Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001816.1 Hibiscus syriacus cultivar Beakdansim tig00003676_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: 67067
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2757 original size:30 final size:30
Alignment explanation
Indices: 2723--2789 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
2713 TATAATTTGG
* *
2723 AAAGTTTAAGGATTAAAAAGGTAATTTTCA
1 AAAGTTTAAGGATAAAAAAGGTAATTTCCA
* *
2753 AAAGTTTGAGGATAAAAAATGTAATTTCCA
1 AAAGTTTAAGGATAAAAAAGGTAATTTCCA
2783 AAA-TTTA
1 AAAGTTTA
2790 GTTGTTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (30 bp):
AAAGTTTAAGGATAAAAAAGGTAATTTCCA
Found at i:21691 original size:54 final size:54
Alignment explanation
Indices: 21626--21733 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 54
21616 CCACTATCAC
* *
21626 AAGCAAGTTCTCCACAATACAACTAGGATGCACGGCATAGCGATCAACAAGTTA
1 AAGCAAGTTCTCCACAATACAACTAGGATGCACGACAGAGCGATCAACAAGTTA
* *
21680 AAGCATGTTCTCTACAATACAACTAGGATGCACGACAGAGCGATCAACAAGTTA
1 AAGCAAGTTCTCCACAATACAACTAGGATGCACGACAGAGCGATCAACAAGTTA
21734 CAAAGTAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (54 bp):
AAGCAAGTTCTCCACAATACAACTAGGATGCACGACAGAGCGATCAACAAGTTA
Found at i:26502 original size:54 final size:54
Alignment explanation
Indices: 26390--26806 Score: 462
Period size: 54 Copynumber: 7.9 Consensus size: 54
26380 TGGATATGGA
* * * * * *
26390 AATTTACAAACTCATTATGAATTTCCGTGGGTTGCACACATAGTGCTAATACGAT
1 AATTCACAAACTCATTATGAA-TTACTTAGGTTGCACACATAGTGCCAATACGGT
* *
26445 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACGTAGTGCCAATATGGT
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
* * * **
26499 AATTCGCAAACTCATTATGAATTATTTAGGTTGCATACATAGTGTTAATACGGT
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
* * * *
26553 AATTCATAAACTC----------A--TAGGTTACACATATAGTTCCAATACGGT
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
*
26595 AATTCATAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
* * *
26649 AATTCACAAACTCATTATGAATTACATAGGTTACACACATAGTTCCAATACGGT
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
* *
26703 AATTCACAAACTCATTATAAATTACTTAGGTTGCACACATAGTGCCAATACAGT
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
* * * * * * * *
26757 CAGTCATAAACTCATTATGAATTTCGTGGGTTGCACAAATAGTGTCAATA
1 AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATA
26807 GTACACATAG
Statistics
Matches: 306, Mismatches: 44, Indels: 25
0.82 0.12 0.07
Matches are distributed among these distances:
42 35 0.11
44 1 0.00
52 1 0.00
54 249 0.81
55 20 0.07
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (54 bp):
AATTCACAAACTCATTATGAATTACTTAGGTTGCACACATAGTGCCAATACGGT
Found at i:26616 original size:150 final size:150
Alignment explanation
Indices: 26419--26717 Score: 447
Period size: 150 Copynumber: 2.0 Consensus size: 150
26409 AATTTCCGTG
* * *
26419 GGTTGCACACATAGTGCTAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACG
1 GGTTACACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACA
* * ** * * *
26484 TAGTGCCAATATGGTAATTCGCAAACTCATTATGAATTATTTAGGTTGCATACATAGTGT-TAAT
66 TAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTACACACATAGT-TCCAAT
*
26548 ACGGTAATTCATAAACTCATA
130 ACGGTAATTCACAAACTCATA
* * * *
26569 GGTTACACATATAGTTCCAATACGGTAATTCATAAACTCATTATGAATTACTTAGGTTGCACACA
1 GGTTACACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACA
26634 TAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTACACACATAGTTCCAATA
66 TAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTACACACATAGTTCCAATA
26699 CGGTAATTCACAAACTCAT
131 CGGTAATTCACAAACTCAT
26718 TATAAATTAC
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
149 1 0.01
150 132 0.99
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (150 bp):
GGTTACACACATAGTGCCAATACGATAATTCACAAACTCATTATGAATTACTTAGGTTGCACACA
TAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACATAGGTTACACACATAGTTCCAATA
CGGTAATTCACAAACTCATA
Found at i:31035 original size:54 final size:54
Alignment explanation
Indices: 30793--31015 Score: 347
Period size: 54 Copynumber: 4.1 Consensus size: 54
30783 TGTGTGGTAC
* * *
30793 ATGAATTACTTAGGTTGCACACATAGTTCCAATACGGTAATTCATAAACTCGTT
1 ATGAATTACTTAGGTTGCACACATAGTGCCAATACGGTAATTCACAAACTCATT
* * *
30847 ATGAATTACTTAGGTTGTACACATAGTGGCAATACGGTAATACACAAACTCATT
1 ATGAATTACTTAGGTTGCACACATAGTGCCAATACGGTAATTCACAAACTCATT
30901 ATGAATTACTTAGGTTGCACACATAGTGCCAATACGGTAATTCACAAACTCATT
1 ATGAATTACTTAGGTTGCACACATAGTGCCAATACGGTAATTCACAAACTCATT
* * * * *
30955 ATGAATTACTTAGGTTGCACACATAGTACCAATATGATCATTCATAAACTCATT
1 ATGAATTACTTAGGTTGCACACATAGTGCCAATACGGTAATTCACAAACTCATT
31009 ATGAATT
1 ATGAATT
31016 TTGTGGGTTG
Statistics
Matches: 155, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 155 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (54 bp):
ATGAATTACTTAGGTTGCACACATAGTGCCAATACGGTAATTCACAAACTCATT
Found at i:34389 original size:81 final size:81
Alignment explanation
Indices: 34285--34847 Score: 702
Period size: 81 Copynumber: 7.0 Consensus size: 81
34275 TATAATTCTT
* *** * * * * * *
34285 TTATTCTTTTACCCAATTATATTTAGCCTTTCATCTAACTTGCATATTTGACACTTTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
* ** ** *
34350 ATGAACAACTAGTCCA
66 TTGCTCAGTTAGGCCA
* * *
34366 TTATTCTTTTACTAAACGGTATTTAA-C--TGATCTAATTGGCATAATTGACACCTTTT-TGCCA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTTATGCCA
34427 ATTGCTCAGTTAGGCCA
65 ATTGCTCAGTTAGGCCA
* * * *
34444 TTATTATTTTACTCAATGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTATGCAAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
*
34509 TTGCTCAGTTAGTCCA
66 TTGCTCAGTTAGGCCA
* *
34525 TTATTCTTTTACTCAACGGTATTTAATCGTTCATCTAACTGGCATAATTGACACATTTATGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
34590 TTGCTCAGTTAGGCCA
66 TTGCTCAGTTAGGCCA
* *
34606 TTATTCTTTTACTCAACGGTATTTAACCGTTTATCTAACTAGCATAATTGACACTTTTATGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
*
34671 TTTCTCAGTTAGGCCA
66 TTGCTCAGTTAGGCCA
* * * * * *
34687 TTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTGATACATATCTGCCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
*
34752 TTGCTCAGTTGGGCCA
66 TTGCTCAGTTAGGCCA
* * * * *
34768 TTATTCTTTTACTCAACGGTATTTAACTGTTCATCTAACTGGCATAATTAACACCTTTCTGTCAA
1 TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
* *
34833 ATGCACAGTTAGGCC
66 TTGCTCAGTTAGGCC
34848 TCAAAGGCAC
Statistics
Matches: 422, Mismatches: 55, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
78 57 0.14
79 6 0.01
80 5 0.01
81 354 0.84
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACTTTTATGCCAA
TTGCTCAGTTAGGCCA
Found at i:34896 original size:68 final size:68
Alignment explanation
Indices: 34797--35119 Score: 540
Period size: 68 Copynumber: 4.8 Consensus size: 68
34787 TATTTAACTG
* *
34797 TTCATCTAACTGGCATAATTAACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
34862 CCT
66 CCT
* * *
34865 TTCATCTAATTGGCATAATTGACACAATTCTGTCAAATCCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
34930 CCT
66 CCT
*
34933 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
34998 CCT
66 CCT
* *
35001 TTCATCTAACTGGCATAATTGACATC-TTTATGTCAAATGCACAGTTAGGACTCAAAGGCACTTA
1 TTCATCTAACTGGCATAATTGACA-CATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
*
35065 TCCT
65 GCCT
*
35069 TTCATCTAACTGGCATAATTGACACATTTATGTCAAATGCACAGTTAGGCC
1 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCC
35120 CATTAATCTT
Statistics
Matches: 239, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
67 1 0.00
68 237 0.99
69 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:35411 original size:54 final size:55
Alignment explanation
Indices: 35332--35478 Score: 206
Period size: 55 Copynumber: 2.7 Consensus size: 55
35322 ACATATATTT
* * * * * *
35332 CCCATACGGAAATTAATATAGTTAGTATGGATTTTTTAG-TTTGCACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTG
*
35386 CCCATACGGATATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTG
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTG
* *
35441 TCCATACCGAAATTCATACACTTAGTATGAATTTCTTA
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTA
35479 AGATTTTGCA
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
54 33 0.40
55 49 0.60
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (55 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTG
Found at i:40163 original size:81 final size:81
Alignment explanation
Indices: 40058--40622 Score: 686
Period size: 81 Copynumber: 7.0 Consensus size: 81
40048 TATAATTCTT
* * ** * * * * * *
40058 TTATTCTTTTACCCGATTATATTTAGCCTTTCATCTAACTTGCATATTTAACACTTTTCT-CTCA
1 TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGC-CA
* ** * *
40122 AATGAACAGCTAGTCCA
65 ATTGCTCAGTTAGGCCA
* *
40139 TTATTATTTTACTCAACGACATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
40204 TTGCTCAGTTAGGCCA
66 TTGCTCAGTTAGGCCA
* * * * * * *
40220 TTATTCTTTTTCTCAAGGGTATTTAACCGTTCATCTAACTGGCATAATTGAAACATTTATGCAAA
1 TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
40285 TTGCTCAGTTAGTCCA
66 TTGCTCAGTTAGGCCA
* * * *
40301 TTATTCTTTTAATCATCG-TATTTAATCGATCATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
40365 TTGCTCAGTTAGGCCA
66 TTGCTCAGTTAGGCCA
* * *
40381 TTATTCTTTTACCCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCTAA
1 TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
*
40446 TTGCTCAGTTAGACCA
66 TTGCTCAGTTAGGCCA
* * * * *
40462 TTATTCTTTTACTCAAC-AGTATTTAACCGTTCATCTAACTAGCATAATTGATACATTTATGCGA
1 TTATTCTTTTACTCAACGA-TATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCA
* *
40526 ATTGCTCAATTGGGCCA
65 ATTGCTCAGTTAGGCCA
* * *
40543 TTATTCTTTTACTCAACGGTATTTAACAGTTCATCTAACTGGCATAATTGACACCTTTCTGTCAA
1 TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
* *
40608 ATGCACAGTTAGGCC
66 TTGCTCAGTTAGGCC
40623 TCAAAGGCAC
Statistics
Matches: 413, Mismatches: 67, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
80 70 0.17
81 342 0.83
82 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.38
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
TTGCTCAGTTAGGCCA
Found at i:40520 original size:242 final size:243
Alignment explanation
Indices: 40088--40622 Score: 779
Period size: 242 Copynumber: 2.2 Consensus size: 243
40078 ATTTAGCCTT
* * * * * * * *
40088 TCATCTAACTTGCATATTTAACACTTTTCT-CTCAAATGAACAGCTAGTCCATTATTATTTTACT
1 TCATCTAACTGGCATAATTGACACCTTTCTGC-CAAATGCACAGTTAGGCCATTATTATTTTACC
*
40152 CAACGACATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCTCAGTTAGG
65 CAACGACATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCTCAGTTAGA
* ** *
40217 CCATTATTCTTTTTCTCAAGGGTATTTAACCGTTCATCTAACTGGCATAATTGAAACATTTATGC
130 CCATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTGAAACATTTATGC
* * *
40282 AAATTGCTCAGTTAGTCCATTATTCTTTTAATCATC-GTATTTAATC-GA
195 AAATTGCTCAATTAGGCCATTATTCTTTTAATCAACGGTATTTAA-CAGA
* * *
40330 TCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCTCAGTTAGGCCATTATTCTTTTACCC
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATTATTATTTTACCC
** *
40395 AACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCTAATTGCTCAGTTAGAC
66 AACGACATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCTCAGTTAGAC
* *
40460 CATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTGATACATTTATGCG
131 CATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTGAAACATTTATGCA
* * *
40525 AATTGCTCAATTGGGCCATTATTCTTTTACTCAACGGTATTTAACAGT
196 AATTGCTCAATTAGGCCATTATTCTTTTAATCAACGGTATTTAACAGA
*
40573 TCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCC
1 TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCC
40623 TCAAAGGCAC
Statistics
Matches: 260, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
242 203 0.78
243 57 0.22
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.37
Consensus pattern (243 bp):
TCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATTATTATTTTACCC
AACGACATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAATTGCTCAGTTAGAC
CATTATTCTTTTACTCAACAGTATTTAACCGTTCATCTAACTAGCATAATTGAAACATTTATGCA
AATTGCTCAATTAGGCCATTATTCTTTTAATCAACGGTATTTAACAGA
Found at i:40663 original size:68 final size:68
Alignment explanation
Indices: 40572--40894 Score: 513
Period size: 68 Copynumber: 4.8 Consensus size: 68
40562 TATTTAACAG
40572 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
40637 CCT
66 CCT
* * *
40640 TTCATCTAATTGGCATAATTGACACCATTCTGTCAGATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
40705 GCT
66 CCT
40708 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
*
40773 -CA
66 CCT
* * * *
40775 TTCATCTAACTAGCATAATTGACATCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
40840 CCT
66 CCT
* * * * *
40843 TTCATCTAATTGGCATAATTGACACATTTATGTGAAATGCACAATTAGGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
40895 ATTAATCTTT
Statistics
Matches: 235, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
67 62 0.26
68 173 0.74
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:40857 original size:135 final size:136
Alignment explanation
Indices: 40572--40894 Score: 513
Period size: 135 Copynumber: 2.4 Consensus size: 136
40562 TATTTAACAG
40572 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
* * * * *
40637 CCTTTCATCTAATTGGCATAATTGACACCATTCTGTCAGATGCACAGTTAGGCCTCAAAGGCACT
66 CCATTCATCTAACTAGCATAATTGACACCATTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
40702 TAGGCT
131 TAGCCT
40708 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
* *
40773 -CATTCATCTAACTAGCATAATTGACATCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
66 CCATTCATCTAACTAGCATAATTGACACCATTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
*
40837 TATCCT
131 TAGCCT
* * * * *
40843 TTCATCTAATTGGCATAATTGACACATTTATGTGAAATGCACAATTAGGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
40895 ATTAATCTTT
Statistics
Matches: 173, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
135 108 0.62
136 65 0.38
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (136 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCATTCATCTAACTAGCATAATTGACACCATTATGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TAGCCT
Found at i:41219 original size:55 final size:55
Alignment explanation
Indices: 41105--41272 Score: 221
Period size: 55 Copynumber: 3.0 Consensus size: 55
41095 ACATATATTT
* * ** * *
41105 CCCATACAGAAATTGATACTGTTAGTATGGATTTTTTAG-TTTGCACACATAGTG
1 CCCATACCGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
* *
41159 CCCATACGGATATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
1 CCCATACCGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
* *
41214 CCCATACCGAAATTCATACACTTAGTATGAATTTCTTAAGTTTTTGCACCCTTAGTG
1 CCCATACCGAAATTCATACACTTAGTATGAATTTCTT-AG-TTTTGCACACATAGTG
41271 CC
1 CC
41273 ATTTGGTAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
54 32 0.32
55 50 0.50
56 2 0.02
57 16 0.16
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (55 bp):
CCCATACCGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACATAGTG
Found at i:46010 original size:81 final size:81
Alignment explanation
Indices: 45906--46400 Score: 630
Period size: 81 Copynumber: 6.1 Consensus size: 81
45896 TCAAATGCAT
* * *
45906 AGTTAGTCCATTATTATTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACC
1 AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
*
45971 TTTCTTCCAATTGCTC
66 TTTCTGCCAATTGCTC
* * * * *
45987 AGTTAGGTCATTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTGGCATAATTGACACT
1 AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
* *
46052 TTTATGCCAATTGCTT
66 TTTCTGCCAATTGCTC
* * * *
46068 AGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACTAATCATCTAACTGGCATAATTGACACA
1 AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
*
46133 TTTCTGCCAATTGCTA
66 TTTCTGCCAATTGCTC
* * * * *
46149 AGTTCGGCCATTATTCTTTTACTCAATGTTATTTAACCATTCATCTAACTTGCAAAATTGACACC
1 AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
* *
46214 TTTATGCCAATTTCTC
66 TTTCTGCCAATTGCTC
* ** * *
46230 AGTTAGGCCATTATTCATTTACTCAACGATATTTAATTATTCATCTAACTGGCATAATTAACACA
1 AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
*
46295 TTTCTACCAATTGCTC
66 TTTCTGCCAATTGCTC
* * * * * * *
46311 ATTTAGGACATTATTCTTTTACTCAACGTTATTTAATCGTTCATCTAACTTGCATAATTAACACC
1 AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
* * * *
46376 TTTATGTCAAATGCAC
66 TTTCTGCCAATTGCTC
46392 AGTTAGGCC
1 AGTTAGGCC
46401 TCAAAGGAAC
Statistics
Matches: 356, Mismatches: 58, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 356 1.00
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (81 bp):
AGTTAGGCCATTATTCTTTTACTCAACGATATTTAACCATTCATCTAACTGGCATAATTGACACC
TTTCTGCCAATTGCTC
Found at i:46103 original size:162 final size:162
Alignment explanation
Indices: 45834--46400 Score: 711
Period size: 162 Copynumber: 3.5 Consensus size: 162
45824 TATAATTCCT
* * * * * * * * * *
45834 TTATTCTTTTACCCAATTGTATTTAGCCTTTCATATAACTTGCATATTTGGCGCTTTTTTTGTCA
1 TTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTTGCATAATTGACAC-CTTTATGCCA
* * * **
45899 AATGCATAGTTAGTCCATTATTATTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAAT
65 AATGCACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACTATTCATCTAACTGGCATAAT
* * *
45964 TGACACCTTTCTTCCAATTGCTCAGTTAGGTCA
130 TGACACATTTCTACCAATTGCTCAGTTAGGACA
* *
45997 TTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTGGCATAATTGACACTTTTATGCCAA
1 TTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTTGCATAATTGACACCTTTATGCCAA
* ** * *
46062 TTGCTTAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACTAATCATCTAACTGGCATAATT
66 ATGCACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACTATTCATCTAACTGGCATAATT
* * * *
46127 GACACATTTCTGCCAATTGCTAAGTTCGGCCA
131 GACACATTTCTACCAATTGCTCAGTTAGGACA
* * *
46159 TTATTCTTTTACTCAATGTTATTTAACCATTCATCTAACTTGCAAAATTGACACCTTTATGCCAA
1 TTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTTGCATAATTGACACCTTTATGCCAA
* * * * *
46224 TTTCTCAGTTAGGCCATTATTCATTTACTCAACGATATTTAATTATTCATCTAACTGGCATAATT
66 ATGCACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACTATTCATCTAACTGGCATAATT
* *
46289 AACACATTTCTACCAATTGCTCATTTAGGACA
131 GACACATTTCTACCAATTGCTCAGTTAGGACA
* * * * * * *
46321 TTATTCTTTTACTCAACGTTATTTAATCGTTCATCTAACTTGCATAATTAACACCTTTATGTCAA
1 TTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTTGCATAATTGACACCTTTATGCCAA
46386 ATGCACAGTTAGGCC
66 ATGCACAGTTAGGCC
46401 TCAAAGGAAC
Statistics
Matches: 355, Mismatches: 49, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
162 309 0.87
163 46 0.13
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41
Consensus pattern (162 bp):
TTATTCTTTTACTCAATGGTATTTAACCATTCATATAACTTGCATAATTGACACCTTTATGCCAA
ATGCACAGTTAGGCCATTATTCTTTTACTCAACGATATTTAACTATTCATCTAACTGGCATAATT
GACACATTTCTACCAATTGCTCAGTTAGGACA
Found at i:46452 original size:68 final size:68
Alignment explanation
Indices: 46350--46537 Score: 245
Period size: 68 Copynumber: 2.8 Consensus size: 68
46340 TATTTAATCG
* * * *
46350 TTCATCTAACTTGCATAATTAAC-ACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGAACTTA
1 TTCATCTAACTAGCATAATTGACGA-ATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTA
46414 GCCT
65 GCCT
* **
46418 TTCATCTAACTATCATAATTGA-GAAATTTCTGTCAAATGCACAGTTAGGCCTCAAAGTCACTTA
1 TTCATCTAACTAGCATAATTGACG-AATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTA
46482 GCCT
65 GCCT
* ** *
46486 TTCATCTAACTGGCATAATTGACGCCTTTCTGTCAAATGTACAGTTAGGCCT
1 TTCATCTAACTAGCATAATTGACGAATTTCTGTCAAATGCACAGTTAGGCCT
46538 ATTAATCATT
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
68 103 0.98
69 2 0.02
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTAGCATAATTGACGAATTTCTGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAG
CCT
Found at i:46869 original size:55 final size:56
Alignment explanation
Indices: 46748--46900 Score: 188
Period size: 55 Copynumber: 2.8 Consensus size: 56
46738 ACATATATTT
* * *
46748 CCCATACAGAAATT-AATACCCTTAGTATGGATTTCTTAA--TTTACACACATAGTG
1 CCCATACAGAAATTCAA-ACACTTAGTATGAATTTCTTAAGTTTTAAACACATAGTG
* * *
46802 CCCATTCGGAAATTCAAACACTTAGTATGAATTTC-TAAGTTTTAAACACGTAGTG
1 CCCATACAGAAATTCAAACACTTAGTATGAATTTCTTAAGTTTTAAACACATAGTG
* * *
46857 CCCATACCGAAATTCATATACTTAGTATGAATTTCTTAAGTTTT
1 CCCATACAGAAATTCAAACACTTAGTATGAATTTCTTAAGTTTT
46901 TGCACCCTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.04
54 28 0.33
55 46 0.54
56 8 0.09
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (56 bp):
CCCATACAGAAATTCAAACACTTAGTATGAATTTCTTAAGTTTTAAACACATAGTG
Found at i:61528 original size:496 final size:496
Alignment explanation
Indices: 60595--61574 Score: 1780
Period size: 496 Copynumber: 2.0 Consensus size: 496
60585 ATAGCTGAAG
60595 AAATTATGCATCATGGTGTCCATCTTCTCCACTCACTCCTTAGTTTCTCAAGAGAAGCCCAATAT
1 AAATTATGCATCATGGTGTCCATCTTCTCCACTCACTCCTTAGTTTCTCAAGAGAAGCCCAATAT
* *
60660 AACTCTCATTCTTGCTACGATAATAGTTTTTGCACCTCTTACCAGGGTCTCCTTAGGTACATCTT
66 AACTCTCATTCTTGCTACGATAATAGTTTTTGCACCTCTTACCAGGGTCTCCTTAGGGACATCAT
* * *
60725 CATCAAAGCCCTTCAGCTCAACAATCAGCTTTACAGTTATGCCAACCTTTATTGGTATCGACTTT
131 CATCAAAGCCCTTCAGCTCAACAATCACCTTTACAGTTATGCCAACCTGTATTGGTATCAACTTT
* *
60790 TCGAACATCACTTCCACCACCTTTTTCTTTTCACATATGGTGATGATCAAGTTTTAAAAGATCAA
196 TCGAACATCACTTCCACCACCTTTTTCCTTTCACATATGGCGATGATCAAGTTTTAAAAGATCAA
* * *
60855 TGTGACCTTTATCTGCTTGATATAATTATATACTTGTCGGTCGATGACCTTGATGATATTGATTG
261 TGTGACCTTTATCTGATTGATATAATTATATACTTGTCGGACGATGACCTTGATGATATTGATCG
* *
60920 GTCATCTAAAAATTATGGAGTACAAAAGAAGCATCTGATGCAATGAGACAGTTGTATGGTGCGAG
326 GTCATCCAAAAATTATGGAGTACAAAACAAGCATCTGATGCAATGAGACAGTTGTATGGTGCGAG
60985 GTAGGCATTAATAGAGTTTTTAAGAAGTGATTCCATACATTTTCTTGGGGCCTAAGATAACTCAT
391 GTAGGCATTAATAGAGTTTTTAAGAAGTGATTCCATACATTTTCTTGGGGCCTAAGATAACTCAT
61050 TTACACACTCCATTTGCTCATGATTTCTCCACTCAGCTCAA
456 TTACACACTCCATTTGCTCATGATTTCTCCACTCAGCTCAA
*
61091 AAATTATGCATCATGGTGTCCATCTTCTCCACTCACTCCTTAGTTTCTCAAGAGAAGCCCACTAT
1 AAATTATGCATCATGGTGTCCATCTTCTCCACTCACTCCTTAGTTTCTCAAGAGAAGCCCAATAT
61156 AACTCTCATTCTTGCTACGATAATAGTTTTTGCACCTCTTACCAGGGTCTCCTTAGGGACATCAT
66 AACTCTCATTCTTGCTACGATAATAGTTTTTGCACCTCTTACCAGGGTCTCCTTAGGGACATCAT
*
61221 CATCAAAGCCCTTCAGCTCAATAATCACCTTTACAGTTATGCCAACCTGTATTGGTATCAACTTT
131 CATCAAAGCCCTTCAGCTCAACAATCACCTTTACAGTTATGCCAACCTGTATTGGTATCAACTTT
*
61286 TCGAACATCACTTCCACCACCTTTTTCCTTTCACATATGGCGGTGATCAAGTTTTAAAAGATCAA
196 TCGAACATCACTTCCACCACCTTTTTCCTTTCACATATGGCGATGATCAAGTTTTAAAAGATCAA
* * *
61351 TGTGCCCTTTTTCTTATTGATATAATTATATACTTGTCGGACGATGACCTTGATGATATTGATCG
261 TGTGACCTTTATCTGATTGATATAATTATATACTTGTCGGACGATGACCTTGATGATATTGATCG
*
61416 GTCATCCAAAAATTATGGAGTGCAAAACAAGCATCTGATGCAATGAGACAGTTGTATGGTGCGAG
326 GTCATCCAAAAATTATGGAGTACAAAACAAGCATCTGATGCAATGAGACAGTTGTATGGTGCGAG
*
61481 GTAGGTATTAATAGAGTTTTTAAGAAGTGATTCCATACATTTTCTTGGGGCCTAAGATAACTCAT
391 GTAGGCATTAATAGAGTTTTTAAGAAGTGATTCCATACATTTTCTTGGGGCCTAAGATAACTCAT
61546 TTACACACTCCATTTGCTCATGATTTCTC
456 TTACACACTCCATTTGCTCATGATTTCTC
61575 ACTTTCATTG
Statistics
Matches: 464, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
496 464 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (496 bp):
AAATTATGCATCATGGTGTCCATCTTCTCCACTCACTCCTTAGTTTCTCAAGAGAAGCCCAATAT
AACTCTCATTCTTGCTACGATAATAGTTTTTGCACCTCTTACCAGGGTCTCCTTAGGGACATCAT
CATCAAAGCCCTTCAGCTCAACAATCACCTTTACAGTTATGCCAACCTGTATTGGTATCAACTTT
TCGAACATCACTTCCACCACCTTTTTCCTTTCACATATGGCGATGATCAAGTTTTAAAAGATCAA
TGTGACCTTTATCTGATTGATATAATTATATACTTGTCGGACGATGACCTTGATGATATTGATCG
GTCATCCAAAAATTATGGAGTACAAAACAAGCATCTGATGCAATGAGACAGTTGTATGGTGCGAG
GTAGGCATTAATAGAGTTTTTAAGAAGTGATTCCATACATTTTCTTGGGGCCTAAGATAACTCAT
TTACACACTCCATTTGCTCATGATTTCTCCACTCAGCTCAA
Found at i:65298 original size:20 final size:20
Alignment explanation
Indices: 65273--65315 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
65263 TCTAAGAGCA
*
65273 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
65293 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
65313 CAT
1 CAT
65316 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Done.