Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 30 of 30
Found at i:5875388 original size:24 final size:24
Alignment explanation
Indices: 5875361--5875414 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5875351 GGATTTGAAA
* *
5875361 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTAGTCAATACCCGGAC
* *
5875385 TTTGATATTAGTCAATACTCGGAT
1 TTTGATATTAGTCAATACCCGGAC
5875409 TTTGAT
1 TTTGAT
5875415 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTAGTCAATACCCGGAC
Found at i:5877690 original size:18 final size:18
Alignment explanation
Indices: 5877667--5877702 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5877657 AAGAAAAAGG
*
5877667 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
5877685 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
5877703 CAACCAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:5878045 original size:20 final size:20
Alignment explanation
Indices: 5878020--5878087 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
5878010 AATCGCAACA
*
5878020 CGAATTTGACTTTCGTGTTG
1 CGAATTTGACTTTCGCGTTG
*
5878040 CGAATTTAACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
5878060 CGAATTT-ACCTTTCGCGTTG
1 CGAATTTGA-CTTTCGCGTTG
*
5878080 TGAATTTG
1 CGAATTTG
5878088 TACCCTTCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.02
20 42 0.98
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:5878229 original size:14 final size:14
Alignment explanation
Indices: 5878210--5878246 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5878200 ATCAAATTAA
5878210 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
5878224 ATAAATAAACTTTT
1 ACAAATCAACTTTT
5878238 ACAAATCAA
1 ACAAATCAA
5878247 TTAAACAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:5879722 original size:42 final size:42
Alignment explanation
Indices: 5879676--5879774 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
5879666 ACGGACGGGA
* * * *
5879676 CCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGAG
1 CCTCTTGAATGATGACAGGGGACTCTTGAACGATAGGAGGAG
* *
5879718 CCTCTTCG-ATGATGAGAGGGGACTCTTGAACGATAGGAGGCG
1 CCTCTT-GAATGATGACAGGGGACTCTTGAACGATAGGAGGAG
*
5879760 ACTCTTGAATGATGA
1 CCTCTTGAATGATGA
5879775 TAGGTGCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.34, T:0.22
Consensus pattern (42 bp):
CCTCTTGAATGATGACAGGGGACTCTTGAACGATAGGAGGAG
Found at i:5879757 original size:21 final size:20
Alignment explanation
Indices: 5879656--5879773 Score: 85
Period size: 21 Copynumber: 5.7 Consensus size: 20
5879646 GTGAATCGGG
* *
5879656 CTCTTGAACGACGGACGGGA
1 CTCTTGAACGATGGAGGGGA
* *
5879676 CCTCTTGAACGATGACAGGGGC
1 -CTCTTGAACGATG-GAGGGGA
* * *
5879698 CTCTTGAACGGTGGGAGGAGC
1 CTCTTGAACGAT-GGAGGGGA
*
5879719 CTCTTCG-ATGATGAGAGGGGA
1 CTCTT-GAACGATG-GAGGGGA
*
5879740 CTCTTGAACGATAGGAGGCGA
1 CTCTTGAACGAT-GGAGGGGA
*
5879761 CTCTTGAATGATG
1 CTCTTGAACGATG
5879774 ATAGGTGCAT
Statistics
Matches: 77, Mismatches: 14, Indels: 13
0.74 0.13 0.12
Matches are distributed among these distances:
20 3 0.04
21 67 0.87
22 7 0.09
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (20 bp):
CTCTTGAACGATGGAGGGGA
Found at i:5879950 original size:4 final size:4
Alignment explanation
Indices: 5879918--5879963 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
5879908 AGGCCGCTGA
* * * *
5879918 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
5879964 TGTCAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:5881967 original size:20 final size:20
Alignment explanation
Indices: 5881944--5881996 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
5881934 AAACTTAAAT
5881944 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
5881964 TCGCAACACAAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
5881984 TCGCAACGCGAAA
1 TCGCAACGCGAAA
5881997 CTAATATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.51, C:0.23, G:0.17, T:0.09
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:5882061 original size:20 final size:20
Alignment explanation
Indices: 5882036--5882206 Score: 120
Period size: 20 Copynumber: 8.6 Consensus size: 20
5882026 AAATTCAGTA
5882036 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGCG
* * *
5882056 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGCG
* * * *
5882076 TTGCGAATTTGTCTTTTGTG
1 TTGCGAATTTGACTATCGCG
*
5882096 TTGCGGATTTGACTATCGCG
1 TTGCGAATTTGACTATCGCG
*
5882116 TTGCGAATTTGACT-TCTGTG
1 TTGCGAATTTGACTATC-GCG
*
5882136 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGAC-TA-TCGCG
* * *
5882156 TTGCGAAATTAGA--AACTGTG
1 TTGCG-AATTTGACTATC-GCG
*
5882176 TTGCGAATTTGGAGT-TCGCG
1 TTGCGAATTT-GACTATCGCG
5882196 TTGCGAATTTG
1 TTGCGAATTTG
5882207 TTGGTCATTT
Statistics
Matches: 121, Mismatches: 19, Indels: 23
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.02
19 12 0.10
20 100 0.83
21 3 0.02
22 3 0.02
23 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:5882099 original size:40 final size:40
Alignment explanation
Indices: 5882036--5882206 Score: 143
Period size: 40 Copynumber: 4.3 Consensus size: 40
5882026 AAATTCAGTA
* * * * * *
5882036 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
* *
5882076 TTGCGAATTTGTCTTTTGTGTTGCGGATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
* *
5882116 TTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCGCG
* *** *
5882156 TTGCGAAATTAGA-AACTGTGTTGCGAATTTGGAGT-TCGCG
1 TTGCG-AATTTGACTTTTGTGTTGCGAATTT-GACTATCGCG
5882196 TTGCGAATTTG
1 TTGCGAATTTG
5882207 TTGGTCATTT
Statistics
Matches: 108, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
38 2 0.02
39 10 0.09
40 85 0.79
41 10 0.09
43 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.40
Consensus pattern (40 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
Found at i:5882159 original size:60 final size:60
Alignment explanation
Indices: 5882014--5882162 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 60
5882004 TGTGTTTCGC
* ** *
5882014 GTTGCGAATTTGAAATTCAGTATTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACATTC-GCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
* * * * *
5882075 GTTGCGAATTTGTCTTTTGTGTTGCGGATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
5882135 GTTGCG-ATTT-ACAGATTCGCGTTGCGAA
1 GTTGCGAATTTGAC--ATTCGCGTTGCGAA
5882163 ATTAGAAACT
Statistics
Matches: 74, Mismatches: 12, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
58 1 0.01
59 4 0.05
60 55 0.74
61 14 0.19
ACGTcount: A:0.19, C:0.15, G:0.26, T:0.41
Consensus pattern (60 bp):
GTTGCGAATTTGACATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
Found at i:5887343 original size:32 final size:31
Alignment explanation
Indices: 5887307--5887401 Score: 84
Period size: 32 Copynumber: 3.0 Consensus size: 31
5887297 GAGCCAACTT
* *
5887307 AAGGGAATATCTTGGTGCATGAGAGCCTACCA
1 AAGGGAATACCTTGG-GCATAAGAGCCTACCA
* * *
5887339 AAGGGAGTACCTTAGGGCTTAAGAGCCTACCC
1 AAGGGAATACCTT-GGGCATAAGAGCCTACCA
* *
5887371 AA-GGAAGTACCTTGGGGCCTTAGAGCCTACC
1 AAGGGAA-TACCTT-GGGCATAAGAGCCTACC
5887402 CAATGAAATG
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 3 0.06
32 47 0.90
33 2 0.04
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (31 bp):
AAGGGAATACCTTGGGCATAAGAGCCTACCA
Found at i:5887402 original size:32 final size:32
Alignment explanation
Indices: 5887328--5887437 Score: 132
Period size: 32 Copynumber: 3.4 Consensus size: 32
5887318 TTGGTGCATG
* * *
5887328 AGAGCCTACCAAAGGGAGTACCTTAGGG-CTT
1 AGAGCCTACCCAAGGAAGTACCTTGGGGCCTT
5887359 AAGAGCCTACCCAAGGAAGTACCTTGGGGCCTT
1 -AGAGCCTACCCAAGGAAGTACCTTGGGGCCTT
* * * *
5887392 AGAGCCTACCCAATGAAATGCCTTGGGGCCTC
1 AGAGCCTACCCAAGGAAGTACCTTGGGGCCTT
*
5887424 AAAGCCTACCCAAG
1 AGAGCCTACCCAAG
5887438 ATCACCTTAG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 65 0.96
33 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.25, T:0.17
Consensus pattern (32 bp):
AGAGCCTACCCAAGGAAGTACCTTGGGGCCTT
Found at i:5890068 original size:2 final size:2
Alignment explanation
Indices: 5890061--5890098 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5890051 TAAAACGATA
5890061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5890099 ATACAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5893055 original size:38 final size:39
Alignment explanation
Indices: 5892979--5893059 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
5892969 GGCAGTTCTG
5892979 TGGTTAACGGGTTTGAACCCGTGAAGAGGAGAGACTCCA
1 TGGTTAACGGGTTTGAACCCGTGAAGAGGAGAGACTCCA
* *
5893018 TGGTTAACGGGTTTGAACCCGTG-AGAGGGGAGGCTCCA
1 TGGTTAACGGGTTTGAACCCGTGAAGAGGAGAGACTCCA
5893056 TGGT
1 TGGT
5893060 AAATTACTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 17 0.43
39 23 0.57
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (39 bp):
TGGTTAACGGGTTTGAACCCGTGAAGAGGAGAGACTCCA
Found at i:5899650 original size:20 final size:20
Alignment explanation
Indices: 5899587--5899653 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
5899577 GTTTCCAAAT
*
5899587 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATTTGTAAA
*
5899607 TCACAACGCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
*
5899627 TCGCAACGCGAATTTGTAAT
1 TCGCAACGCGAATTTGTAAA
5899647 TCGCAAC
1 TCGCAAC
5899654 ACAGAAGTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:5899667 original size:20 final size:20
Alignment explanation
Indices: 5899644--5899688 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5899634 GCGAATTTGT
*
5899644 AATTCGCAACACAGAAGTTA
1 AATTCGCAACACAGAAGTCA
5899664 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
5899684 AATTC
1 AATTC
5899689 ACAAAGTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.13, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:5899671 original size:40 final size:41
Alignment explanation
Indices: 5899583--5899673 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 41
5899573 CTCAGTTTCC
* *
5899583 AAATTCGCAACGCGAATATGTAAATCACAACGCGAATTTGT
1 AAATTCGCAACGCGAATATGTAAATCACAACACGAATGTGT
* * *
5899624 AAA-TCGCAACGCGAATTTGTAATTCGCAACACAGAA-GT-T
1 AAATTCGCAACGCGAATATGTAAATCACAACAC-GAATGTGT
5899663 AAATTCGCAAC
1 AAATTCGCAAC
5899674 ACAGAAGTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 4 0.09
40 33 0.77
41 6 0.14
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (41 bp):
AAATTCGCAACGCGAATATGTAAATCACAACACGAATGTGT
Found at i:5899872 original size:22 final size:22
Alignment explanation
Indices: 5899847--5899897 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
5899837 CAACGGCGAC
5899847 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
5899869 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
5899891 ATCCGTC
1 ATCCGTC
5899898 TATCTCCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:5900287 original size:19 final size:20
Alignment explanation
Indices: 5900263--5900316 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
5900253 AAATCGCAAC
5900263 GCGATTTT-AGTTTCACGTT
1 GCGATTTTAAGTTTCACGTT
* *
5900282 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTAAGTTTCACGTT
5900301 GCGATTTTAAGTTTCA
1 GCGATTTTAAGTTTCA
5900317 GAAACTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (20 bp):
GCGATTTTAAGTTTCACGTT
Found at i:5902216 original size:21 final size:21
Alignment explanation
Indices: 5902192--5902284 Score: 107
Period size: 21 Copynumber: 4.4 Consensus size: 21
5902182 CTTGTCATAG
*
5902192 TTCAAGAGGCCTCTC-CTATCA
1 TTCAAGAGGCCCCTCTC-ATCA
* * *
5902213 TTCAAGATGCCCCTATCATCC
1 TTCAAGAGGCCCCTCTCATCA
*
5902234 TTCAAGAGGCCCCTCTCACCA
1 TTCAAGAGGCCCCTCTCATCA
* *
5902255 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCTCATCA
5902276 TTCAAGAGG
1 TTCAAGAGG
5902285 TATCTCCCAC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
21 59 0.98
22 1 0.02
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCATCA
Found at i:5902257 original size:42 final size:42
Alignment explanation
Indices: 5902192--5902284 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
5902182 CTTGTCATAG
* * *
5902192 TTCAAGAGGCCTCTCCTATCATTCAAGATGCCCCTATCATCC
1 TTCAAGAGGCCCCTCCTACCATTCAAGAGGCCCCTATCATCC
* *
5902234 TTCAAGAGGCCCCT-CTCACCATTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCT-ACCATTCAAGAGGCCCCTATCATCC
5902276 TTCAAGAGG
1 TTCAAGAGG
5902285 TATCTCCCAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 2 0.04
42 43 0.96
ACGTcount: A:0.24, C:0.34, G:0.17, T:0.25
Consensus pattern (42 bp):
TTCAAGAGGCCCCTCCTACCATTCAAGAGGCCCCTATCATCC
Found at i:5903702 original size:64 final size:64
Alignment explanation
Indices: 5903629--5903777 Score: 253
Period size: 64 Copynumber: 2.3 Consensus size: 64
5903619 AAATTGATGT
5903629 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
* * ***
5903693 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
5903757 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
5903778 GTTTTAAATT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
Found at i:5903867 original size:20 final size:20
Alignment explanation
Indices: 5903836--5903940 Score: 138
Period size: 20 Copynumber: 5.2 Consensus size: 20
5903826 AAGGTACACT
5903836 TTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*** **
5903856 TTCGCGTTGCGATGGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
5903876 TTCGCAACGTGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
5903896 TTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
*
5903916 TTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAA
5903936 TTCGC
1 TTCGC
5903941 GTTGCGATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTCAAA
Found at i:5903891 original size:40 final size:40
Alignment explanation
Indices: 5903836--5903948 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
5903826 AAGGTACACT
*
5903836 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATGGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
* **** *
5903876 TTCGCAACGTGAAAGTCAAATTCGCAACACGAAAGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
*
5903916 TTCGCAACACGAAAGTCAAATTCGCGTTGCGAT
1 TTCGCAACGCGAAAGTCAAATTCGCGTTGCGAT
5903949 TTCCCGTTTC
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (40 bp):
TTCGCAACGCGAAAGTCAAATTCGCGTTGCGATAGTCAAA
Found at i:5906468 original size:24 final size:24
Alignment explanation
Indices: 5906434--5906511 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
5906424 CTGAAACATC
* *
5906434 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAGTCCGGGTATTGACCAAT
5906458 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAGTCCGGGTATTGACCAAT
*
5906482 ATCAAAGTCTGGGTATTGACCAAT
1 ATCAAAGTCCGGGTATTGACCAAT
5906506 ATCAAA
1 ATCAAA
5906512 TTTTGAATAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (24 bp):
ATCAAAGTCCGGGTATTGACCAAT
Found at i:5906525 original size:24 final size:24
Alignment explanation
Indices: 5906450--5906525 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
5906440 ATCCGAGTAT
* ** *
5906450 TGACCAATATCAAAGTCCGGGTAT
1 TGACCAATATCAAAGTCTGAATAC
** *
5906474 TGACCAATATCAAAGTCTGGGTAT
1 TGACCAATATCAAAGTCTGAATAC
* *
5906498 TGACCAATATCAAATTTTGAATAC
1 TGACCAATATCAAAGTCTGAATAC
5906522 TGAC
1 TGAC
5906526 TAGTACTCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (24 bp):
TGACCAATATCAAAGTCTGAATAC
Found at i:5922847 original size:19 final size:20
Alignment explanation
Indices: 5922813--5922851 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5922803 ATATCCCTTC
5922813 TCCAAAAACTTGTAGTTTAT
1 TCCAAAAACTTGTAGTTTAT
5922833 TCCAAAAACTT-TAGTTTAT
1 TCCAAAAACTTGTAGTTTAT
5922852 AAAAAAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (20 bp):
TCCAAAAACTTGTAGTTTAT
Found at i:5922858 original size:19 final size:19
Alignment explanation
Indices: 5922816--5922864 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
5922806 TCCCTTCTCC
***
5922816 AAAAACTTGTAGTTTATTCC
1 AAAAACTT-TAGTTTATAAA
5922836 AAAAACTTTAGTTTATAAA
1 AAAAACTTTAGTTTATAAA
5922855 AAAATACTTT
1 AAAA-ACTTT
5922865 TTTGGTGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.39
Consensus pattern (19 bp):
AAAAACTTTAGTTTATAAA
Found at i:5930999 original size:21 final size:21
Alignment explanation
Indices: 5930973--5931012 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5930963 CCCCCTTTGA
*
5930973 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
5930994 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
5931013 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:5941102 original size:21 final size:21
Alignment explanation
Indices: 5941076--5941130 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
5941066 ATTTACCGTG
*
5941076 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGACGCT
*
5941097 ATTGCGGTCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGACGCT
5941118 ATTGCGGCCGTCG
1 ATTGCGGCCGTCG
5941131 TGGGTAACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.07, C:0.31, G:0.40, T:0.22
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGACGCT
Found at i:5942647 original size:10 final size:10
Alignment explanation
Indices: 5942632--5942658 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
5942622 GAAAGGGTGA
5942632 ACCACCAACG
1 ACCACCAACG
5942642 ACCACCAACG
1 ACCACCAACG
5942652 ACCACCA
1 ACCACCA
5942659 CCCCCATCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.52, G:0.07, T:0.00
Consensus pattern (10 bp):
ACCACCAACG
Found at i:5949194 original size:21 final size:21
Alignment explanation
Indices: 5949164--5949208 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
5949154 ATATTTTAAA
*
5949164 AAAATTTATT-TTTATATTATT
1 AAAATATATTATTTA-ATTATT
5949185 AAAATATATTATTTAATTATT
1 AAAATATATTATTTAATTATT
5949206 AAA
1 AAA
5949209 TATTATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATATATTATTTAATTATT
Found at i:5952364 original size:3 final size:3
Alignment explanation
Indices: 5952356--5952383 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5952346 AATTACAAGA
5952356 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5952384 TTTTTAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5952930 original size:66 final size:66
Alignment explanation
Indices: 5952770--5953327 Score: 625
Period size: 65 Copynumber: 8.6 Consensus size: 66
5952760 AGGGATAATG
* * * *
5952770 GTTTCAAGACAAACCGTCTCAAGAGAGATC-AAAC-TTGTTTCAAGGGAAACAACCTCAATG-TT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGA-CAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATT
5952832 TGT
65 T-T
* * * * *
5952835 ATTTAAAGGGAAACTGTCTCAAGAGAGACAAAAC-TTGTTTAAAGGGAAACAAACTAAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
5952899 GT
66 -T
* * *
5952901 GTTTCAAGAGAAACTGTCTTAAGGGAGACAAAAC-TTGTTTCAAGGGAAAC-AACTCAAAGATTA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
5952964 T
66 T
* * * * *
5952965 -TTTCAAGAAAAACTATCTC-A-AGAGACAAATCTTTGTTTCAAGAGAAACATACTCAAAGACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA-TT
5953027 TT
65 TT
* * *
5953029 GTTTCAAGAG-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACAGACTCAAAAACTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA-TT
5953093 TT
65 TT
* * *
5953095 GTTTCAATAGAAATTGTCTC-A-AGAGACAAAACTTTGTTTCAAGAGAAACAAACTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA-TT
5953158 TT
65 TT
* * *
5953160 ATTTCAA-A-ATAA-TGTCTCAAGAGAGATAAAACTTTGTTTCAAGGGAAACATACTCAAAGATT
1 GTTTCAAGAGA-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGA-T
5953222 TTT
64 TTT
* *
5953225 ATTTCAA-A-ATAA-TGTCTCAAAAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATT
1 GTTTCAAGAGA-AACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATT
5953287 TT
65 TT
* *
5953289 -TTTCAAGAGAAATTGTCTCAAGAGAGATAAAA-TTTGTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTT
5953328 TGAGTAAAAA
Statistics
Matches: 430, Mismatches: 48, Indels: 31
0.84 0.09 0.06
Matches are distributed among these distances:
61 9 0.02
62 16 0.04
63 38 0.09
64 31 0.07
65 230 0.53
66 98 0.23
67 8 0.02
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.28
Consensus pattern (66 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACAAACTCAAAGATTT
T
Found at i:5953030 original size:30 final size:30
Alignment explanation
Indices: 5952935--5953040 Score: 103
Period size: 35 Copynumber: 3.5 Consensus size: 30
5952925 GAGACAAAAC
*
5952935 TTGTTTCAAGGGAAACA-ACTCAAAGA-TT
1 TTGTTTCAAGAGAAACATACTCAAAGACTT
* *
5952963 AT-TTTCAAGAAAAAC-TATCTCAAGAGACAAATCT
1 TTGTTTCAAGAGAAACATA-CTCAA-AGAC---T-T
5952997 TTGTTTCAAGAGAAACATACTCAAAGACTT
1 TTGTTTCAAGAGAAACATACTCAAAGACTT
5953027 TTGTTTCAAGAGAA
1 TTGTTTCAAGAGAA
5953041 CTGTCTCAAG
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
27 12 0.19
28 6 0.10
29 3 0.05
30 15 0.24
31 1 0.02
33 1 0.02
34 6 0.10
35 17 0.27
36 2 0.03
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (30 bp):
TTGTTTCAAGAGAAACATACTCAAAGACTT
Found at i:5954809 original size:24 final size:24
Alignment explanation
Indices: 5954759--5954810 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5954749 TCTTGTCCCC
* *
5954759 TTTTCTTTGTTTTTCTTTGCTTAT
1 TTTTCTTTGTTTTTATTTCCTTAT
*
5954783 TTTTCTTGTTTTTTTATTTCCTT-T
1 TTTTCTT-TGTTTTTATTTCCTTAT
5954807 TTTT
1 TTTT
5954811 ATTTTCGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.04, C:0.12, G:0.06, T:0.79
Consensus pattern (24 bp):
TTTTCTTTGTTTTTATTTCCTTAT
Found at i:5954829 original size:14 final size:13
Alignment explanation
Indices: 5954758--5954849 Score: 60
Period size: 13 Copynumber: 6.7 Consensus size: 13
5954748 TTCTTGTCCC
5954758 CTTTTCTTTGTTTTT
1 CTTTT-TTT-TTTTT
* *
5954773 CTTTGCTTATTTTT
1 CTTT-TTTTTTTTT
5954787 CTTGTTTTTTTATTT
1 CTT-TTTTTTT-TTT
*
5954802 CCTTTTTTTATTTT
1 -CTTTTTTTTTTTT
*
5954816 CGTTTTTTTTTTT
1 CTTTTTTTTTTTT
* *
5954829 -TTTTTCTTCTTT
1 CTTTTTTTTTTTT
*
5954841 ATTTTTTTT
1 CTTTTTTTT
5954850 CTTCTTTCTC
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
12 9 0.15
13 18 0.30
14 15 0.25
15 16 0.26
16 3 0.05
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.80
Consensus pattern (13 bp):
CTTTTTTTTTTTT
Found at i:5954845 original size:16 final size:16
Alignment explanation
Indices: 5954826--5954856 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5954816 CGTTTTTTTT
5954826 TTTTTTTTCTTCTTTA
1 TTTTTTTTCTTCTTTA
5954842 TTTTTTTTCTTCTTT
1 TTTTTTTTCTTCTTT
5954857 CTCTTCGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTTTTCTTCTTTA
Found at i:5954849 original size:19 final size:17
Alignment explanation
Indices: 5954758--5954856 Score: 63
Period size: 18 Copynumber: 5.2 Consensus size: 17
5954748 TTCTTGTCCC
*
5954758 CTTTTCTTTGTTTTTCTTTG
1 CTTTT-TTT-TTTTT-TTTT
5954778 CTTATTTTTCTTGTTTTTTT
1 CTT-TTTTT-TT-TTTTTTT
* * *
5954798 ATTTCCTTTTTTTATTTT
1 CTTT-TTTTTTTTTTTTT
5954816 CGTTTTTTTTTTTTTTTT
1 C-TTTTTTTTTTTTTTTT
*
5954834 CTTCTTTATTTTTTTTCTT
1 CTT-TTT-TTTTTTTTTTT
5954853 CTTT
1 CTTT
5954857 CTCTTCGCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.03
18 22 0.34
19 19 0.30
20 16 0.25
21 5 0.08
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.80
Consensus pattern (17 bp):
CTTTTTTTTTTTTTTTT
Found at i:5960747 original size:3 final size:3
Alignment explanation
Indices: 5960739--5960789 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
5960729 AATTATAAGA
* *
5960739 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT -AT AAT AAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5960786 AAT A
1 AAT A
5960790 TTTTAAGACC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Done.