Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008624.1 Hibiscus syriacus cultivar Beakdansim tig00111587_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: 642794
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:537503 original size:20 final size:21
Alignment explanation
Indices: 537466--537505 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
537456 AAATTAAGTT
537466 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
537487 AAATG-ATTTTATA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
537506 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:537760 original size:19 final size:19
Alignment explanation
Indices: 537736--537774 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
537726 TCGAATGCAT
537736 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
537755 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
537774 T
1 T
537775 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:537875 original size:64 final size:65
Alignment explanation
Indices: 537722--537882 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
537712 GAATTAATTG
* * *** *
537722 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
537787 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATA-TTTTCA
537850 A
65 A
537851 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
537883 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:537897 original size:64 final size:64
Alignment explanation
Indices: 537722--537902 Score: 220
Period size: 64 Copynumber: 2.8 Consensus size: 64
537712 GAATTAATTG
* * * *
537722 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
537787 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
537851 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
537903 AGTGTTCCAA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 48 0.48
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:543698 original size:20 final size:21
Alignment explanation
Indices: 543669--543724 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
543659 TTTGTGCTTC
*
543669 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
543689 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
543711 ATGCATCGATGCAT
1 ATGCATCGATGCAT
543725 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:543721 original size:42 final size:42
Alignment explanation
Indices: 543669--543748 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
543659 TTTGTGCTTC
* *
543669 ATGCACCGATGCATTTA-ACAATGCATCGATGCATCCTTGAAT
1 ATGCACCGATGCA-TAAGACAATGCACCGATGCATCCTTGAAT
* *
543711 ATGCATCGATGCATAAGACCATGCACCGATGCATCCTT
1 ATGCACCGATGCATAAGACAATGCACCGATGCATCCTT
543749 CGGGTTTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.06
42 31 0.94
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCACCGATGCATAAGACAATGCACCGATGCATCCTTGAAT
Found at i:545293 original size:21 final size:21
Alignment explanation
Indices: 545251--545294 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
545241 ACCCCGGGAG
*
545251 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
545272 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
545293 CT
1 CT
545295 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:546294 original size:20 final size:20
Alignment explanation
Indices: 546269--546307 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
546259 TATTCAAAGG
546269 CATGCACCGATGCATCAATA
1 CATGCACCGATGCATCAATA
*
546289 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
546308 GAATTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (20 bp):
CATGCACCGATGCATCAATA
Found at i:546356 original size:19 final size:19
Alignment explanation
Indices: 546332--546370 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
546322 TCGAATGCAT
546332 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
546351 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
546370 T
1 T
546371 AAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:546387 original size:65 final size:64
Alignment explanation
Indices: 546269--546476 Score: 208
Period size: 65 Copynumber: 3.2 Consensus size: 64
546259 TATTCAAAGG
* ** ** *
546269 CATGCACCGATGCATCAATACATGCATCGATGCATCAATGAAT-TAATT-GAACATCGAATGCAT
1 CATGCATCGATGCA-CAAGCCATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCAT
*
546332 TC
63 TT
* ***
546334 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTA-AATA-TTTTCAAAACATCGAATGCAT
1 CATGCATCGATGCACAAGCCATGCATCGATGCA-TC-AGAATATTTTTC-AAACATCGAATGCAT
546397 TT
63 TT
* **
546399 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
546463 CATGCATCGATGCA
1 CATGCATCGATGCA
546477 TACTTGGTGC
Statistics
Matches: 121, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
63 6 0.05
64 50 0.41
65 65 0.54
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:547954 original size:18 final size:18
Alignment explanation
Indices: 547926--547966 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
547916 CCCAGCAGCC
*
547926 ACCGTAGCCATATATGAT
1 ACCGCAGCCATATATGAT
*
547944 GCCGCAGCCATATATGAT
1 ACCGCAGCCATATATGAT
547962 ACCGC
1 ACCGC
547967 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (18 bp):
ACCGCAGCCATATATGAT
Found at i:552699 original size:31 final size:31
Alignment explanation
Indices: 552671--552762 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
552661 ACTCTTAATA
* * *
552671 TTTAGACAAAATGTTAATATGACCCTTAAAT
1 TTTAGATAAAATATCAATATGACCCTTAAAT
*
552702 TTTAGATAAAATATCAA-ATTAACCCTTAAAT
1 TTTAGATAAAATATCAATA-TGACCCTTAAAT
*
552733 TTTAGATAAAATATCAAAATGACCCTTAAA
1 TTTAGATAAAATATCAATATGACCCTTAAA
552763 CATAAAATGA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.02
31 52 0.96
32 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.34
Consensus pattern (31 bp):
TTTAGATAAAATATCAATATGACCCTTAAAT
Found at i:553723 original size:20 final size:20
Alignment explanation
Indices: 553668--553716 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
553658 CCTATTCCCT
553668 GGTAATCTTTTATTCCCACC
1 GGTAATCTTTTATTCCCACC
* *
553688 AGTAATCTTTTATTCCTACC
1 GGTAATCTTTTATTCCCACC
553708 GGTAATCTT
1 GGTAATCTT
553717 ACATTCCCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.43
Consensus pattern (20 bp):
GGTAATCTTTTATTCCCACC
Found at i:560898 original size:30 final size:31
Alignment explanation
Indices: 560839--560899 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
560829 AAGAAGTGAA
* **
560839 CATTTTGTTATAAATCGATAATGTTAATAAC
1 CATTTTGTTACAAATCGATAACATTAATAAC
*
560870 CATTTTGTTACAAATCG-TCACATTAATAAC
1 CATTTTGTTACAAATCGATAACATTAATAAC
560900 GTTAGTGACT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (31 bp):
CATTTTGTTACAAATCGATAACATTAATAAC
Found at i:577150 original size:20 final size:20
Alignment explanation
Indices: 577122--577193 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
577112 TTCCCAATTT
*
577122 GCAATGCGAATAAGTAAATC
1 GCAACGCGAATAAGTAAATC
** *
577142 GCAACGCGAATTGGGAAAATC
1 GCAACGCGAA-TAAGTAAATC
*
577163 GCAATGCGAATAAGTAAATC
1 GCAACGCGAATAAGTAAATC
577183 GCAACGCGAAT
1 GCAACGCGAAT
577194 TGGGAAAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
GCAACGCGAATAAGTAAATC
Found at i:577163 original size:21 final size:21
Alignment explanation
Indices: 577137--577212 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
577127 GCGAATAAGT
577137 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
577158 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
577178 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
577199 AAATCGCAATGCGA
1 AAATCGCAACGCGA
577213 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:577167 original size:41 final size:41
Alignment explanation
Indices: 577122--577212 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
577112 TTCCCAATTT
577122 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATC
1 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATC
577163 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATC
1 GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATC
577204 GCAATGCGA
1 GCAATGCGA
577213 TACTGACTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (41 bp):
GCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATC
Found at i:577225 original size:41 final size:42
Alignment explanation
Indices: 577139--577278 Score: 137
Period size: 41 Copynumber: 3.4 Consensus size: 42
577129 GAATAAGTAA
* *
577139 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGATATTGGGAAAATCGCAATGCG-ATACTG-ACT
577180 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGATATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
577221 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGATATTGGGAAAATCGCAATGCGATACTGACT
*
577262 TTCGCAACGCGATATTG
1 ATCGCAACGCGATATTG
577279 ACTTTCGCAA
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
40 4 0.05
41 77 0.93
42 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (42 bp):
ATCGCAACGCGATATTGGGAAAATCGCAATGCGATACTGACT
Found at i:577226 original size:20 final size:20
Alignment explanation
Indices: 577201--577315 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
577191 AATTGGGAAA
* *
577201 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATAATGACT
* * **
577221 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATAAT-GACT
* * *
577242 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAATGACT
* *
577262 TTCGCAACGCGATATTGACT
1 ATCGCAACGCGATAATGACT
*
577282 TTCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATAATGAC-T
*
577302 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
577316 TTTCAAAGTG
Statistics
Matches: 75, Mismatches: 17, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
19 2 0.03
20 48 0.64
21 25 0.33
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATAATGACT
Found at i:577511 original size:22 final size:22
Alignment explanation
Indices: 577483--577526 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
577473 CACTCTCTCA
577483 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
577505 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
577527 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:577815 original size:20 final size:20
Alignment explanation
Indices: 577790--577827 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
577780 CGATTCTCTC
577790 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
577810 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
577828 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:579168 original size:18 final size:18
Alignment explanation
Indices: 579147--579191 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
579137 TCCACTTCGG
*
579147 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
579165 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
579183 GAGCCATCA
1 GAGCCATCA
579192 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:579721 original size:19 final size:20
Alignment explanation
Indices: 579667--579733 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
579657 TAGTTTACTT
* *
579667 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
579687 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
579707 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
579726 TCGCAACG
1 TCGCAACG
579734 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:579779 original size:19 final size:19
Alignment explanation
Indices: 579667--579787 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
579657 TAGTTTACTT
* **
579667 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
579687 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
579707 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
579726 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
579740 TCGCAATGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
579758 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
579777 TCGCAATGCGA
1 TCGCAACGCGA
579788 TTTGTGTTTC
Statistics
Matches: 84, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 18 0.21
19 26 0.31
20 24 0.29
21 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:579818 original size:14 final size:14
Alignment explanation
Indices: 579799--579856 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
579789 TTGTGTTTCG
579799 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
579813 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
579829 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
579845 CGTTGCGATTTT
1 CGTTGCGATTTT
579857 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:579833 original size:32 final size:33
Alignment explanation
Indices: 579794--579872 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
579784 GCGATTTGTG
579794 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
579826 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
579859 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
579873 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:579871 original size:19 final size:19
Alignment explanation
Indices: 579813--579928 Score: 82
Period size: 20 Copynumber: 6.3 Consensus size: 19
579803 GCGATTTTGT
579813 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
579831 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
579845 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
579864 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
579884 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
579903 CGTTGTGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
579923 TGTTGC
1 CGTTGC
579929 AAAAGTAAAC
Statistics
Matches: 77, Mismatches: 14, Indels: 12
0.75 0.14 0.12
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 11 0.14
19 25 0.32
20 26 0.34
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:583853 original size:33 final size:33
Alignment explanation
Indices: 583796--583883 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
583786 ACGAGATAAT
*
583796 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
583830 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* *
583863 GACAATCACAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
583884 AAATCACAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 36 0.72
34 14 0.28
ACGTcount: A:0.40, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:583914 original size:39 final size:38
Alignment explanation
Indices: 583866--583955 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 38
583856 GCGACCAGAC
*
583866 AATCACAACGCGAAATGAAAATCACAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCACAA-CGCGAAATAAA
* *
583905 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCACAACGCGAAATAAA
*
583943 AATCGCAATGCGA
1 AATCGCAACGCGA
583956 TTTTGGTTTC
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 22 0.47
39 25 0.53
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCACAACGCGAAATAAA
Found at i:583947 original size:19 final size:19
Alignment explanation
Indices: 583771--583955 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
583761 TCTTTTGGTT
*
583771 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
583790 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
583810 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
583828 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
583844 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
* *
583862 ---A-GACAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
583877 GAAATGAAAATCACAACCGC
1 GAAATGAAAATCGCAA-CGC
*
583897 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
583916 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
583935 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
583954 GA
1 GA
583956 TTTTGGTTTC
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 18 0.13
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.46
20 44 0.32
21 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:583984 original size:19 final size:19
Alignment explanation
Indices: 583951--584017 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
583941 AAAATCGCAA
**
583951 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
583970 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
583989 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
584009 TGCGATTTT
1 TGCGATTTT
584018 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:584564 original size:20 final size:20
Alignment explanation
Indices: 584539--584586 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
584529 ATGTAAATCG
584539 CGTTGCGAAAGTCAG-AGTCA
1 CGTTGCGAAAGTCAGTA-TCA
*
584559 CGTTGCGAAAGTCAGTATCT
1 CGTTGCGAAAGTCAGTATCA
584579 CGTTGCGA
1 CGTTGCGA
584587 TTTTGTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCA
Found at i:584979 original size:15 final size:16
Alignment explanation
Indices: 584945--584980 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
584935 TTGTGTTCTC
584945 AAAATTGAAATTCCCA
1 AAAATTGAAATTCCCA
*
584961 AAAATTGAAATTCCTA
1 AAAATTGAAATTCCCA
584977 AAAA
1 AAAA
584981 CGTTCATTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (16 bp):
AAAATTGAAATTCCCA
Found at i:587017 original size:12 final size:12
Alignment explanation
Indices: 587000--587038 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
586990 TTTATCTTTT
587000 AAATTTTATAAA
1 AAATTTTATAAA
587012 AAA-TTTATATAA
1 AAATTTTATA-AA
587024 AAATTTTATTAAA
1 AAATTTTA-TAAA
587037 AA
1 AA
587039 GTATATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.25
12 8 0.33
13 8 0.33
14 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATTTTATAAA
Found at i:587022 original size:13 final size:13
Alignment explanation
Indices: 587000--587038 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
586990 TTTATCTTTT
587000 AAATTT-TATAAA
1 AAATTTATATAAA
587012 AAATTTATATAAA
1 AAATTTATATAAA
*
587025 AATTTTAT-TAAA
1 AAATTTATATAAA
587037 AA
1 AA
587039 GTATATAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.48
13 13 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTTATATAAA
Found at i:587043 original size:23 final size:24
Alignment explanation
Indices: 587000--587047 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
586990 TTTATCTTTT
*
587000 AAATTTTATAAAAAATTTATATAA
1 AAATTTTATAAAAAATGTATATAA
*
587024 AAATTTTATTAAAAA-GTATATAA
1 AAATTTTATAAAAAATGTATATAA
587047 A
1 A
587048 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
AAATTTTATAAAAAATGTATATAA
Found at i:591272 original size:171 final size:172
Alignment explanation
Indices: 590986--591324 Score: 608
Period size: 171 Copynumber: 2.0 Consensus size: 172
590976 CTTAGTATCT
*
590986 TTTTATAGGGATATATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
1 TTTTATAGGGATAGATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
*
591051 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCGA
66 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
* * *
591116 GTCAAACTTTATTAAATCTCCTCTTTAACATGAATTCTAAAA
131 GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCTAAAA
* *
591158 TTTTATATGGATAGATACTTGATTACAAAGAAAACTAAATAAA-TAAAAAATTACTTTAATAAAG
1 TTTTATAGGGATAGATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
591222 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
66 TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
591287 GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCT
131 GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCT
591325 GAAGGTGCAA
Statistics
Matches: 160, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
171 120 0.75
172 40 0.25
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (172 bp):
TTTTATAGGGATAGATACTTGATCACAAAGAAAACTAAATAAAGTAAAAAATTACTTTAATAAAG
TTCTCTACTTTTAATCAAAATAGGTTTATTACTTTCCCAATTAAATTATGTCACTTTGAATTCAA
GTCAAACTTTAATAAATCTCCACTTTAACACGAATTCTAAAA
Found at i:594074 original size:42 final size:42
Alignment explanation
Indices: 594020--594117 Score: 178
Period size: 42 Copynumber: 2.3 Consensus size: 42
594010 CTAAATTTTA
594020 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTTT
1 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTTT
594062 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTTT
1 TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTTT
*
594104 TTCCTTATCAAATA
1 TT-CTTCTCAAATA
594118 CATTATTTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 44 0.81
43 10 0.19
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.41
Consensus pattern (42 bp):
TTCTTCTCAAATATGTTATGCCCACATAACTAAACTCTCTTT
Found at i:594733 original size:14 final size:15
Alignment explanation
Indices: 594701--594733 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
594691 CTGCTCGTGT
594701 TTTTTCACGAAAAAG
1 TTTTTCACGAAAAAG
*
594716 TTTTTCACGTAAAA-
1 TTTTTCACGAAAAAG
594730 TTTT
1 TTTT
594734 GGTGTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTTTCACGAAAAAG
Found at i:596320 original size:18 final size:17
Alignment explanation
Indices: 596299--596336 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
596289 AATTATAAAG
*
596299 TTATCCTAATATATATAA
1 TTATACTAATAT-TATAA
596317 TTATACTAATATTATAA
1 TTATACTAATATTATAA
596334 TTA
1 TTA
596337 GTCTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATACTAATATTATAA
Found at i:596516 original size:2 final size:2
Alignment explanation
Indices: 596509--596542 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
596499 TCATAAATAC
596509 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
596543 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:597516 original size:8 final size:8
Alignment explanation
Indices: 597500--597551 Score: 52
Period size: 8 Copynumber: 6.1 Consensus size: 8
597490 TAAAATTGTA
597500 ATAATTAAT
1 ATAA-TAAT
597509 ATAATAAT
1 ATAATAAT
597517 ATAA-AAT
1 ATAATAAT
597524 AATAATATATT
1 -ATAATA-A-T
597535 ATAATAAT
1 ATAATAAT
*
597543 ATTATAAT
1 ATAATAAT
597551 A
1 A
597552 CTTATAACGA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
7 3 0.08
8 21 0.55
9 6 0.16
10 7 0.18
11 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:597527 original size:13 final size:13
Alignment explanation
Indices: 597498--597544 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
597488 TGTAAAATTG
597498 TAATAAT-TAATA
1 TAATAATATAATA
*
597510 TAATAATATAAAA
1 TAATAATATAATA
*
597523 TAATAATATATTA
1 TAATAATATAATA
597536 TAATAATAT
1 TAATAATAT
597545 TATAATACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
12 7 0.23
13 24 0.77
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:597782 original size:36 final size:36
Alignment explanation
Indices: 597734--597857 Score: 160
Period size: 36 Copynumber: 3.4 Consensus size: 36
597724 GATTTGTTCA
**
597734 TGCTTCACTACTCTTTTGTGAAGGCTGAAGGTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGAATTTGCAT
* * *
597770 CGCTTCACTACTCTTTTGTGAAGGCTTAATTTGTAT
1 TGCTTCACTACTCTTTTGTGAAGGCTGAATTTGCAT
* *
597806 TGCTTCATTACTCGTTTGTGAAGGCTTG-ATTTGCAT
1 TGCTTCACTACTCTTTTGTGAAGGC-TGAATTTGCAT
597842 TGCTTCCACTACTCTT
1 TGCTT-CACTACTCTT
597858 CCGTGGAGAT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
36 65 0.88
37 9 0.12
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (36 bp):
TGCTTCACTACTCTTTTGTGAAGGCTGAATTTGCAT
Found at i:604563 original size:18 final size:18
Alignment explanation
Indices: 604540--604574 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
604530 TTCCATCCGG
*
604540 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
604558 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
604575 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:605689 original size:8 final size:8
Alignment explanation
Indices: 605673--605707 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
605663 GTCAACAGTA
605673 GTCAACGG
1 GTCAACGG
*
605681 GTTAACGG
1 GTCAACGG
605689 GTCAACGG
1 GTCAACGG
605697 GTCAACGG
1 GTCAACGG
605705 GTC
1 GTC
605708 GGGTCAACGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.23, C:0.23, G:0.37, T:0.17
Consensus pattern (8 bp):
GTCAACGG
Found at i:605712 original size:13 final size:13
Alignment explanation
Indices: 605694--605756 Score: 63
Period size: 13 Copynumber: 4.5 Consensus size: 13
605684 AACGGGTCAA
605694 CGGGTCAACGGGT
1 CGGGTCAACGGGT
605707 CGGGTCAACGAGTCGAGT
1 CGGGTCAAC--G--G-GT
*
605725 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
605738 CGGGTAAACGGGT
1 CGGGTCAACGGGT
605751 CGGGTC
1 CGGGTC
605757 GGGTAAACGG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
13 29 0.67
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 10 0.23
ACGTcount: A:0.19, C:0.21, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:605728 original size:18 final size:18
Alignment explanation
Indices: 605705--605765 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
605695 GGGTCAACGG
*
605705 GTCGGGTCAACGAGTCGA
1 GTCGGGTAAACGAGTCGA
605723 GTCGGGTAAAC--G--G-
1 GTCGGGTAAACGAGTCGA
* *
605736 GTCGGGTAAACGGGTCGG
1 GTCGGGTAAACGAGTCGA
605754 GTCGGGTAAACG
1 GTCGGGTAAACG
605766 GGTTGGGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 22 0.59
ACGTcount: A:0.21, C:0.18, G:0.44, T:0.16
Consensus pattern (18 bp):
GTCGGGTAAACGAGTCGA
Found at i:605735 original size:31 final size:31
Alignment explanation
Indices: 605694--605774 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
605684 AACGGGTCAA
*
605694 CGGGTCAACGGGTCGGGTCAACGAGTCGAGT
1 CGGGTAAACGGGTCGGGTCAACGAGTCGAGT
* * *
605725 CGGGTAAACGGGTCGGGTAAACGGGTCGGGT
1 CGGGTAAACGGGTCGGGTCAACGAGTCGAGT
*
605756 CGGGTAAACGGGTTGGGTC
1 CGGGTAAACGGGTCGGGTC
605775 GGGTTGTGAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.46, T:0.17
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTCAACGAGTCGAGT
Found at i:605766 original size:18 final size:18
Alignment explanation
Indices: 605733--605778 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
605723 GTCGGGTAAA
605733 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
605751 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
605769 TGGGTCGGGT
1 CGGGTCGGGT
605779 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:605773 original size:13 final size:13
Alignment explanation
Indices: 605723--605755 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
605713 AACGAGTCGA
605723 GTCGGGTAAACGG
1 GTCGGGTAAACGG
605736 GTCGGGTAAACGG
1 GTCGGGTAAACGG
605749 GTCGGGT
1 GTCGGGT
605756 CGGGTAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.48, T:0.18
Consensus pattern (13 bp):
GTCGGGTAAACGG
Found at i:612780 original size:18 final size:17
Alignment explanation
Indices: 612759--612796 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
612749 AATTATAAAG
*
612759 TTATCCTAATATATATAA
1 TTATACTAATAT-TATAA
612777 TTATACTAATATTATAA
1 TTATACTAATATTATAA
612794 TTA
1 TTA
612797 GTCTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATACTAATATTATAA
Found at i:613812 original size:19 final size:19
Alignment explanation
Indices: 613788--613833 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
613778 GGCGGAATAG
*
613788 CCCTAGTGTGTAATGAAAA
1 CCCTAGGGTGTAATGAAAA
613807 CCCTAGGGTGTAATGAAAA
1 CCCTAGGGTGTAATGAAAA
613826 CCCTAGGG
1 CCCTAGGG
613834 ATCCTGCTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (19 bp):
CCCTAGGGTGTAATGAAAA
Found at i:615539 original size:22 final size:22
Alignment explanation
Indices: 615514--615562 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
615504 ATATCATATC
615514 AATGTCCATTTGTTTATTTTCT
1 AATGTCCATTTGTTTATTTTCT
615536 AATGTCCATTTGTTTATTTTCT
1 AATGTCCATTTGTTTATTTTCT
615558 AATGT
1 AATGT
615563 ATTCATATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (22 bp):
AATGTCCATTTGTTTATTTTCT
Found at i:618177 original size:29 final size:29
Alignment explanation
Indices: 618143--618201 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
618133 CTTAAATTAA
618143 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
618172 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
618201 T
1 T
618202 AGGTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:622785 original size:29 final size:29
Alignment explanation
Indices: 622751--622809 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
622741 CCTAAATTAA
* *
622751 TTTGATGTTATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
622780 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
622809 T
1 T
622810 AGGTAAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:623998 original size:23 final size:23
Alignment explanation
Indices: 623970--624058 Score: 160
Period size: 23 Copynumber: 3.9 Consensus size: 23
623960 CTTACCAATT
*
623970 TTCTCCCTTCATTTTCTCTTTTC
1 TTCTCCCTTCATTTTCTCTCTTC
623993 TTCTCCCTTCATTTTCTCTCTTC
1 TTCTCCCTTCATTTTCTCTCTTC
*
624016 TTCTCCCTTTATTTTCTCTCTTC
1 TTCTCCCTTCATTTTCTCTCTTC
624039 TTCTCCCTTCATTTTCTCTC
1 TTCTCCCTTCATTTTCTCTC
624059 CAAGAGTCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.04, C:0.37, G:0.00, T:0.58
Consensus pattern (23 bp):
TTCTCCCTTCATTTTCTCTCTTC
Found at i:624033 original size:36 final size:36
Alignment explanation
Indices: 623967--624051 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
623957 TGGCTTACCA
* *
623967 ATTTTCTCCCTTCATTTTCTCTTTTCTTCTCCCTTC
1 ATTTTCTCCCTTCATTCTCCCTTTTCTTCTCCCTTC
* * *
624003 ATTTTCTCTCTTC-TTCTCCCTTTATTTTCTCTCTTC
1 ATTTTCTCCCTTCATTCTCCCTTT-TCTTCTCCCTTC
624039 ---TTCTCCCTTCATT
1 ATTTTCTCCCTTCATT
624052 TTCTCTCCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
33 9 0.22
34 2 0.05
35 8 0.20
36 22 0.54
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (36 bp):
ATTTTCTCCCTTCATTCTCCCTTTTCTTCTCCCTTC
Found at i:634141 original size:8 final size:8
Alignment explanation
Indices: 634128--634166 Score: 78
Period size: 8 Copynumber: 4.9 Consensus size: 8
634118 GCATAGGCCA
634128 TAATTCAC
1 TAATTCAC
634136 TAATTCAC
1 TAATTCAC
634144 TAATTCAC
1 TAATTCAC
634152 TAATTCAC
1 TAATTCAC
634160 TAATTCA
1 TAATTCA
634167 ATCATAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (8 bp):
TAATTCAC
Found at i:636642 original size:2 final size:2
Alignment explanation
Indices: 636635--636659 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
636625 CTCATCATTG
636635 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
636660 CAGGTTTCAG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Done.