Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009616.1 Hibiscus syriacus cultivar Beakdansim tig00117002_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: 692457
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:555255 original size:303 final size:303
Alignment explanation
Indices: 554708--555316 Score: 1002
Period size: 303 Copynumber: 2.0 Consensus size: 303
554698 ACATCGGAAC
554708 CCAAAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAAAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
* *
554773 GAATAAATCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGAATGGA
66 GAATAAATCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGCCCAGAATAGA
* * *
554838 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
*
554903 TGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTTTAC
196 TGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
*
554968 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * * * *
555011 CCAAAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCTGTTTTATTAGC
1 CCAAAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
** * ** * *
555076 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTCTGTTTGTATTTTATGTCCAGAATAGA
66 GAATAAATCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGCCCAGAATAGA
555141 AGAAAAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
* * * * *
555206 TGTACTAGATAATTTTGTAATATAATCGGTATAAGTATACCGGTTTTATGAGTGAATAGGTCTAC
196 TGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
555271 AACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
555314 CCA
1 CCA
555317 GAATGGAAGA
Statistics
Matches: 282, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
303 282 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (303 bp):
CCAAAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAAATCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGCCCAGAATAGA
AGAAAAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
TGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
AACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:555328 original size:183 final size:183
Alignment explanation
Indices: 555015--555485 Score: 780
Period size: 183 Copynumber: 2.6 Consensus size: 183
555005 TTATGTCCAA
* *
555015 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCTGTTTTATTAGCGAAT
1 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAAT
* * ** *
555080 AGGTCTACAACCTATGTCGACACTTTTTAATATTCTGTTTGTATTTTATGTCCAGAATAGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAA
* *
555145 AAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAG
131 AAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAG
* *
555198 AATTATAATGTACTAGATAATTTTGTAATATAATCGGTATAAGTATACCGGTTTTATGAGTGAAT
1 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAAT
*
555263 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAA
* * *
555328 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAG
131 AAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAG
* * *
555381 AATTATAATGTAATTGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAAT
555446 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCG
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCG
555486 CTAATTTTAA
Statistics
Matches: 268, Mismatches: 20, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
183 268 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35
Consensus pattern (183 bp):
AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATAGAAGAA
AAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAG
Found at i:555440 original size:486 final size:486
Alignment explanation
Indices: 554529--555485 Score: 1637
Period size: 486 Copynumber: 2.0 Consensus size: 486
554519 CGGAACCCAT
*
554529 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATGCTGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATCCTGGTTTTATGAGCGAAT
* *
554594 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGTCCAGAATAGAAGAA
* * *
554659 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
131 AAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
554724 ATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAAATCTACAACC
196 ATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAAATCTACAACC
554789 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGAATGGAAGAAAAATGTGTCGAT
261 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGAATGGAAGAAAAATGTGTCGAT
* *
554854 ACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTT
326 ACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAGAATTATAATGTAATAGATAATTTT
*
554919 ATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTTTACAACCTATATCGACACT
391 ATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACT
*
554984 TTTTAATTTTGTGTCGGTACTTTATGTCCAA
456 TTTTAATATTGTGTCGGTACTTTATGTCCAA
* * * *
555015 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCT-GTTTTATTAGCGAA
1 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATAT-CCTGGTTTTATGAGCGAA
* ** *
555079 TAGGTCTACAACCTATGTCGACACTTTTTAATATTCTGTTTGTATTTTATGTCCAGAATAGAAGA
65 TAGGTCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGTCCAGAATAGAAGA
*
555144 AAAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGT
130 AAAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGT
* * * * * **
555209 ACTAGATAATTTTGTAATATAATCGGTATAAGTATACCGGTTTTATGAGTGAATAGGTCTACAAC
195 AATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAAATCTACAAC
*
555274 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGA
260 CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGAATGGAAGAAAAATGTGTCGA
*
555339 TACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAGAATTATAATGTAATTGATAATTT
325 TACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAGAATTATAATGTAATAGATAATTT
*
555404 TGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC
390 TATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACAC
555469 TTTTTAATATTGTGTCG
455 TTTTTAATATTGTGTCG
555486 CTAATTTTAA
Statistics
Matches: 441, Mismatches: 29, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
486 439 1.00
487 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (486 bp):
AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATCCTGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGTCCAGAATAGAAGAA
AAAAGTATCAATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTA
ATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAAATCTACAACC
TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGAATGGAAGAAAAATGTGTCGAT
ACCTTGTCAAAAAGTGTCGACATTTACACACCGAAACCCAGAATTATAATGTAATAGATAATTTT
ATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACT
TTTTAATATTGTGTCGGTACTTTATGTCCAA
Found at i:556562 original size:16 final size:16
Alignment explanation
Indices: 556541--556572 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
556531 AATAAATAAG
556541 CGAACATAAACGAACA
1 CGAACATAAACGAACA
556557 CGAACATAAACGAACA
1 CGAACATAAACGAACA
556573 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:556656 original size:16 final size:16
Alignment explanation
Indices: 556635--556701 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
556625 TAAATAAATG
556635 AACATAAACGAACACA
1 AACATAAACGAACACA
*
556651 AACATAAACGAACACG
1 AACATAAACGAACACA
* *
556667 AACATAAATGAACACG
1 AACATAAACGAACACA
*
556683 AACATAAACGAACATA
1 AACATAAACGAACACA
556699 AAC
1 AAC
556702 GTTGGAGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:556670 original size:32 final size:32
Alignment explanation
Indices: 556634--556696 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
556624 ATAAATAAAT
556634 GAACATAAACGAACACAAACATAAACGAACAC
1 GAACATAAACGAACACAAACATAAACGAACAC
* *
556666 GAACATAAATGAACACGAACATAAACGAACA
1 GAACATAAACGAACACAAACATAAACGAACA
556697 TAAACGTTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.08
Consensus pattern (32 bp):
GAACATAAACGAACACAAACATAAACGAACAC
Found at i:558271 original size:24 final size:24
Alignment explanation
Indices: 558210--558271 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
558200 TATTAGGTTA
*
558210 AACATAAATGAACGCACATAAACG
1 AACATAACTGAACGCACATAAACG
* *
558234 AACATAACTAAACGCATATAAACG
1 AACATAACTGAACGCACATAAACG
*
558258 AACATAACCGAACG
1 AACATAACTGAACG
558272 TTCACGAACG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.53, C:0.23, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAACTGAACGCACATAAACG
Found at i:560840 original size:23 final size:23
Alignment explanation
Indices: 560811--560858 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
560801 AAATAGGTCA
*
560811 ATATAAGCGCTACCTATTACGTT
1 ATATAAGCGCTACCTAATACGTT
*
560834 ATATAAGCGCTACCTAATATGTT
1 ATATAAGCGCTACCTAATACGTT
560857 AT
1 AT
560859 TGTACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACGTT
Found at i:560915 original size:87 final size:87
Alignment explanation
Indices: 560811--560973 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
560801 AAATAGGTCA
* *
560811 ATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
560876 CCTGTTAAATACCTATTTTATT
66 CCAGTTAAATACCTATTTTATT
* *
560898 ATATAAACGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
560963 TCAGTTAAATA
66 CCAGTTAAATA
560974 ATATAACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAACGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATACCTATTTTATT
Found at i:568376 original size:27 final size:29
Alignment explanation
Indices: 568346--568411 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
568336 TTTCTTTTGG
568346 AAATAAACTTT-A-ATATATATATCCTTA
1 AAATAAACTTTAATATATATATATCCTTA
568373 AAATAAACTTTAATATATATATATCCTTA
1 AAATAAACTTTAATATATATATATCCTTA
*
568402 AAACAAACTT
1 AAATAAACTT
568412 CAAATCACTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 11 0.31
28 1 0.03
29 24 0.67
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATAAACTTTAATATATATATATCCTTA
Found at i:585580 original size:18 final size:18
Alignment explanation
Indices: 585554--585589 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
585544 TTTGTTCGTA
*
585554 TTTATCTTTTGATTGAGT
1 TTTAACTTTTGATTGAGT
585572 TTTAACTTTTGATTGAGT
1 TTTAACTTTTGATTGAGT
585590 CCTTAACTAA
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:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (18 bp):
TTTAACTTTTGATTGAGT
Found at i:585597 original size:19 final size:18
Alignment explanation
Indices: 585559--585597 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
585549 TCGTATTTAT
*
585559 CTTTTGATTGAGTTTTAA
1 CTTTTGATTGAGTCTTAA
585577 CTTTTGATTGAGTCCTTAA
1 CTTTTGATTGAGT-CTTAA
585596 CT
1 CT
585598 AAGTATAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (18 bp):
CTTTTGATTGAGTCTTAA
Found at i:586231 original size:22 final size:22
Alignment explanation
Indices: 586206--586247 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
586196 TAGTAGAACT
586206 AATTTAACTCATATGTCATGCC
1 AATTTAACTCATATGTCATGCC
586228 AATTTAACTCATATGTCATG
1 AATTTAACTCATATGTCATG
586248 TCATTCGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (22 bp):
AATTTAACTCATATGTCATGCC
Found at i:589122 original size:17 final size:17
Alignment explanation
Indices: 589100--589245 Score: 98
Period size: 17 Copynumber: 8.4 Consensus size: 17
589090 CATTTTATAT
589100 CTGTAAATATATGATAA
1 CTGTAAATATATGATAA
* * *
589117 CTGT-AATCATCTTATAT
1 CTGTAAAT-ATATGATAA
*
589134 CTATAAATA-ACTGATAA
1 CTGTAAATATA-TGATAA
* * *
589151 CCGAAAATCATTTGATAA
1 CTGTAAAT-ATATGATAA
589169 CTGTAAATATATGATAA
1 CTGTAAATATATGATAA
**
589186 CTAAAAATCATATGATAA
1 CTGTAAAT-ATATGATAA
* *
589204 TTGTAAATATCTGATAA
1 CTGTAAATATATGATAA
* * *
589221 CGGTGAAATGTTTGATAA
1 CTGT-AAATATATGATAA
*
589239 TTGTAAA
1 CTGTAAA
589246 CATTTATAAT
Statistics
Matches: 96, Mismatches: 26, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
16 3 0.03
17 50 0.52
18 43 0.45
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (17 bp):
CTGTAAATATATGATAA
Found at i:589122 original size:35 final size:36
Alignment explanation
Indices: 589076--589221 Score: 137
Period size: 35 Copynumber: 4.2 Consensus size: 36
589066 AATATATGTC
* *
589076 TGATAATTGTAAAA-CATTTTATATCTGTAAATATA
1 TGATAACTGTAAAATCATTTGATATCTGTAAATATA
*
589111 TGATAACTGT--AATCATCTT-ATATCTATAAATA-A
1 TGATAACTGTAAAATCAT-TTGATATCTGTAAATATA
* *
589144 CTGATAACCG-AAAATCATTTGATAACTGTAAATATA
1 -TGATAACTGTAAAATCATTTGATATCTGTAAATATA
* * *
589180 TGATAACT-AAAAATCATATGATAAT-TGTAAATATC
1 TGATAACTGTAAAATCATTTGAT-ATCTGTAAATATA
589215 TGATAAC
1 TGATAAC
589222 GGTGAAATGT
Statistics
Matches: 93, Mismatches: 9, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
33 3 0.03
34 25 0.27
35 63 0.68
36 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (36 bp):
TGATAACTGTAAAATCATTTGATATCTGTAAATATA
Found at i:589168 original size:18 final size:18
Alignment explanation
Indices: 589145--589221 Score: 77
Period size: 18 Copynumber: 4.4 Consensus size: 18
589135 TATAAATAAC
* *
589145 TGATAACCGAAAATCATT
1 TGATAACTGAAAATCATA
*
589163 TGATAACTGTAAAT-ATA
1 TGATAACTGAAAATCATA
*
589180 TGATAACTAAAAATCATA
1 TGATAACTGAAAATCATA
* * *
589198 TGATAATTGTAAAT-ATC
1 TGATAACTGAAAATCATA
589215 TGATAAC
1 TGATAAC
589222 GGTGAAATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
17 22 0.46
18 26 0.54
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (18 bp):
TGATAACTGAAAATCATA
Found at i:589245 original size:70 final size:69
Alignment explanation
Indices: 589086--589221 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 69
589076 TGATAATTGT
* * ** * *
589086 AAAA-CATTTTATATCTGTAAATATATGATAACTGTAATCATCTTATATCTATAAATAACTGATA
1 AAAATCATTTGATAACTGTAAATATATGATAACTAAAATCATATGATATCTATAAATAACTGATA
589150 ACCG
66 ACCG
* *
589154 AAAATCATTTGATAACTGTAAATATATGATAACTAAAAATCATATGATAAT-TGTAAATATCTGA
1 AAAATCATTTGATAACTGTAAATATATGATAACT-AAAATCATATGAT-ATCTATAAATAACTGA
589218 TAAC
64 TAAC
589222 GGTGAAATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
68 4 0.07
69 27 0.47
70 24 0.42
71 2 0.04
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (69 bp):
AAAATCATTTGATAACTGTAAATATATGATAACTAAAATCATATGATATCTATAAATAACTGATA
ACCG
Found at i:598849 original size:17 final size:17
Alignment explanation
Indices: 598824--598857 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
598814 TCTCGAGGAA
598824 ATAAATTTTAATAAAAT
1 ATAAATTTTAATAAAAT
* *
598841 ATAATTTTTATTAAAAT
1 ATAAATTTTAATAAAAT
598858 TTTTAAATAA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAATTTTAATAAAAT
Found at i:606983 original size:30 final size:30
Alignment explanation
Indices: 606948--607007 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
606938 AAAATAGAGT
606948 AAGTATAAGATAATATATGTTCAAAAATAA
1 AAGTATAAGATAATATATGTTCAAAAATAA
606978 AAGTATAAGATAATATATGTTCAAAAATAA
1 AAGTATAAGATAATATATGTTCAAAAATAA
607008 CTATCAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (30 bp):
AAGTATAAGATAATATATGTTCAAAAATAA
Found at i:615478 original size:3 final size:3
Alignment explanation
Indices: 615470--615533 Score: 114
Period size: 3 Copynumber: 22.0 Consensus size: 3
615460 GAGCATATCT
615470 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
615516 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
615534 AACTTGCTGT
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 55 0.93
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:615534 original size:20 final size:20
Alignment explanation
Indices: 615474--615535 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
615464 ATATCTTAAT
615474 AATAATAATAATAATAATAA
1 AATAATAATAATAATAATAA
615494 TAAT-ATAATAATAATAATAA
1 -AATAATAATAATAATAATAA
615514 AATAATAATAATAATAATAA
1 AATAATAATAATAATAATAA
615534 AA
1 AA
615536 CTTGCTGTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAATAATAATAATAATAA
Found at i:623571 original size:7 final size:7
Alignment explanation
Indices: 623559--624019 Score: 716
Period size: 7 Copynumber: 68.7 Consensus size: 7
623549 CTACACACAT
623559 GTAAGCA
1 GTAAGCA
623566 GTAAGCA
1 GTAAGCA
*
623573 GTACGCA
1 GTAAGCA
623580 -TAAGCA
1 GTAAGCA
623586 GTAAGCA
1 GTAAGCA
623593 GTAAGCA
1 GTAAGCA
623600 GTAAGCA
1 GTAAGCA
623607 GTAAGCA
1 GTAAGCA
623614 GTAAGCA
1 GTAAGCA
623621 GT-AGCA
1 GTAAGCA
623627 -TAAGCA
1 GTAAGCA
623633 GTAAGCA
1 GTAAGCA
623640 GTAAGCA
1 GTAAGCA
623647 GTAAGCA
1 GTAAGCA
623654 GTAAGCA
1 GTAAGCA
623661 GTAAGCA
1 GTAAGCA
623668 GTAAG-A
1 GTAAGCA
623674 GT-A--A
1 GTAAGCA
623678 GTAAGCA
1 GTAAGCA
623685 GTAAGCA
1 GTAAGCA
623692 GTAAGCA
1 GTAAGCA
623699 GTAAGCA
1 GTAAGCA
623706 GTAAGCA
1 GTAAGCA
*
623713 GTACGCA
1 GTAAGCA
623720 GTAAGCA
1 GTAAGCA
623727 GTAAGC-
1 GTAAGCA
623733 --AAGCA
1 GTAAGCA
623738 GTAAGCA
1 GTAAGCA
623745 GTAAGCA
1 GTAAGCA
623752 GTAAGCA
1 GTAAGCA
623759 GTAAGCA
1 GTAAGCA
623766 -TAAGCA
1 GTAAGCA
623772 GTAAGCA
1 GTAAGCA
623779 GTAAGCA
1 GTAAGCA
623786 GT-A--A
1 GTAAGCA
623790 GTAAGCA
1 GTAAGCA
623797 GTAAGCA
1 GTAAGCA
623804 GTAAGCA
1 GTAAGCA
623811 -T-AGCA
1 GTAAGCA
623816 GTAAGCA
1 GTAAGCA
623823 GTAAGCA
1 GTAAGCA
623830 GTAAGCA
1 GTAAGCA
623837 -TAAGCA
1 GTAAGCA
623843 GTAAGCA
1 GTAAGCA
623850 GTAAGCA
1 GTAAGCA
623857 GTAAGCA
1 GTAAGCA
623864 GTAAGCA
1 GTAAGCA
623871 GT-AGCA
1 GTAAGCA
623877 GTAAGCA
1 GTAAGCA
623884 GTAAGCA
1 GTAAGCA
623891 GTAAGCA
1 GTAAGCA
623898 GTAAGCA
1 GTAAGCA
623905 -TAAGCA
1 GTAAGCA
623911 GTAAGCA
1 GTAAGCA
623918 GTAAGCA
1 GTAAGCA
623925 GTAAGCA
1 GTAAGCA
623932 GTAAGC-
1 GTAAGCA
623938 -TAAGCA
1 GTAAGCA
623944 GTAAGCA
1 GTAAGCA
623951 GTAAGCA
1 GTAAGCA
623958 GTAAGCA
1 GTAAGCA
623965 GTAAGCA
1 GTAAGCA
623972 GT-A-CA
1 GTAAGCA
623977 GTAAGCA
1 GTAAGCA
623984 GTAAGCAGCA
1 GT-A--AGCA
623994 GTAAGCA
1 GTAAGCA
624001 GTAAGCA
1 GTAAGCA
624008 GTAAGCA
1 GTAAGCA
624015 GTAAG
1 GTAAG
624020 TAATCATCAT
Statistics
Matches: 425, Mismatches: 4, Indels: 50
0.89 0.01 0.10
Matches are distributed among these distances:
4 10 0.02
5 17 0.04
6 45 0.11
7 345 0.81
8 1 0.00
9 1 0.00
10 6 0.01
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.15
Consensus pattern (7 bp):
GTAAGCA
Found at i:627385 original size:20 final size:20
Alignment explanation
Indices: 627360--627409 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
627350 TTTCATACTC
627360 TTGCCCAAAAACTCACAAAT
1 TTGCCCAAAAACTCACAAAT
*
627380 TTGCCCAAAAACTCACATAT
1 TTGCCCAAAAACTCACAAAT
627400 TTGCCCAAAA
1 TTGCCCAAAA
627410 CGAAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.30, G:0.06, T:0.22
Consensus pattern (20 bp):
TTGCCCAAAAACTCACAAAT
Found at i:628041 original size:16 final size:18
Alignment explanation
Indices: 628010--628043 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
628000 CTCACTTTAG
628010 GAAAGAATGAAGAAGATA
1 GAAAGAATGAAGAAGATA
628028 GAAAG-ATG-AGAAGATA
1 GAAAGAATGAAGAAGATA
628044 TGAAGAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (18 bp):
GAAAGAATGAAGAAGATA
Found at i:629448 original size:18 final size:17
Alignment explanation
Indices: 629427--629469 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
629417 ATAAAAAAAT
* *
629427 AATAAAAAATAATTTTAA
1 AATAAAAAAAAATTGT-A
629445 AATAACAAAAAAATTGTA
1 AATAA-AAAAAAATTGTA
629463 AATAAAA
1 AATAAAA
629470 TCACTACAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 11 0.50
19 9 0.41
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
AATAAAAAAAAATTGTA
Found at i:633938 original size:15 final size:15
Alignment explanation
Indices: 633898--633941 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
633888 TGTTATGTCC
633898 ATATTTTTTAAATAAA
1 ATATTTTTTAAA-AAA
* *
633914 ATATTATTTAAAAAT
1 ATATTTTTTAAAAAA
633929 ATATTTTTTAAAA
1 ATATTTTTTAAAA
633942 TATGGACGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTTTAAAAAA
Found at i:639684 original size:2 final size:2
Alignment explanation
Indices: 639668--639711 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
639658 ATCATAATCC
*
639668 TA TA TG TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
639709 TA T
1 TA T
639712 TGTTAAATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:639968 original size:21 final size:21
Alignment explanation
Indices: 639939--639985 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
639929 ATTCTGACTA
639939 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
639960 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
639981 TCGCA
1 TCGCA
639986 ACGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:640018 original size:20 final size:20
Alignment explanation
Indices: 639993--640044 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
639983 GCAACGCGAA
*
639993 TACGTATTCGCATTGCAATT
1 TACGTAATCGCATTGCAATT
* *
640013 TACGTAATCGCGTTGCGATT
1 TACGTAATCGCATTGCAATT
640033 TA-GTAAATCGCA
1 TACGT-AATCGCA
640045 ACGAGATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (20 bp):
TACGTAATCGCATTGCAATT
Found at i:643522 original size:33 final size:33
Alignment explanation
Indices: 643485--643665 Score: 200
Period size: 33 Copynumber: 5.3 Consensus size: 33
643475 GGAAATTACT
*
643485 ATCGCAATGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* * * * *
643518 ATCGCAACGTGAAAATCGTAACGCGAATATGAAT
1 ATCGCAACGAGAGAATCGCAATGCGAA-ATGAAA
*
643552 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAA
1 ATCGCAA--C-GAGA-GA--ATCGCAATGCGAAATGAAA
* *
643591 ATCGCAACGAGAGAATCACAATGCGAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
* *
643624 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
643657 ATCGCAACG
1 ATCGCAACG
643666 CGAATTTAGT
Statistics
Matches: 122, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
33 77 0.63
34 12 0.10
35 2 0.02
36 4 0.03
37 3 0.02
38 1 0.01
39 12 0.10
40 11 0.09
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
Found at i:643550 original size:20 final size:19
Alignment explanation
Indices: 643498--643669 Score: 104
Period size: 19 Copynumber: 9.7 Consensus size: 19
643488 GCAATGAGAG
*
643498 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
643517 AATCGCAA--CG---TGAA
1 AATCGCAACGCGAAATGAA
*
643531 AATCGTAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
* *
643551 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAA
* *
643571 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
643590 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
* * *
643604 AATCACAATGCGAAATAAA
1 AATCGCAACGCGAAATGAA
**
643623 AATCGCAA--CG--A-GGG
1 AATCGCAACGCGAAATGAA
*
643637 AATCGCAAAGCGAAATGAA
1 AATCGCAACGCGAAATGAA
643656 AATCGCAACGCGAA
1 AATCGCAACGCGAA
643670 TTTAGTTTCG
Statistics
Matches: 118, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
14 28 0.24
15 2 0.02
16 6 0.05
17 6 0.05
18 2 0.02
19 44 0.37
20 27 0.23
21 3 0.03
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:643585 original size:73 final size:66
Alignment explanation
Indices: 643485--643665 Score: 200
Period size: 73 Copynumber: 2.6 Consensus size: 66
643475 GGAAATTACT
* * * ** *
643485 ATCGCAATGAGAGAATCGCAATGCGAAATGAAAATCGCAACGTGAAAATCGTAACGCGAATATGA
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAACGCGAA-ATAA
*
643550 AT
65 AA
* * *
643552 ATCGCAACGCGGAAATGACTATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCACAATGCGA
1 ATCGCAACGAGG----GA--ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAACGCGA
643617 AATAAAA
60 AATAAAA
*
643624 ATCGCAACGAGGGAATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACG
643666 CGAATTTAGT
Statistics
Matches: 96, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
66 27 0.28
67 9 0.09
68 2 0.02
71 2 0.02
72 15 0.16
73 41 0.43
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (66 bp):
ATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCACAACGCGAAATAAA
A
Found at i:643709 original size:19 final size:19
Alignment explanation
Indices: 643685--643766 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
643675 TTTCGCGTTG
643685 CGCGTTGCGATTTT-AGTTT
1 CGCGTTGCGATTTTCA-TTT
643704 CGCGTTGCGATTTTCATTT
1 CGCGTTGCGATTTTCATTT
*
643723 CGCATTGCGA--TTC---T
1 CGCGTTGCGATTTTCATTT
*
643737 CTCGTTGCGATTTTCATTT
1 CGCGTTGCGATTTTCATTT
*
643756 CGCATTGCGAT
1 CGCGTTGCGAT
643767 AGTCACTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
14 9 0.17
16 3 0.06
17 3 0.06
19 36 0.69
20 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
CGCGTTGCGATTTTCATTT
Found at i:643892 original size:14 final size:13
Alignment explanation
Indices: 643873--643911 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
643863 CATCAATTAA
643873 ACAAATCAACTTTT
1 ACAAATCAA-TTTT
643887 ACAAATCATATTTT
1 ACAAATCA-ATTTT
643901 ACAAATCAATT
1 ACAAATCAATT
643912 AAACAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 3 0.12
14 20 0.83
15 1 0.04
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (13 bp):
ACAAATCAATTTT
Found at i:647216 original size:33 final size:33
Alignment explanation
Indices: 647174--647251 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
647164 GGAAATGACT
647174 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
647207 ATCGCAACGCGAAATTAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
647240 ATCACAATGCGA
1 ATCGCAACGCGA
647252 TTTTGGTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:647230 original size:19 final size:19
Alignment explanation
Indices: 647125--647234 Score: 95
Period size: 20 Copynumber: 5.9 Consensus size: 19
647115 TCTTTTGGTT
* *
647125 GAAATAAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
647144 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
647164 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
647184 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
647201 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
647217 GAAATTAAAATCGCAACG
1 GAAATGAAAATCGCAACG
647235 AGAGAATCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 27 0.36
20 30 0.40
21 2 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:647271 original size:19 final size:19
Alignment explanation
Indices: 647247--647291 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
647237 AGAATCACAA
**
647247 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTAATTTCGCGT
647266 TGCGATTTTAATTTCGCGT
1 TGCGATTTTAATTTCGCGT
*
647285 TGTGATT
1 TGCGATT
647292 CTCTTGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTAATTTCGCGT
Found at i:647343 original size:20 final size:20
Alignment explanation
Indices: 647296--647368 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
647286 GTGATTCTCT
647296 TGTTGCGATTTTCATTTCTC-
1 TGTTGCGATTTTCATTT-TCA
**
647316 TCGTTGCGATAGTCATTTTCA
1 T-GTTGCGATTTTCATTTTCA
647337 TGTTGCGATTTTCATTTTCA
1 TGTTGCGATTTTCATTTTCA
647357 TGTTGCGATTTT
1 TGTTGCGATTTT
647369 AAGTTTAGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
20 32 0.68
21 15 0.32
ACGTcount: A:0.14, C:0.16, G:0.18, T:0.52
Consensus pattern (20 bp):
TGTTGCGATTTTCATTTTCA
Found at i:647816 original size:27 final size:27
Alignment explanation
Indices: 647786--647851 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
647776 GAGATGGGAC
647786 TGAGTTGTGATTTTAGGTTTTAGGTTA
1 TGAGTTGTGATTTTAGGTTTTAGGTTA
647813 TGAGTTGTGATTTTAGGTTTTAGGTTA
1 TGAGTTGTGATTTTAGGTTTTAGGTTA
*
647840 TGAGTTGCGATT
1 TGAGTTGTGATT
647852 ACGGGATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.18, C:0.02, G:0.30, T:0.50
Consensus pattern (27 bp):
TGAGTTGTGATTTTAGGTTTTAGGTTA
Found at i:647978 original size:20 final size:20
Alignment explanation
Indices: 647953--648166 Score: 225
Period size: 20 Copynumber: 10.6 Consensus size: 20
647943 CTTTAAAAAT
647953 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
647973 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
647993 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
648014 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* * *
648034 CTCGTTACGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
648054 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
648074 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
648094 CGCATTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
648114 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
648135 CGCGTTGTGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
648156 CTCGTTGCGAT
1 CGCGTTGCGAT
648167 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 105 0.67
21 51 0.33
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:648012 original size:41 final size:41
Alignment explanation
Indices: 647955--648166 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
647945 TTAAAAATCG
*
647955 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
647996 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
648036 CGTTACGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
648076 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
648117 CGTTGCGATTTACGGATACGCGTTGTGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
648158 CGTTGCGAT
1 CGTTGCGAT
648167 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 73 0.47
41 83 0.53
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:648306 original size:20 final size:20
Alignment explanation
Indices: 648261--648310 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
648251 TTCATAATTA
648261 CGTTGCGATTCTGGGAACTG
1 CGTTGCGATTCTGGGAACTG
** *
648281 ATTTGCGATTCTGGAGATC-G
1 CGTTGCGATTCTGG-GAACTG
648301 CGTTGCGATT
1 CGTTGCGATT
648311 TTTATTTCGC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTCTGGGAACTG
Found at i:653868 original size:15 final size:16
Alignment explanation
Indices: 653836--653868 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
653826 AATCTAAGCT
*
653836 TAAATATAAAATTCGA
1 TAAAAATAAAATTCGA
653852 TAAAAATAAAA-TCGA
1 TAAAAATAAAATTCGA
653867 TA
1 TA
653869 CTTGAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAAATAAAATTCGA
Found at i:653904 original size:27 final size:27
Alignment explanation
Indices: 653848--653905 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
653838 AATATAAAAT
*
653848 TCGATAAAAATAAAATCGATACTTGAA
1 TCGATAAAAATAAAATCGATACTTCAA
*
653875 TCGATACAAAACT-AAATCG-TACTTCCA
1 TCGATA-AAAA-TAAAATCGATACTTCAA
653902 TCGA
1 TCGA
653906 AATTTCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 16 0.59
28 10 0.37
29 1 0.04
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (27 bp):
TCGATAAAAATAAAATCGATACTTCAA
Found at i:657030 original size:26 final size:27
Alignment explanation
Indices: 656973--657030 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
656963 AAATGTTAAG
*
656973 TTATACATCCAAACCCTAAATCTTAAA
1 TTATACATCCAAACCCTAAATCTCAAA
* *
657000 CTATACCT-CAAACCCT-AATCCTCAAA
1 TTATACATCCAAACCCTAAAT-CTCAAA
657026 TTATA
1 TTATA
657031 ACTTCTGCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 3 0.12
26 17 0.65
27 6 0.23
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.29
Consensus pattern (27 bp):
TTATACATCCAAACCCTAAATCTCAAA
Found at i:657643 original size:21 final size:20
Alignment explanation
Indices: 657623--657662 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
657613 TATATCAAAT
*
657623 TCAATAAATAAATTAAAAAA
1 TCAATAAATAAAATAAAAAA
**
657643 TCCGTAAATAAAATAAAAAA
1 TCAATAAATAAAATAAAAAA
657663 AGAGAAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.23
Consensus pattern (20 bp):
TCAATAAATAAAATAAAAAA
Found at i:668622 original size:23 final size:24
Alignment explanation
Indices: 668591--668635 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
668581 CATTTCTTGC
668591 ATTTAATATTTT-CATGTTTTTTT
1 ATTTAATATTTTCCATGTTTTTTT
*
668614 ATTTTATATTTTCCATGTTTTT
1 ATTTAATATTTTCCATGTTTTT
668636 ACATTCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (24 bp):
ATTTAATATTTTCCATGTTTTTTT
Found at i:672139 original size:15 final size:17
Alignment explanation
Indices: 672112--672145 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
672102 TCTTTTTGAA
672112 TTCATTGTCCATTT-TC
1 TTCATTGTCCATTTCTC
672128 TTCATT-TCCATTTCTC
1 TTCATTGTCCATTTCTC
672144 TT
1 TT
672146 TCAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.12, C:0.26, G:0.03, T:0.59
Consensus pattern (17 bp):
TTCATTGTCCATTTCTC
Found at i:675810 original size:11 final size:11
Alignment explanation
Indices: 675796--675823 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
675786 AAAGGAAAAG
675796 AGAAAAAGAAA
1 AGAAAAAGAAA
675807 AGAAAAAGAAA
1 AGAAAAAGAAA
675818 AGAAAA
1 AGAAAA
675824 TAAGGTGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:675813 original size:74 final size:74
Alignment explanation
Indices: 675670--675813 Score: 193
Period size: 74 Copynumber: 1.9 Consensus size: 74
675660 AGTACTTCGC
* * *
675670 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAATAAAAAAAGAGGAAAAAAATA
1 TTAGGATGAAAACCCGAAAGGGCGTCCTAAATTGAAAAAAAAAATAAAAAAAGAGGAAAAAAAAA
675735 AAAAATCGT
66 AAAAATCGT
* * **
675744 TTAGGGTGAAAACCCGAAAGGGCGTCCTAAATTGAAAAAATAAA-AGGAAAAGA-GAAAAAGAAA
1 TTAGGATGAAAACCCGAAAGGGCGTCCTAAATTGAAAAAAAAAATAAAAAAAGAGGAAAAA-AAA
675807 AGAAAAA
65 A-AAAAA
675814 GAAAAGAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
72 6 0.10
73 10 0.16
74 45 0.74
ACGTcount: A:0.56, C:0.09, G:0.22, T:0.13
Consensus pattern (74 bp):
TTAGGATGAAAACCCGAAAGGGCGTCCTAAATTGAAAAAAAAAATAAAAAAAGAGGAAAAAAAAA
AAAAATCGT
Found at i:676822 original size:120 final size:120
Alignment explanation
Indices: 676637--676853 Score: 289
Period size: 120 Copynumber: 1.8 Consensus size: 120
676627 TGTTCGAGAG
* * * *
676637 TAGATTTCAACTTCACGACGAATGATATCTAGCTCGAAGCCAAACTTCACAATGAAAGGGTCATC
1 TAGATTTCAACTTCACGACGAAGGATATCAAGCTCGAAGCCAAACTTCACAATCAAAGGGCCATC
*
676702 CACGGTTTCAACTTCACGGCGAAGGGAATCGTGTCCACCCGCAACATACAATACT
66 CACGGTTTCAACTTCACGACGAAGGGAATCGTGTCCACCCGCAACATACAATACT
* *
676757 TAGATTTCAACTTCACGATGAAGGATATTCAAG-TC-AAGGCTC-AACTTCACGA-CAAAGGGGC
1 TAGATTTCAACTTCACGACGAAGGATA-TCAAGCTCGAA-GC-CAAACTTCACAATCAAA-GGGC
* *
676818 CATCCATGGTTTCAACTTCACGATGAAGGGAATCGT
62 CATCCACGGTTTCAACTTCACGACGAAGGGAATCGT
676854 ACCCACACAT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
119 5 0.06
120 74 0.88
121 5 0.06
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (120 bp):
TAGATTTCAACTTCACGACGAAGGATATCAAGCTCGAAGCCAAACTTCACAATCAAAGGGCCATC
CACGGTTTCAACTTCACGACGAAGGGAATCGTGTCCACCCGCAACATACAATACT
Found at i:677115 original size:106 final size:104
Alignment explanation
Indices: 676930--677188 Score: 396
Period size: 106 Copynumber: 2.5 Consensus size: 104
676920 ACGAAGAGGC
* *
676930 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTGGACTCAAGACAGCACAAGCT
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCT
* * *
676995 CAACTTCACAGCGAATGGGCGGCTGACTGTCAACAAA-T
66 CAACTTCACAGCGAAGGGGCGACTGACTATCAACAAACT
677033 AAGTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAA
1 ---TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAA
677098 GCTCAACTTCACAGCGAAGGGGCGACTGACTATCAACAAACT
63 GCTCAACTTCACAGCGAAGGGGCGACTGACTATCAACAAACT
* * * *
677140 TT-CCAGTTTCAGAGTCAATTTCAACTTCACAACGGAGGATATTAGACTC
1 TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
677189 GGAACAATAC
Statistics
Matches: 143, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
103 43 0.30
104 2 0.01
106 97 0.68
107 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (104 bp):
TTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCT
CAACTTCACAGCGAAGGGGCGACTGACTATCAACAAACT
Found at i:679061 original size:2 final size:2
Alignment explanation
Indices: 679054--679078 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
679044 TTATTATTAA
679054 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
679079 CTTTTTGTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:686271 original size:35 final size:34
Alignment explanation
Indices: 686227--686339 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
686217 AAAACAATTC
*
686227 TCAATTTCATTCTAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
*
686262 TCAATTTCATTCTAAACTCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAAC-CCAAATTCCAAAATAAT
* * *
686297 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
686332 TCAATTTC
1 TCAATTTC
686340 TGTCTTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
35 64 0.93
36 5 0.07
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:687397 original size:35 final size:34
Alignment explanation
Indices: 687349--687460 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 34
687339 ATTTCTCCTT
*
687349 AAATTGAAGTATTTTAGAATTTGGGATTTAGAATG
1 AAATTGAATTATTTT-GAATTTGGGATTTAGAATG
*
687384 TAATTGAATTATTTTGGAATTTAGGG-TTTAGAATG
1 AAATTGAATTATTTT-GAATTT-GGGATTTAGAATG
* *
687419 AAATTGAATTACTTTGAAATTTGGGATTTATAATG
1 AAATTGAATTATTTTG-AATTTGGGATTTAGAATG
687454 AAATTGA
1 AAATTGA
687461 GGAATGTTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
34 4 0.06
35 61 0.90
36 3 0.04
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.42
Consensus pattern (34 bp):
AAATTGAATTATTTTGAATTTGGGATTTAGAATG
Done.