Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006890.1 Hibiscus syriacus cultivar Beakdansim tig00017583_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: 227650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:192324 original size:14 final size:15
Alignment explanation
Indices: 192286--192325 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
192276 AGCAATCATT
192286 AAAAAAATTATATAG
1 AAAAAAATTATATAG
*
192301 AAATAAAATTATGTA-
1 AAA-AAAATTATATAG
192316 AAAAAAATTA
1 AAAAAAATTA
192326 GAGATGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 6 0.26
16 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAAAATTATATAG
Found at i:192528 original size:20 final size:20
Alignment explanation
Indices: 192505--192602 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
192495 AATTTGTGTC
192505 GCGAATTCGAAAATCGAGTT
1 GCGAATTCGAAAATCGAGTT
**
192525 GCGAAAAC-AAAATTC-ACGTT
1 GCGAATTCGAAAA-TCGA-GTT
*
192545 GCGAATT-TAGAAATCGAGTT
1 GCGAATTCGA-AAATCGAGTT
* * *
192565 GCGAATTTGAAATTCAGTGTT
1 GCGAATTCGAAAATC-GAGTT
*
192586 GCGAATTTGGAAAATCG
1 GCGAA-TTCGAAAATCG
192603 CAATGCGATT
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
19 5 0.08
20 33 0.54
21 15 0.25
22 8 0.13
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (20 bp):
GCGAATTCGAAAATCGAGTT
Found at i:192578 original size:40 final size:41
Alignment explanation
Indices: 192515--192598 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 41
192505 GCGAATTCGA
192515 AAATCGAGTTGCGAAAACAAAATTCA-CGTTGCGAATTTAG
1 AAATCGAGTTGCGAAAACAAAATTCAGCGTTGCGAATTTAG
**** * *
192555 AAATCGAGTTGCGAATTTGAAATTCAGTGTTGCGAATTTGG
1 AAATCGAGTTGCGAAAACAAAATTCAGCGTTGCGAATTTAG
192596 AAA
1 AAA
192599 ATCGCAATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 22 0.59
41 15 0.41
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.29
Consensus pattern (41 bp):
AAATCGAGTTGCGAAAACAAAATTCAGCGTTGCGAATTTAG
Found at i:192588 original size:21 final size:21
Alignment explanation
Indices: 192534--192594 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
192524 TGCGAAAACA
*
192534 AAATTCA-CGTTGCGAATTTAG
1 AAATTCAGAGTTGCGAATTT-G
192555 AAA-TC-GAGTTGCGAATTTG
1 AAATTCAGAGTTGCGAATTTG
*
192574 AAATTCAGTGTTGCGAATTTG
1 AAATTCAGAGTTGCGAATTTG
192595 GAAAATCGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 4 0.11
20 15 0.43
21 16 0.46
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (21 bp):
AAATTCAGAGTTGCGAATTTG
Found at i:194315 original size:60 final size:60
Alignment explanation
Indices: 194239--194376 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
194229 GATAAAATCA
* ***
194239 AAATATTCAAAAAGTTTAAGGACCAATTTAGAATTA-AGATCACAATTTGGGGATGAAAATG
1 AAATATTC-AAAAGTTTAAGGACCAATTTAGAATGATAG-TCACAATTTAAAGATGAAAATG
* * * * *
194300 AAATATTCAAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAAAGATGAAATTG
1 AAATATTCAAAAGTTTAAGGACCAATTTAGAATGATAGTCACAATTTAAAGATGAAAATG
*
194360 AAATATTTAAAAGTTTA
1 AAATATTCAAAAGTTTA
194377 GAGATCAATA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
60 55 0.85
61 10 0.15
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.32
Consensus pattern (60 bp):
AAATATTCAAAAGTTTAAGGACCAATTTAGAATGATAGTCACAATTTAAAGATGAAAATG
Found at i:194394 original size:60 final size:60
Alignment explanation
Indices: 194290--194403 Score: 135
Period size: 60 Copynumber: 1.9 Consensus size: 60
194280 ACAATTTGGG
* * *
194290 GATGAAAATGAAATATTCAAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAAA
1 GATGAAAATGAAATATTCAAAAGTTTGAGGACTAATTGAGAATGAGAATCATAGTTTAAA
* *
194350 GATGAAATTGAAATATTTAAAAGTTT-AGAGA-TCAATATGA-AATGAGAATCATAG
1 GATGAAAATGAAATATTCAAAAGTTTGAG-GACT-AAT-TGAGAATGAGAATCATAG
194404 ATTAGAGACA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
59 3 0.07
60 41 0.89
61 2 0.04
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.31
Consensus pattern (60 bp):
GATGAAAATGAAATATTCAAAAGTTTGAGGACTAATTGAGAATGAGAATCATAGTTTAAA
Found at i:197228 original size:19 final size:19
Alignment explanation
Indices: 197204--197257 Score: 92
Period size: 19 Copynumber: 2.8 Consensus size: 19
197194 AATGAACCCT
197204 AAAAACACTTT-GAAACTCC
1 AAAAACA-TTTCGAAACTCC
197223 AAAAACATTTCGAAACTCC
1 AAAAACATTTCGAAACTCC
197242 AAAAACATTTCGAAAC
1 AAAAACATTTCGAAAC
197258 ATGCAAGCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 3 0.09
19 31 0.91
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (19 bp):
AAAAACATTTCGAAACTCC
Found at i:199281 original size:3 final size:3
Alignment explanation
Indices: 199273--199318 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
199263 TACATCAAAA
199273 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
199319 CATAAGAAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:201419 original size:12 final size:13
Alignment explanation
Indices: 201383--201426 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
201373 GCCCCGATTA
201383 CCCGATTACCCGC
1 CCCGATTACCCGC
201396 CCCGATTACCCGC
1 CCCGATTACCCGC
*
201409 CCCGA-TACCCGA
1 CCCGATTACCCGC
201421 CCCGAT
1 CCCGAT
201427 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:201480 original size:32 final size:33
Alignment explanation
Indices: 201444--201529 Score: 113
Period size: 32 Copynumber: 2.7 Consensus size: 33
201434 AAAAATAATT
*
201444 ATTTATATATATATATA-ATATTAATAAATTTA
1 ATTTAAATATATATATATATATTAATAAATTTA
* * * *
201476 ATTTAAATA-AAAAATATATATTTATATATTTA
1 ATTTAAATATATATATATATATTAATAAATTTA
201508 ATTTAAATATATATATATATAT
1 ATTTAAATATATATATATATAT
201530 ATATATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 5 0.11
32 30 0.67
33 10 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATTTAAATATATATATATATATTAATAAATTTA
Found at i:201494 original size:2 final size:2
Alignment explanation
Indices: 201489--201546 Score: 73
Period size: 2 Copynumber: 29.5 Consensus size: 2
201479 TAAATAAAAA
* * * *
201489 AT AT AT AT TT AT AT AT TT A- AT TT AA 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
201530 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
201547 CCCGGCCCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:201582 original size:12 final size:12
Alignment explanation
Indices: 201567--201598 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
201557 TTCTCGGCCT
201567 AATACCCGACCC
1 AATACCCGACCC
*
201579 AATACCCGGCCC
1 AATACCCGACCC
201591 AATACCCG
1 AATACCCG
201599 TTTAAATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.31, C:0.47, G:0.12, T:0.09
Consensus pattern (12 bp):
AATACCCGACCC
Found at i:204024 original size:21 final size:21
Alignment explanation
Indices: 203925--204024 Score: 53
Period size: 21 Copynumber: 4.8 Consensus size: 21
203915 AACGTGATCC
** *
203925 CCAGAATCGCAAATC-AGTTT
1 CCAGAATCGCAACGCGATTTT
*
203945 CCAAAATCGCAACGCGATTCTT
1 CCAGAATCGCAACGCGATT-TT
* * * **
203967 -GACAATCGCAATGCGATAGT
1 CCAGAATCGCAACGCGATTTT
* **
203987 ACA-AATTCGCATTGCGATTTT
1 CCAGAA-TCGCAACGCGATTTT
204008 CCAGAATCGCAACGCGA
1 CCAGAATCGCAACGCGA
204025 ATATGAAAAT
Statistics
Matches: 59, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
20 15 0.25
21 40 0.68
22 4 0.07
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (21 bp):
CCAGAATCGCAACGCGATTTT
Found at i:204037 original size:20 final size:20
Alignment explanation
Indices: 204012--204162 Score: 117
Period size: 20 Copynumber: 7.5 Consensus size: 20
204002 GATTTTCCAG
*
204012 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
*
204032 AATCGCAACGCGAACAC-ATA
1 AATCGCAACGCGAATACGA-A
* * *
204052 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
204072 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* * * *
204092 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
204112 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
204133 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
204153 AATCGCAACG
1 AATCGCAACG
204163 TGATTTTTAA
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 1 0.01
20 93 0.85
21 16 0.15
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:204075 original size:40 final size:40
Alignment explanation
Indices: 204012--204162 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
204002 GATTTTCCAG
* ** * *
204012 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTA
* *
204052 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATC-CGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACGTA
* *
204092 TATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGAACACGT-A
204133 AATCGCAACGCGTATCCGTAAATCGCAACG
1 AATCGCAACGCGTATCCGTAAATCGCAACG
204163 TGATTTTTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.01
40 61 0.64
41 33 0.35
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACGTA
Found at i:204581 original size:33 final size:33
Alignment explanation
Indices: 204542--204612 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
204532 TTCACTTAGA
204542 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
204575 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
204608 TTTCA
1 TTTCA
204613 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:204718 original size:21 final size:21
Alignment explanation
Indices: 204692--204768 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
204682 TGCAGAAGAG
204692 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
204713 TCGCAACGTGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
*
204733 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
204755 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
204769 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:204772 original size:14 final size:14
Alignment explanation
Indices: 204753--204809 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
204743 GAAAAATGAA
204753 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
204767 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
204786 AATCGCAACGAGAG
1 AATCGCAACGAGAG
204800 AATCGCAACG
1 AATCGCAACG
204810 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:204784 original size:33 final size:33
Alignment explanation
Indices: 204746--204825 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
204736 GCAACGAGAA
204746 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
204779 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
204812 AAACCAAAATCGCA
1 AAATGAAAATCGCA
204826 TTGCAATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:204862 original size:14 final size:14
Alignment explanation
Indices: 204843--204899 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
204833 TTTCATTTCG
204843 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
204857 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
204876 CGTTGCGATTCTTT
1 CGTTGCGATTCTCT
204890 CGTTGCGATT
1 CGTTGCGATT
204900 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:204873 original size:33 final size:33
Alignment explanation
Indices: 204826--204948 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
204816 CAAAATCGCA
*
204826 TTGCAATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
204859 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
204892 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
204933 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
204949 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
33 43 0.55
34 2 0.03
35 6 0.08
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 20 0.26
ACGTcount: A:0.11, C:0.24, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:204908 original size:21 final size:21
Alignment explanation
Indices: 204884--204948 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
204874 CGCGTTGCGA
*
204884 TTCTTTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
204905 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
204925 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
204946 TTC
1 TTC
204949 AACCAAAAGA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.49
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:206792 original size:93 final size:93
Alignment explanation
Indices: 206633--206855 Score: 428
Period size: 93 Copynumber: 2.4 Consensus size: 93
206623 TAGATTGCTT
*
206633 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
206698 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
206726 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
206791 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
206819 AGTAAATTTGTTCGGTTGCTACCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
206856 AATACCCTGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 128 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:206990 original size:14 final size:14
Alignment explanation
Indices: 206971--207027 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
206961 CGAAACTTAA
206971 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
206985 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
207004 AATCGCAACGACAG
1 AATCGCAACGAGAG
207018 AATCGCAACG
1 AATCGCAACG
207028 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:207009 original size:19 final size:18
Alignment explanation
Indices: 206985--207076 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
206975 GCAACGAGAG
206985 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
207004 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
207018 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
207037 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
207051 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
207070 AATCGCA
1 AATCGCA
207077 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:207011 original size:33 final size:33
Alignment explanation
Indices: 206953--207076 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
206943 TAGTTTACTT
* * *
206953 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
206987 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
207020 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
207053 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
207077 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:207053 original size:14 final size:14
Alignment explanation
Indices: 207002--207060 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
206992 ACGCGAAATG
207002 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
207016 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
207035 AAAATCGCAACGAC
1 AAAATCGCAACGAC
207049 AAAATCGCAACG
1 AAAATCGCAACG
207061 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:207094 original size:19 final size:19
Alignment explanation
Indices: 207072--207230 Score: 175
Period size: 19 Copynumber: 8.6 Consensus size: 19
207062 GAAACCAAAA
*
207072 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
207091 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
207110 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
207126 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
207143 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
207162 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
207181 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
207200 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
207220 TCGTGTTGCGA
1 TCGCGTTGCGA
207231 AAGTAAACTA
Statistics
Matches: 119, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
14 7 0.06
16 5 0.04
17 5 0.04
19 90 0.76
20 12 0.10
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:207139 original size:52 final size:54
Alignment explanation
Indices: 207077--207214 Score: 190
Period size: 52 Copynumber: 2.5 Consensus size: 54
207067 CAAAATCGCA
207077 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCG
** * *
207129 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGG--T-TCG
*
207186 TTGCGATTCTCATTTCGCGTTGCGATTTT
1 TTGCGATTTTCATTTCGCGTTGCGATTTT
207215 AAGTTTCGTG
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
52 44 0.58
53 1 0.01
57 31 0.41
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.48
Consensus pattern (54 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCG
Found at i:209172 original size:14 final size:14
Alignment explanation
Indices: 209153--209188 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
209143 ATTGTTTAAT
209153 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
209167 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
209181 TGATTTGT
1 TGATTTGT
209189 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:209303 original size:19 final size:19
Alignment explanation
Indices: 209279--209368 Score: 127
Period size: 19 Copynumber: 4.9 Consensus size: 19
209269 GCATTATGTT
209279 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
209298 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
209315 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
209331 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
209350 GGAAATGAAAATCGCAATG
1 -GAAATGAAAATCGCAATG
209369 AGAGAATTGC
Statistics
Matches: 63, Mismatches: 2, Indels: 11
0.83 0.03 0.14
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.46
20 18 0.29
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:209398 original size:53 final size:53
Alignment explanation
Indices: 209279--209385 Score: 189
Period size: 53 Copynumber: 2.0 Consensus size: 53
209269 GCATTATGTT
209279 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
* *
209331 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGAGAGAATTGCAATGC
1 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
209384 GA
1 GA
209386 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
52 19 0.37
53 33 0.63
ACGTcount: A:0.46, C:0.15, G:0.24, T:0.15
Consensus pattern (53 bp):
GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:209444 original size:53 final size:53
Alignment explanation
Indices: 209381--209617 Score: 331
Period size: 53 Copynumber: 4.5 Consensus size: 53
209371 AGAATTGCAA
209381 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
209434 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
* * * * *
209486 TGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCCGCA-TTGCGATTCTCTCGT
* *
209539 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCTTGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
*
209592 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
209618 CTCTCGTTGC
Statistics
Matches: 164, Mismatches: 11, Indels: 18
0.85 0.06 0.09
Matches are distributed among these distances:
50 2 0.01
51 8 0.05
52 49 0.30
53 91 0.55
54 7 0.04
55 7 0.04
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
Found at i:209506 original size:86 final size:86
Alignment explanation
Indices: 209399--209564 Score: 332
Period size: 86 Copynumber: 1.9 Consensus size: 86
209389 TCATTTCGCA
209399 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
209464 TTTCGCATTGCGATTCTCTCG
66 TTTCGCATTGCGATTCTCTCG
209485 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
209550 TTTCGCATTGCGATT
66 TTTCGCATTGCGATT
209565 TTCATTTCCG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (86 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
TTTCGCATTGCGATTCTCTCG
Found at i:209573 original size:72 final size:71
Alignment explanation
Indices: 209381--209617 Score: 292
Period size: 72 Copynumber: 3.4 Consensus size: 71
209371 AGAATTGCAA
* * *
209381 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCG-ATTTTC
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATT-T-TCATTTCCGCA-TTGC
* *
209444 -ATTTCGCAT
62 GATTTCTCGT
*
209453 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
209513 CTCTCGT
66 -TCTCGT
209520 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGA-T
*
209585 TTCTTGT
65 TTCTCGT
*
209592 TGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
209618 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 9, Indels: 20
0.83 0.05 0.11
Matches are distributed among these distances:
64 2 0.01
65 8 0.05
66 12 0.08
67 28 0.19
68 2 0.01
69 5 0.03
70 7 0.05
72 80 0.55
73 2 0.01
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (71 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT
TCTCGT
Found at i:209639 original size:33 final size:33
Alignment explanation
Indices: 209452--209631 Score: 261
Period size: 33 Copynumber: 5.2 Consensus size: 33
209442 TCATTTCGCA
209452 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
209485 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
209519 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* *
209555 CATTGCGATTTTCATTTCCGCATTGCGATTTTCTTG
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
209591 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
209624 TTGCGATT
1 TTGCGATT
209632 GTAATTTCCG
Statistics
Matches: 132, Mismatches: 8, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
33 48 0.36
34 47 0.36
35 3 0.02
36 7 0.05
37 2 0.02
38 15 0.11
39 10 0.08
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:212146 original size:24 final size:24
Alignment explanation
Indices: 212112--212158 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
212102 CTGAAACATC
212112 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
212136 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
212159 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:212879 original size:20 final size:20
Alignment explanation
Indices: 212851--213079 Score: 226
Period size: 20 Copynumber: 11.4 Consensus size: 20
212841 AAATTTCAGT
* * *
212851 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
212871 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
212891 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
212911 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
212931 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
212951 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
212971 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
212991 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
213011 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
213031 GTTGCGATTTATGTG-TTCAC
1 GTTGCGATTTACG-GATTCGC
* **
213051 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
213071 GTTGCGATT
1 GTTGCGATT
213080 CTTGAAAATC
Statistics
Matches: 179, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 178 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:217283 original size:17 final size:17
Alignment explanation
Indices: 217263--217296 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
217253 TTTTTTTATC
*
217263 TATTTTAAAATTTTAAA
1 TATTCTAAAATTTTAAA
*
217280 TATTCTAATATTTTAAA
1 TATTCTAAAATTTTAAA
217297 ATTATTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTCTAAAATTTTAAA
Found at i:218517 original size:47 final size:47
Alignment explanation
Indices: 218417--218517 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 47
218407 ATTTGAGTTG
* * *
218417 GAAGAAGGAGAAGGATTTTGGGTTTTGCTTAGTTTGAGTTGGGAGGA
1 GAAGAAGAAGAAGGATTTTGGGTTTTGCTTAGTTTGAGTTGGAAGAA
* * * * * *
218464 GGAGAAGAATAAGGGTTTTGGGTTTTGGTTGGTTTTAGTTGGAAGAA
1 GAAGAAGAAGAAGGATTTTGGGTTTTGCTTAGTTTGAGTTGGAAGAA
218511 GAAGAAG
1 GAAGAAG
218518 TCAAACTATC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.28, C:0.01, G:0.40, T:0.32
Consensus pattern (47 bp):
GAAGAAGAAGAAGGATTTTGGGTTTTGCTTAGTTTGAGTTGGAAGAA
Found at i:224186 original size:20 final size:19
Alignment explanation
Indices: 224140--224187 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
224130 ATGACCAACA
*
224140 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
224159 AAATCGCAACGCGATCTCT
1 AAATCGCAACGCGATCTCT
224178 AATATCGCAA
1 AA-ATCGCAA
224188 ATCAGTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:224389 original size:21 final size:20
Alignment explanation
Indices: 224352--224432 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 20
224342 AAATTTACGT
*
224352 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
224371 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
** * *
224392 TTTTTCAAATT-CGTTGCGA
1 TAGTCCAAGTTCCGTTGCGA
*
224411 TAGTCAAAGTTCGCGTTGCGA
1 TAGTCCAAGTTC-CGTTGCGA
224432 T
1 T
224433 TTTGAAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
19 24 0.50
21 24 0.50
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
TAGTCCAAGTTCCGTTGCGA
Found at i:224412 original size:40 final size:40
Alignment explanation
Indices: 224357--224435 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
224347 TACGTTAGTC
*
224357 CAAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATTTTT
1 CAAATTCGTTGCGATAGTCAAAGTTCACGTTGCGATTTTT
*
224397 CAAATTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTT
1 CAAATTCGTTGCGATAGTCAAAGTTCACGTTGCGATTTT
224436 GAAAAATCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (40 bp):
CAAATTCGTTGCGATAGTCAAAGTTCACGTTGCGATTTTT
Done.