * * * * * ** *
33864 CAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGC
1 CAATCGAAAATGTTATGAAGAATGACAC-ATTTTAAGTT-A
33905 CAATCG-AAATGGTTATGAAGAATGACACATTTTAAGTTA
1 CAATCGAAAAT-GTTATGAAGAATGACACATTTTAAGTTA
*
33944 CAATCGAAAATGTTATGAAGAATGTCACATTTTA
1 CAATCGAAAATGTTATGAAGAATGACACATTTTA
33978 GGTTGTCCAA
Statistics
Matches: 89, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
39 50 0.56
40 22 0.25
41 17 0.19
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (39 bp):
CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTA
Found at i:34240 original size:39 final size:39
Alignment explanation
Indices: 34197--34401 Score: 137
Period size: 41 Copynumber: 5.2 Consensus size: 39
34187 CTTCGTAACA
34197 TTTTTT-GTTGCAATCTAAAATGTAACGAAAAATGTCAC
1 TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
* * * * * * *
34235 TTTTTTCGGTTTCCAATCGAAAATGTTATGAAGAATGACAC
1 TTTTTT-AG-TTGCAATCTAAAATGTAACGAAAAATGTCAC
* * *
34276 ATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCAC
1 TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
* * * * * *
34315 TTTTTTCGGTTGCCAATC-GAAATGGTTATGAAGAATGACAC
1 TTTTTT-AGTTG-CAATCTAAAAT-GTAACGAAAAATGTCAC
* * * * * *
34356 ATTTTAAATTGCAATCGAAAATGTTATGAAAAATGTCA-
1 TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
*
34394 TATTTTAG
1 TTTTTTAG
34402 GTTATGTCCA
Statistics
Matches: 124, Mismatches: 36, Indels: 14
0.71 0.21 0.08
Matches are distributed among these distances:
38 10 0.08
39 47 0.38
40 17 0.14
41 50 0.40
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (39 bp):
TTTTTTAGTTGCAATCTAAAATGTAACGAAAAATGTCAC
Found at i:34258 original size:41 final size:41
Alignment explanation
Indices: 34207--34336 Score: 138
Period size: 41 Copynumber: 3.2 Consensus size: 41
34197 TTTTTTGTTG
*
34207 CAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
1 CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
* * * * * ** *
34248 CAATCGAAAATGTTATGAAGAATGACAC-ATTTTAAG-TTG
1 CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
* * *
34287 CAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGC
1 CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
34328 CAATCGAAA
1 CAATCGAAA
34337 TGGTTATGAA
Statistics
Matches: 66, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
39 24 0.36
40 10 0.15
41 32 0.48
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (41 bp):
CAATCGAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTC
Found at i:34288 original size:80 final size:80
Alignment explanation
Indices: 34194--34393 Score: 312
Period size: 80 Copynumber: 2.5 Consensus size: 80
34184 CTTCTTCGTA
** *
34194 ACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTTCCAATCGAAAAT
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCG-AAAT
34259 -GTTATGAAGAATGAC
65 GGTTATGAAGAATGAC
*
34274 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGGTCACTTTTTTCGGTTGCCAATCGAAATG
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
34339 GTTATGAAGAATGAC
66 GTTATGAAGAATGAC
* * * *
34354 ACATTTTAAATTGCAATCGAAAATGTTATGAAAAATGTCA
1 ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCA
34394 TATTTTAGGT
Statistics
Matches: 110, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 4 0.04
80 106 0.96
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (80 bp):
ACATTTTAAGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTTGCCAATCGAAATG
GTTATGAAGAATGAC
Found at i:34289 original size:423 final size:425
Alignment explanation
Indices: 33328--34614 Score: 2391
Period size: 423 Copynumber: 3.0 Consensus size: 425
33318 ACTTAAAATA
33328 TGACATTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGT
1 TGAC-TTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGT
*
33393 TGCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
65 TTCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
33458 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAA
130 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAA
*
33523 AATGTTATGAAGAATGTCACATTTTAGGTTGTGTCCAACCTAAAATATTATGTATTTTTATCATA
195 AATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATA
*
33588 TTTTCTGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTA
260 TTTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTA
*
33653 CCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTCCCCCCCCCCCAAGTGAT
325 CCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTT----TCCCCCCAAGTGAT
33718 TGTGCTTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCGC
386 TGTGCTTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCGC
*
33758 TTACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
1 TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
33823 GT-CAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
66 -TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAG
*
33887 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTACAATCGAA
130 GTCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAA
33952 AATGTTATGAAGAATGTCACATTTTAGG-T-TGTCCAACCTAAAATATTATGTATTTTTATCATA
195 AATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATA
34015 TTTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTA
260 TTTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTA
*
34080 CCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGCGATTGTG
325 CCCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGTGATTGTG
34145 CTTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCGC
390 CTTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCGC
34181 TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
1 TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
34246 TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGG
66 TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGG
*
34311 TCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAATTGCAATCGAAA
131 TCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAAA
* *
34376 ATGTTATGAAAAATGTCATATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATAT
196 ATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATAT
34441 TTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTAC
261 TTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTAC
*
34506 CCGAGGCAATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGTGATTGTGC
326 CCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGTGATTGTGC
*
34571 TTCATGCTGCCATCTTTTTGTCTGTTAGGGGGCGC
391 TTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCGC
34606 TGACTTCTT
1 TGACTTCTT
34615 GCAGTAATGT
Statistics
Matches: 839, Mismatches: 14, Indels: 13
0.97 0.02 0.02
Matches are distributed among these distances:
422 1 0.00
423 267 0.32
424 1 0.00
425 206 0.25
427 145 0.17
428 1 0.00
429 215 0.26
430 3 0.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (425 bp):
TGACTTCTTCGTAACATTTTTTGTTGCAATCTAAAATGTAACGAAAAATGTCACTTTTTTCGGTT
TCCAATCGAAAATGTTATGAAGAATGACACATTTTAAGTTGCAATCTAAAATGTAACGAAAAAGG
TCACTTTTTTCGGTTGCCAATCGAAATGGTTATGAAGAATGACACATTTTAAGTTGCAATCGAAA
ATGTTATGAAGAATGTCACATTTTAGGTTATGTCCAACCTAAAATATTATGTATTTTTATCATAT
TTTCGGTCGCTTCATGTATGCATCGGTTTTTAGTCATGTATGCATAGGTTGTACCGCAAAATTAC
CCGAGGCCATGAATGTTGAGTATGACTGTGGCTTGTACTTGCATTTTCCCCCCAAGTGATTGTGC
TTCATGCTGCCATTTTTTTGTCTGTTAGGGGGCGC
Found at i:47899 original size:23 final size:23
Alignment explanation
Indices: 47873--47917 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47863 CACCACAGCT
*
47873 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
47896 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
47918 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:54710 original size:23 final size:23
Alignment explanation
Indices: 54684--54728 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
54674 CACCACAGCT
*
54684 CGTATAAATGCACC-TAAGTGCCC
1 CGTAGAAATGCACCGT-AGTGCCC
*
54707 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGTAGTGCC
54729 ATATAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCCC
Found at i:57452 original size:17 final size:19
Alignment explanation
Indices: 57410--57452 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
57400 AATATTTGGG
57410 AAATTGTGAAGCAGATATC
1 AAATTGTGAAGCAGATATC
*
57429 AAGTTGTGAAGCAG-T-TC
1 AAATTGTGAAGCAGATATC
57446 AAATTGT
1 AAATTGT
57453 ACATAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 13 0.59
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (19 bp):
AAATTGTGAAGCAGATATC
Found at i:58591 original size:7 final size:7
Alignment explanation
Indices: 58571--58640 Score: 54
Period size: 7 Copynumber: 10.1 Consensus size: 7
58561 TCACATAATC
58571 GGATTTA
1 GGATTTA
*
58578 GGGTTTA
1 GGATTTA
*
58585 TGATTTA
1 GGATTTA
58592 GGATTTA
1 GGATTTA
* *
58599 AGAGTTA
1 GGATTTA
*
58606 GGGTTTA
1 GGATTTA
58613 GGA-TTA
1 GGATTTA
58619 TGG-TTTA
1 -GGATTTA
*
58626 GGTTTTA
1 GGATTTA
*
58633 GGGTTTA
1 GGATTTA
58640 G
1 G
58641 TGTTAATTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
6 5 0.10
7 44 0.90
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (7 bp):
GGATTTA
Found at i:58591 original size:14 final size:14
Alignment explanation
Indices: 58571--58640 Score: 79
Period size: 14 Copynumber: 5.1 Consensus size: 14
58561 TCACATAATC
58571 GGATTTAGGGTTTA
1 GGATTTAGGGTTTA
* *
58585 TGATTTAGGATTTA
1 GGATTTAGGGTTTA
* *
58599 AGAGTTAGGGTTTA
1 GGATTTAGGGTTTA
*
58613 GGA-TTATGGTTTA
1 GGATTTAGGGTTTA
*
58626 GGTTTTAGGGTTTA
1 GGATTTAGGGTTTA
58640 G
1 G
58641 TGTTAATTAC
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
13 11 0.24
14 35 0.76
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (14 bp):
GGATTTAGGGTTTA
Found at i:58767 original size:11 final size:11
Alignment explanation
Indices: 58751--58813 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
58741 GTATTATAGA
58751 ATTTTTAATAT
1 ATTTTTAATAT
58762 ATTTTTAA-A-
1 ATTTTTAATAT
58771 ATTTTATAAT-T
1 ATTTT-TAATAT
*** *
58782 ATCAATAATGT
1 ATTTTTAATAT
58793 ATTTTTAATAT
1 ATTTTTAATAT
58804 ATTTTTAATA
1 ATTTTTAATA
58814 ATGTAATTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:62289 original size:18 final size:19
Alignment explanation
Indices: 62257--62296 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
62247 TATAACTTTT
*
62257 AAAATAAATAGAATCTTAA
1 AAAATAAATAGAATCATAA
*
62276 AAAATAACTA-AATCATAA
1 AAAATAAATAGAATCATAA
62294 AAA
1 AAA
62297 TTAAGAGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAATAAATAGAATCATAA
Found at i:62370 original size:72 final size:70
Alignment explanation
Indices: 62270--62402 Score: 160
Period size: 72 Copynumber: 1.9 Consensus size: 70
62260 ATAAATAGAA
* * * *
62270 TCTTAAAAAATAACTAAATCATAAAAATTAAGAGACTGTAA-GTTTAATTTCATTAATTTTAAAA
1 TCTTAAAAAATAACTAAACCAGAAAAATT-AGAGA-T-TAAGGCTTAATTCCATTAATTTTAAAA
62334 CTCAAATG
63 CTCAAATG
* * * *
62342 TCTTAAAATATAATTAAACCAGATAAATTTGAGATTAAGGCTTAATTCCATTAATTTTAAA
1 TCTTAAAAAATAACTAAACCAGAAAAATTAGAGATTAAGGCTTAATTCCATTAATTTTAAA
62403 CTTTACAGTG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
69 3 0.06
70 21 0.40
71 4 0.08
72 24 0.46
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (70 bp):
TCTTAAAAAATAACTAAACCAGAAAAATTAGAGATTAAGGCTTAATTCCATTAATTTTAAAACTC
AAATG
Found at i:62445 original size:71 final size:70
Alignment explanation
Indices: 62313--62446 Score: 166
Period size: 70 Copynumber: 1.9 Consensus size: 70
62303 GACTGTAAGT
* *
62313 TTAATTTCATTAATTTTAAAACTCAAATGTCTTAAAATATAATTAAACCAGATAAATTTGAGATT
1 TTAATTCCATTAATTTTAAAACTCAAATGTCTAAAAATATAATTAAACCAGATAAATTTGAGATT
62378 AAGGC
66 AAGGC
* * *
62383 TTAATTCCATTAATTTT-AAACTTTACAGTGTCCTAAAAAT-TAATTATACCAGA-AAATGTTGA
1 TTAATTCCATTAATTTTAAAAC-TCA-AATGT-CTAAAAATATAATTAAACCAGATAAAT-TTGA
62445 GA
62 GA
62447 GGAATAAAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
69 4 0.07
70 22 0.40
71 22 0.40
72 7 0.13
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (70 bp):
TTAATTCCATTAATTTTAAAACTCAAATGTCTAAAAATATAATTAAACCAGATAAATTTGAGATT
AAGGC
Found at i:63803 original size:6 final size:6
Alignment explanation
Indices: 63792--63816 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
63782 TAATTTAATT
63792 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
63817 ATATTTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:63826 original size:20 final size:21
Alignment explanation
Indices: 63779--63828 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
63769 CATATTATTA
* *
63779 ATTTAATTTAATTATATAAAT
1 ATTTAATATAAATATATAAAT
*
63800 A-TAAATATAAATATA-AAAT
1 ATTTAATATAAATATATAAAT
63819 ATTTAATATA
1 ATTTAATATA
63829 TTAATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.21
20 18 0.75
21 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTAATATAAATATATAAAT
Found at i:84015 original size:41 final size:41
Alignment explanation
Indices: 83936--84016 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
83926 TATTTTTAAG
* **
83936 TTATATTAAGAATAAAATATTTTTTTAATTAAACATATATT
1 TTATATTAAGAATAAAATATATTAATAATTAAACATATATT
83977 TTATATTAA-AATAAAATATATTAATAAGTTAAGA-ATATAT
1 TTATATTAAGAATAAAATATATTAATAA-TTAA-ACATATAT
84017 ATATAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 15 0.43
41 19 0.54
42 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (41 bp):
TTATATTAAGAATAAAATATATTAATAATTAAACATATATT
Done.