Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008041.1 Hibiscus syriacus cultivar Beakdansim tig00110528_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: 4970990
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 21
Found at i:4896392 original size:60 final size:60
Alignment explanation
Indices: 4896302--4896495 Score: 246
Period size: 60 Copynumber: 3.1 Consensus size: 60
4896292 TTCAATGTGA
* * * *
4896302 ATCGATGCATCCTCAAGTAATTGAACATCGAATGTCGTCGTGCATCGATGCATAAGGAGTGC
1 ATCGATGCAT-TTCAATTAA-TGAACATCGAATGCCCTCGTGCATCGATGCATAAGGAGTGC
4896364 ATCGATGCATTTCAATTAATGAACATCGAATGCCCTCAGTGC-TCGATGCATAAGGAGTGC
1 ATCGATGCATTTCAATTAATGAACATCGAATGCCCTC-GTGCATCGATGCATAAGGAGTGC
* * * * *
4896424 ATCGATGCATTTTCAATTAAATAAACATCGAATGACCTTAGTGCATCGATGAATAAAGAGTGC
1 ATCGATGCA-TTTCAATT-AATGAACATCGAATG-CCCTCGTGCATCGATGCATAAGGAGTGC
4896487 ATCGATGCA
1 ATCGATGCA
4896496 CATCCTTAAG
Statistics
Matches: 118, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
60 43 0.36
61 19 0.16
62 28 0.24
63 28 0.24
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (60 bp):
ATCGATGCATTTCAATTAATGAACATCGAATGCCCTCGTGCATCGATGCATAAGGAGTGC
Found at i:4896562 original size:21 final size:21
Alignment explanation
Indices: 4896536--4896580 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
4896526 TGTGTACGAT
4896536 ACACATGT-AGTGCATCGATGC
1 ACACAT-TAAGTGCATCGATGC
4896557 ACACATTAAGAGTGCATCGATGC
1 ACACATT-A-AGTGCATCGATGC
4896580 A
1 A
4896581 TACCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 1 0.05
21 6 0.29
23 14 0.67
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (21 bp):
ACACATTAAGTGCATCGATGC
Found at i:4897192 original size:23 final size:23
Alignment explanation
Indices: 4897161--4897217 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
4897151 AATCTTATGG
*
4897161 CACTACGGTGCAATTCTACGCGA
1 CACTTCGGTGCAATTCTACGCGA
* *
4897184 CACTTCGGTGCAATTCTACGTGG
1 CACTTCGGTGCAATTCTACGCGA
4897207 CACTTC-GTGCA
1 CACTTCGGTGCA
4897218 TTTATACGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 5 0.16
23 26 0.84
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (23 bp):
CACTTCGGTGCAATTCTACGCGA
Found at i:4897846 original size:2 final size:2
Alignment explanation
Indices: 4897839--4897876 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4897829 TGTATAAACC
4897839 TA TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4897877 TATCGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4898028 original size:2 final size:2
Alignment explanation
Indices: 4898021--4898060 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4898011 TGTATAAACC
4898021 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4898061 TATTTTCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4898098 original size:176 final size:181
Alignment explanation
Indices: 4897799--4898155 Score: 613
Period size: 177 Copynumber: 2.0 Consensus size: 181
4897789 AGAATGTTAA
4897799 ATTGTGTATGCTCTGAGTATTTGTGAACTTTGTATAAACCTATATATAATAATATATATATATAT
1 ATTGTGTATGCTCTGAGTATTTGTGAACTTTGTATAAACCTATATATAATAATATATATATATAT
4897864 ATATAATATATATTATCGTATTTTCTCAATATAATTCAATGTTTTGTTATTTTGTTAAGAATAAT
66 ATATAATATATATTATC-TATTTTCTCAATATAATTCAATGTTTTGTTATTTTGTTAAGAATAAT
*
4897929 GCTTT-AAAAGGTAATGTGACCTCTCGGACTCGTATCCAGGTCGAGTACGGT
130 GCTTTAAAAAGGTAATGTGACATCTCGGACTCGTATCCAGGTCGAGTACGGT
4897980 ATTGTGTATGCTCTGAGTATTTTGTGAACTTTGTATAAACCTATATAT-AT-ATATATATATATA
1 ATTGTGTATGCTCTGAGTA-TTTGTGAACTTTGTATAAACCTATATATAATAATATATATATATA
4898043 TATAT-ATATATTATATAT-TA-TTT-TC-ATATAATTCAATGTTTTGTTATTTTGTTAAGAATA
65 TATATAATATA-TAT-TATCTATTTTCTCAATATAATTCAATGTTTTGTTATTTTGTTAAGAATA
4898103 ATGCTTTAAAAAGGTAATGTGACATCTCGGACTCGTATCCAGGTCGAGTACGG
128 ATGCTTTAAAAAGGTAATGTGACATCTCGGACTCGTATCCAGGTCGAGTACGG
4898156 GTTGGGGGTG
Statistics
Matches: 171, Mismatches: 1, Indels: 12
0.93 0.01 0.07
Matches are distributed among these distances:
176 42 0.25
177 46 0.27
178 3 0.02
179 7 0.04
180 21 0.12
181 24 0.14
182 28 0.16
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (181 bp):
ATTGTGTATGCTCTGAGTATTTGTGAACTTTGTATAAACCTATATATAATAATATATATATATAT
ATATAATATATATTATCTATTTTCTCAATATAATTCAATGTTTTGTTATTTTGTTAAGAATAATG
CTTTAAAAAGGTAATGTGACATCTCGGACTCGTATCCAGGTCGAGTACGGT
Found at i:4900986 original size:123 final size:126
Alignment explanation
Indices: 4900767--4901016 Score: 479
Period size: 123 Copynumber: 2.0 Consensus size: 126
4900757 ACAATTGCAC
4900767 TTGAAACCAAAACCTTGAGACAAGAGACTTTGTCGAGCATCATAACTCATACTGACGTCGATGTA
1 TTGAAACCAAAACCTTGAGACAAGAGACTTTGTCGAGCATCATAACTCATACTGACGTCGATGTA
4900832 ACATATCCGAAGCTCTTCACCTACAAGATGCCAAG-A-ACGTGTCATTCAT-AAATCAGGA
66 ACATATCCGAAGCTCTTCACCTACAAGATGCCAAGAAGACGTGTCATTCATAAAATCAGGA
4900890 TTGAAACCAAAACCTTGAGACAAGAGACTTTGTCGAGCATCATAACTCATACTGACGTCGATGTA
1 TTGAAACCAAAACCTTGAGACAAGAGACTTTGTCGAGCATCATAACTCATACTGACGTCGATGTA
4900955 ACATATCCGAAGCTCTTCACCTACAAGATGCCAAGAAGACGTGTCATTCATAAAATCAGGA
66 ACATATCCGAAGCTCTTCACCTACAAGATGCCAAGAAGACGTGTCATTCATAAAATCAGGA
4901016 T
1 T
4901017 ACCTTTGAAG
Statistics
Matches: 124, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
123 100 0.81
124 1 0.01
125 13 0.10
126 10 0.08
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (126 bp):
TTGAAACCAAAACCTTGAGACAAGAGACTTTGTCGAGCATCATAACTCATACTGACGTCGATGTA
ACATATCCGAAGCTCTTCACCTACAAGATGCCAAGAAGACGTGTCATTCATAAAATCAGGA
Found at i:4916090 original size:2 final size:2
Alignment explanation
Indices: 4916083--4916171 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
4916073 AATGAAGTAA
4916083 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
4916125 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
4916167 AT AT A
1 AT AT A
4916172 AGAAGGATAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4917542 original size:19 final size:19
Alignment explanation
Indices: 4917518--4917562 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4917508 TGGTGCATCA
* *
4917518 GAGGCGGCTGGAGATAGTT
1 GAGGCGGCTGCAGATAGCT
4917537 GAGGCGGCTGCAGATAGCT
1 GAGGCGGCTGCAGATAGCT
4917556 GAGGCGG
1 GAGGCGG
4917563 TGGCGGCGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.49, T:0.16
Consensus pattern (19 bp):
GAGGCGGCTGCAGATAGCT
Found at i:4923033 original size:77 final size:77
Alignment explanation
Indices: 4922906--4923059 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
4922896 TCTGATGGGT
* *
4922906 CTAAGCCAGTTGGACAACCCAGATACGGTATCACTGTTTTTGATCCAGTTAGTGGGTTCTGGGGT
1 CTAAGCAAGTAGGACAACCCAGATACGGTATCACTGTTTTTGATCCAGTTAGTGGGTTCTGGGGT
4922971 CGAATTGACCCG
66 CGAATTGACCCG
4922983 CTAAGCAAGTAGGACAACCCAGATACGGTATCACTGTTTTTGATCCAGTTAGTGGGTTCTGGGGT
1 CTAAGCAAGTAGGACAACCCAGATACGGTATCACTGTTTTTGATCCAGTTAGTGGGTTCTGGGGT
*
4923048 CGAGTTGACCCG
66 CGAATTGACCCG
4923060 GTTCCAAAGT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (77 bp):
CTAAGCAAGTAGGACAACCCAGATACGGTATCACTGTTTTTGATCCAGTTAGTGGGTTCTGGGGT
CGAATTGACCCG
Found at i:4923849 original size:37 final size:37
Alignment explanation
Indices: 4923797--4923915 Score: 184
Period size: 37 Copynumber: 3.2 Consensus size: 37
4923787 ACATATATGT
* * * *
4923797 ACAACAAAAACGCCTGTGCAGACAGTTCAGTTAAAGC
1 ACAACAAAAATGCCTGTTCAGCCAGTGCAGTTAAAGC
4923834 ACAACAAAAATGCCTGTTCAGCCAGTGCAGTTAAAGC
1 ACAACAAAAATGCCTGTTCAGCCAGTGCAGTTAAAGC
*
4923871 ACAACAAAAATGCCTGTTCAGCCAGTGCTGTTAAAGC
1 ACAACAAAAATGCCTGTTCAGCCAGTGCAGTTAAAGC
*
4923908 ACTACAAA
1 ACAACAAA
4923916 TCTGTGGGGG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.18
Consensus pattern (37 bp):
ACAACAAAAATGCCTGTTCAGCCAGTGCAGTTAAAGC
Found at i:4924700 original size:60 final size:60
Alignment explanation
Indices: 4924607--4924757 Score: 223
Period size: 60 Copynumber: 2.5 Consensus size: 60
4924597 CCAAGTTATT
* *
4924607 ACTCTCATTTTAAATTAGTCCTTAAACTTTTAAACATTTCAATTTCATCCCAAAACTATG
1 ACTCTCATTTTAAATTAGTTCTTAAACTTTTAAACATTCCAATTTCATCCCAAAACTATG
* *
4924667 ACTCTCATTTTAAATTAGTTCTTAAACTTTTAAACATTCCAATTTCATCCCTAAATTATG
1 ACTCTCATTTTAAATTAGTTCTTAAACTTTTAAACATTCCAATTTCATCCCAAAACTATG
* * *
4924727 -CATATCATTCTAAATTAGTTCCTAAACTTTT
1 AC-TCTCATTTTAAATTAGTTCTTAAACTTTT
4924758 GCATATTTAG
Statistics
Matches: 83, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
59 1 0.01
60 82 0.99
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (60 bp):
ACTCTCATTTTAAATTAGTTCTTAAACTTTTAAACATTCCAATTTCATCCCAAAACTATG
Found at i:4928052 original size:16 final size:17
Alignment explanation
Indices: 4928020--4928053 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4928010 GGGTCTACAA
*
4928020 AAATATTATTATATTTT
1 AAATATTAATATATTTT
4928037 AAATATTAAT-TATTTT
1 AAATATTAATATATTTT
4928053 A
1 A
4928054 TTTATCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATATTAATATATTTT
Found at i:4928100 original size:19 final size:18
Alignment explanation
Indices: 4928030--4928100 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
4928020 AAATATTATT
4928030 ATATTTTA--AATATTAA
1 ATATTTTATTAATATTAA
* * *
4928046 TTATTTTATTTATCATTAT
1 ATATTTTATTAAT-ATTAA
*
4928065 ATATTATTATTATTATTAA
1 ATATT-TTATTAATATTAA
4928084 ATATTTTATTACATATT
1 ATATTTTATTA-ATATT
4928101 TTGCAAGCCA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
16 7 0.17
18 8 0.19
19 21 0.50
20 6 0.14
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATTTTATTAATATTAA
Found at i:4931738 original size:29 final size:28
Alignment explanation
Indices: 4931667--4931738 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
4931657 TTGTATTTAC
4931667 TTTTCAGTCCTTTAAGTTTTTTTTTTGCTA
1 TTTT-AGTCCTTT-AGTTTTTTTTTTGCTA
*
4931697 -TTTAGCCCATTTA-TTTTTGTTTTTGGCTA
1 TTTTAGTCC-TTTAGTTTTT-TTTTT-GCTA
4931726 TTTTAGTCCTTTA
1 TTTTAGTCCTTTA
4931739 ACTATCTGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 5 0.14
28 10 0.28
29 14 0.39
30 7 0.19
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (28 bp):
TTTTAGTCCTTTAGTTTTTTTTTTGCTA
Found at i:4933977 original size:44 final size:43
Alignment explanation
Indices: 4933905--4934004 Score: 150
Period size: 43 Copynumber: 2.3 Consensus size: 43
4933895 TTGGACCCTT
4933905 AGTGCATCGATGCATAAAATGCATTCGATGTTT-TAAAATAGCCTG
1 AGTGCATCGATGCATAAAATGCATTCGAT-TTTATAAAA-A-CCTG
4933950 AGTGCATCGATGCA-AAAATGCATTCGATTTTCATAAAAACCTG
1 AGTGCATCGATGCATAAAATGCATTCGATTTT-ATAAAAACCTG
4933993 AGTGCATCGATG
1 AGTGCATCGATG
4934005 AATGGTATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
43 19 0.36
44 15 0.28
45 19 0.36
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (43 bp):
AGTGCATCGATGCATAAAATGCATTCGATTTTATAAAAACCTG
Found at i:4938610 original size:67 final size:65
Alignment explanation
Indices: 4938437--4938709 Score: 268
Period size: 66 Copynumber: 4.1 Consensus size: 65
4938427 ATTTTTACTC
*
4938437 AAAACAAAGTTTATGTCT-TTCTTGAGACAGTGTCTTTTGAA-ACACAAATCTTTGAGTATGTTT
1 AAAACAAAGTTT-TGTCTCTTC-TGAGACAGTTTCTTTTGAAGA-A-AAATCTTTGAGTATGTTT
4938500 CATTT
62 C-TTT
* * * *
4938505 AAAACAAA-TTTTATCTCTTCTGAGACAGATTCTTTTGAAGAAAAATCTTTGAGTCTATTTCTTT
1 AAAACAAAGTTTTGTCTCTTCTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCTTT
* *
4938569 ATAAACCAAAGTTTTGTCTCTTCTGAAACAGTTTCTGTTGAAGAAAAATCTTTGAGTATGTTTCT
1 A-AAA-CAAAGTTTTGTCTCTTCTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCT
4938634 TT
64 TT
* * * * * * * * *
4938636 GGAAACAAAATTTTATC-CCTCTTGAGATAATATCTTTTGAAGGAAAATCTTTAAGT-TGTTTCT
1 -AAAACAAAGTTTTGTCTCTTC-TGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCT
4938699 CTT
64 -TT
*
4938702 GAAACAAA
1 AAAACAAA
4938710 ACCATCTTTG
Statistics
Matches: 175, Mismatches: 22, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
64 4 0.02
65 38 0.22
66 65 0.37
67 60 0.34
68 8 0.05
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (65 bp):
AAAACAAAGTTTTGTCTCTTCTGAGACAGTTTCTTTTGAAGAAAAATCTTTGAGTATGTTTCTTT
Found at i:4938728 original size:31 final size:31
Alignment explanation
Indices: 4938682--4938740 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
4938672 TTGAAGGAAA
* *
4938682 ATCTTTAAGTTGTTTCTCTTGAAACAAAACC
1 ATCTTTAAGTCGTTTCCCTTGAAACAAAACC
*
4938713 ATCTTTGAGTCGTTTCCCTTGAAACAAA
1 ATCTTTAAGTCGTTTCCCTTGAAACAAA
4938741 TTGTCTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (31 bp):
ATCTTTAAGTCGTTTCCCTTGAAACAAAACC
Found at i:4939353 original size:135 final size:134
Alignment explanation
Indices: 4938806--4939556 Score: 914
Period size: 135 Copynumber: 5.6 Consensus size: 134
4938796 GAAACCATTA
* **
4938806 TCCCTAAAAATGGTCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGA--T-CTC
1 TCCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCCTC
* * * *
4938868 ATCACGTAAGAGCCTTGTCACCCCTATATAACCAGTCGTCCTCATCATGTATGAACCGAGTTATC
66 ATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTATC
4938933 ACCC
131 ACCC
* *
4938937 TCCCTAAAGATGGA--AGAACTCTTCATCACATATGAGTCGTGTCATCCCCCGACCAGATCTCCT
1 TCCCTAAAGAT-GACCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCCT
* ** *
4939000 CATCACGTACGAGCCGTGTCACCCCTAGATAACCAGTCAACCTCATCGCGTAAGAACCGA--TAT
65 CATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTAT
4939063 CACCC
130 CACCC
* * * *
4939068 TTCCTAAAGAT-AGTCAGAATTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCTT
1 TCCCTAAAGATGA-CCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCCT
* * * * * * * * *
4939132 CATCAGGTAGGAGTCGTGTCATCCCTAAATAACCA-CCGTCCTCATCACTTAGGAATCGAGTTAT
65 CATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTAT
4939196 CACCC
130 CACCC
* * * * *
4939201 TTCCTAAAGATGGCCAGAACTCTTCATCACTTATGAGTTGTGTCATCCACCGACCAGATCTCCTA
1 TCCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCCTC
** *
4939266 ATCACGTAAGATTCGTATCACACCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTAT
66 ATCACGTAAGAGCCGTGTCAC-CCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTAT
4939331 CACCC
130 CACCC
* * * *
4939336 TCCCTAAAGATGACCAGAACTCTTTATCACATATGAGTCT-TGTCATCCACTGACCAGATCTCCT
1 TCCCTAAAGATGACCAGAACTCTTCATCACGTATGAGT-TGTGTCATCCCCCGACCAGATCTCCT
* * * * *
4939400 CATCACGTATGAGCCGTGTCACCCCTTGATAATCA-TCCGTCCTCATCACGTAGGAACCTAGTTA
65 CATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGT-CGTCCTCATCACGTAAGAACCGAGTTA
4939464 TCACCC
129 TCACCC
** * * *
4939470 TCCCTAAAGATTG-CCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCCAACCATATCTCA
1 TCCCTAAAGA-TGACC-AGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCC
*
4939534 TCATCACGTAGGAGCCGTGTCAC
64 TCATCACGTAAGAGCCGTGTCAC
4939557 TCTTAGACGA
Statistics
Matches: 533, Mismatches: 70, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
129 1 0.00
130 41 0.08
131 45 0.08
132 77 0.14
133 136 0.26
134 66 0.12
135 166 0.31
136 1 0.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.26
Consensus pattern (134 bp):
TCCCTAAAGATGACCAGAACTCTTCATCACGTATGAGTTGTGTCATCCCCCGACCAGATCTCCTC
ATCACGTAAGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAACCGAGTTATC
ACCC
Found at i:4939770 original size:17 final size:17
Alignment explanation
Indices: 4939748--4939808 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
4939738 GGTCTACCAA
4939748 AAATATTATTATATTTT
1 AAATATTATTATATTTT
*
4939765 AAATATTAAT-TATTTT
1 AAATATTATTATATTTT
** *
4939781 ATTTATCATTATATTATT
1 AAATATTATTATATT-TT
*
4939799 -ATTATTATTA
1 AAATATTATTA
4939809 AATATTTTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
16 12 0.34
17 21 0.60
18 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATATTATTATATTTT
Found at i:4939776 original size:21 final size:22
Alignment explanation
Indices: 4939750--4939820 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 22
4939740 TCTACCAAAA
4939750 ATATTATTATATTTTAAATATT
1 ATATTATTATATTTTAAATATT
*
4939772 A-ATTATTTTA-TTT--ATCATT
1 ATATTATTATATTTTAAAT-ATT
4939791 ATATTATTATTATTATTAAATATT
1 ATATTATTA-TATT-TTAAATATT
*
4939815 TTATTA
1 ATATTA
4939821 CACATTTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.23
21 10 0.26
22 2 0.05
23 2 0.05
24 8 0.21
25 2 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTATTATATTTTAAATATT
Found at i:4941696 original size:19 final size:20
Alignment explanation
Indices: 4941674--4941725 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4941664 TTATTAAAAT
4941674 AATATTATTTTTTAATT-TA
1 AATATTATTTTTTAATTATA
* * *
4941693 AATAATATTTTTAAATTATT
1 AATATTATTTTTTAATTATA
*
4941713 AATTTTATTTTTT
1 AATATTATTTTTT
4941726 TAAATCCCAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATATTATTTTTTAATTATA
Found at i:4945678 original size:24 final size:24
Alignment explanation
Indices: 4945651--4945717 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 24
4945641 AAGGATTGCG
*
4945651 TAGAATTTTTCCCGAATGACCACA
1 TAGAATTTATCCCGAATGACCACA
* *
4945675 TAGAA-TTATCCCAAAGGACCACA
1 TAGAATTTATCCCGAATGACCACA
*
4945698 TAG-ATTTGTCCCGAATGACC
1 TAGAATTTATCCCGAATGACC
4945718 GCGTAGAACC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.03
23 30 0.83
24 5 0.14
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (24 bp):
TAGAATTTATCCCGAATGACCACA
Found at i:4947331 original size:24 final size:24
Alignment explanation
Indices: 4947259--4947332 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
4947249 TTCGAGATAT
* **
4947259 TTCTACATGGTCCTTAAGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
4947283 TTCTACGTGGTCCTTCGGGAAAAA
1 TTCTACGTGGTCCTTCGGGACAAA
*
4947307 TTCTACGTGG-CACTTCGGTACAAA
1 TTCTACGTGGTC-CTTCGGGACAAA
4947331 TT
1 TT
4947333 ATATGATTGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 42 0.98
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:4955597 original size:19 final size:20
Alignment explanation
Indices: 4955575--4955626 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4955565 TTATTAAAAT
4955575 AATATTATTTTTTAATT-TA
1 AATATTATTTTTTAATTATA
* * *
4955594 AATAATATTTTTAAATTATT
1 AATATTATTTTTTAATTATA
*
4955614 AATTTTATTTTTT
1 AATATTATTTTTT
4955627 TTAAATCCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
AATATTATTTTTTAATTATA
Found at i:4959033 original size:24 final size:24
Alignment explanation
Indices: 4959006--4959074 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 24
4958996 TGAAGGATTG
*
4959006 CATAGAATTTTTCCCGAATGACCA
1 CATAGAATTTATCCCGAATGACCA
* *
4959030 CATAGAA-TTATCCCAAAGGACCA
1 CATAGAATTTATCCCGAATGACCA
*
4959053 CATAG-ATTTGTCCCGAATGACC
1 CATAGAATTTATCCCGAATGACC
4959075 GCGTAGAACC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 1 0.03
23 30 0.79
24 7 0.18
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (24 bp):
CATAGAATTTATCCCGAATGACCA
Found at i:4959049 original size:47 final size:46
Alignment explanation
Indices: 4958972--4959074 Score: 111
Period size: 47 Copynumber: 2.2 Consensus size: 46
4958962 ATAAATTGCA
* * *** *
4958972 CCGAAGTG-CCACATAGATTTACCCTGAAGGATTGCATAGAATTTTTC
1 CCGAA-TGACCACATAGAATTACCCTAAAGGACCACATAG-ATTTGTC
4959019 CCGAATGACCACATAGAATTATCCC-AAAGGACCACATAGATTTGTC
1 CCGAATGACCACATAGAATTA-CCCTAAAGGACCACATAGATTTGTC
4959065 CCGAATGACC
1 CCGAATGACC
4959075 GCGTAGAACC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
46 18 0.38
47 27 0.56
48 3 0.06
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (46 bp):
CCGAATGACCACATAGAATTACCCTAAAGGACCACATAGATTTGTC
Found at i:4959081 original size:23 final size:23
Alignment explanation
Indices: 4958972--4959074 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
4958962 ATAAATTGCA
4958972 CCGAAGTG-CCACATAGATTTA-C
1 CCGAA-TGACCACATAGATTTATC
* *** *
4958994 CCTGAAGGATTGCATAGAATTTTTC
1 CC-GAATGACCACATAG-ATTTATC
*
4959019 CCGAATGACCACATAGAATTATC
1 CCGAATGACCACATAGATTTATC
* * *
4959042 CCAAAGGACCACATAGATTTGTC
1 CCGAATGACCACATAGATTTATC
4959065 CCGAATGACC
1 CCGAATGACC
4959075 GCGTAGAACC
Statistics
Matches: 60, Mismatches: 17, Indels: 7
0.71 0.20 0.08
Matches are distributed among these distances:
22 3 0.05
23 40 0.67
24 14 0.23
25 3 0.05
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (23 bp):
CCGAATGACCACATAGATTTATC
Found at i:4960645 original size:24 final size:24
Alignment explanation
Indices: 4960617--4960670 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
4960607 TTCGGGATAT
* *
4960617 TTCTACATAGTCCTTATGGACAAA
1 TTCTACATAGTCCTTAGGGAAAAA
* * *
4960641 TTCTACGTGGTCCTTCGGGAAAAA
1 TTCTACATAGTCCTTAGGGAAAAA
4960665 TTCTAC
1 TTCTAC
4960671 GTGGTACTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (24 bp):
TTCTACATAGTCCTTAGGGAAAAA
Found at i:4960689 original size:24 final size:24
Alignment explanation
Indices: 4960634--4960690 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
4960624 TAGTCCTTAT
*
4960634 GGACAAATTCTACGTGGTCCTTCG
1 GGACAAATTCTACGTGGTACTTCG
*
4960658 GGAAAAATTCTACGTGGTACTTCG
1 GGACAAATTCTACGTGGTACTTCG
*
4960682 GTACAAATT
1 GGACAAATT
4960691 ATATGATCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
GGACAAATTCTACGTGGTACTTCG
Done.