Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005911.1 Hibiscus syriacus cultivar Beakdansim tig00013881_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: 123103
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:8246 original size:9 final size:10
Alignment explanation
Indices: 8222--8264 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
8212 TCATTTTTGT
8222 TAAAAATAAA
1 TAAAAATAAA
*
8232 TAAAAATGAA
1 TAAAAATAAA
* *
8242 TAAAATTCAA
1 TAAAAATAAA
8252 TAAAAATATAA
1 TAAAAATA-AA
8263 TA
1 TA
8265 TAAAGCTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
10 23 0.85
11 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:17953 original size:2 final size:2
Alignment explanation
Indices: 17948--17979 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
17938 AAAAATACGA
17948 AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17980 GGTTATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:19656 original size:4 final size:4
Alignment explanation
Indices: 19647--19677 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
19637 ACAATACATG
19647 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
19678 TGGTGCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:21151 original size:13 final size:13
Alignment explanation
Indices: 21129--21161 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21119 GTTATCTTTT
21129 TTTTTGTTTTTTAG
1 TTTTT-TTTTTTAG
21143 TTTTTTTTTTTAG
1 TTTTTTTTTTTAG
21156 TTTTTT
1 TTTTTT
21162 AATAAGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.06, C:0.00, G:0.09, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTTTAG
Found at i:21201 original size:20 final size:20
Alignment explanation
Indices: 21176--21234 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
21166 AGAATAATTA
*
21176 TGTCTTTGTGACATGTTCTC
1 TGTCTTTGTGACATGTTATC
* *
21196 TGTCTTTATGACACGTTTATC
1 TGTCTTTGTGACATG-TTATC
*
21217 TCGTATTTGTGACATGTT
1 T-GTCTTTGTGACATGTT
21235 TTTTTTGCCT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 13 0.42
21 7 0.23
22 11 0.35
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.49
Consensus pattern (20 bp):
TGTCTTTGTGACATGTTATC
Found at i:23657 original size:17 final size:17
Alignment explanation
Indices: 23635--23685 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
23625 TATATTTATA
23635 ATATAAGTGTATAATAT
1 ATATAAGTGTATAATAT
* *
23652 ATATAAGTATATATTAT
1 ATATAAGTGTATAATAT
23669 ATATAAGTGTAT-ATAT
1 ATATAAGTGTATAATAT
23685 A
1 A
23686 ATTATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (17 bp):
ATATAAGTGTATAATAT
Found at i:23899 original size:7 final size:8
Alignment explanation
Indices: 23885--23924 Score: 50
Period size: 7 Copynumber: 5.4 Consensus size: 8
23875 ATGCATATGC
23885 ATAAGTAT
1 ATAAGTAT
23893 A-AAGTAT
1 ATAAGTAT
23900 ATAA-TAT
1 ATAAGTAT
23907 ATAAGTAT
1 ATAAGTAT
*
23915 A-AAATAT
1 ATAAGTAT
23922 ATA
1 ATA
23925 CATAAGCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
7 20 0.71
8 8 0.29
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (8 bp):
ATAAGTAT
Found at i:23912 original size:15 final size:15
Alignment explanation
Indices: 23885--23924 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
23875 ATGCATATGC
23885 ATAAGTATA-AAGTAT
1 ATAA-TATATAAGTAT
23900 ATAATATATAAGTAT
1 ATAATATATAAGTAT
*
23915 AAAATATATA
1 ATAATATATA
23925 CATAAGCATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (15 bp):
ATAATATATAAGTAT
Found at i:24150 original size:2 final size:2
Alignment explanation
Indices: 23523--24131 Score: 155
Period size: 2 Copynumber: 313.5 Consensus size: 2
23513 GAAACAATTA
* *
23523 AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT GT -T AT GAC A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
* * * *
23562 AT AT A- AT AT AT GT AT GT AT AT -T AT A- AT GT AC AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* ** * * *
23600 TT AT GC AT AC A- AT AT A- AGT AT AC AT -T AT AT TT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
23639 A- AGT GT AT A- AT AT AT AT A- AGT AT AT AT -T AT AT AT A- AGT
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T
* * *
23677 GT AT AT AT A- AT -T AT AT AA AT AT AT AT AT GT AT AT ACT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * * * *
23717 GT GT AT AT AT AT -T AT AC GT GT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
23758 AT AT AT AT AT AT GT -T AC AC AT AT AT GT AT AT AT GT A- AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * ** * **
23797 AT GT AT GAT CA- ACG AT GC AT GT AT GAT AT A- AGT AT GAT GC AT
1 AT AT AT -AT -AT A-T AT AT AT AT AT -AT AT AT A-T AT -AT AT AT
* * ** **
23839 GT AT GT GC AT A- AT AT AT AT AT AT AT AT AT AT AT AT A- AT GC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * *
23879 AT AT GC AT A- AGT AT AA AGT AT AT A- AT AT AT A- AGT AT A- AA
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
23918 AT AT AT AC AT A- AGC AT GT AT AC AT AT A- AGT AT AT AT AT GT GAT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT
* * * * * * * *
23961 GT AT GT AC AC A- AGT AT AT AT AT AT GT AT GT AT GT AT AT AT AG
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
24003 AT A- AT -T AT AT AT A- AGT AT AT AT AT A- AGT AC AT AT AT A- AGT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T
* * * * * * *
24043 AT AT AC AT AG GT GT GT GT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24127 AT AT A
1 AT AT A
24132 AGCATTATAT
Statistics
Matches: 443, Mismatches: 103, Indels: 122
0.66 0.15 0.18
Matches are distributed among these distances:
1 40 0.09
2 380 0.86
3 23 0.05
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (2 bp):
AT
Found at i:25854 original size:18 final size:18
Alignment explanation
Indices: 25816--25879 Score: 92
Period size: 18 Copynumber: 3.4 Consensus size: 18
25806 AAATATTTTG
*
25816 AAATAAATTATTATAAAAAT
1 AAATAAATTA-T-TCAAAAT
25836 AAATAAATTATTCAAAAT
1 AAATAAATTATTCAAAAT
*
25854 AAATAAATTATTCAAAGT
1 AAATAAATTATTCAAAAT
25872 AAATAAAT
1 AAATAAAT
25880 AAATAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
18 31 0.74
19 1 0.02
20 10 0.24
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATAAATTATTCAAAAT
Found at i:27507 original size:20 final size:20
Alignment explanation
Indices: 27482--27524 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
27472 AAATCGTCAA
27482 AAGCGAATATCTAATACGTT
1 AAGCGAATATCTAATACGTT
27502 AAGCGAATATCTAATACGTT
1 AAGCGAATATCTAATACGTT
27522 AAG
1 AAG
27525 ACAACTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (20 bp):
AAGCGAATATCTAATACGTT
Found at i:29530 original size:13 final size:13
Alignment explanation
Indices: 29512--29538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29502 CAGCTATCCC
29512 TCTTTGCTCATTG
1 TCTTTGCTCATTG
29525 TCTTTGCTCATTG
1 TCTTTGCTCATTG
29538 T
1 T
29539 TGTGAAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.15, T:0.56
Consensus pattern (13 bp):
TCTTTGCTCATTG
Found at i:29932 original size:42 final size:42
Alignment explanation
Indices: 29846--29953 Score: 148
Period size: 42 Copynumber: 2.6 Consensus size: 42
29836 ACCCGAAGGT
* * * *
29846 CTTATAGATGGCCCGAAGGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
*
29887 CTTATAGATGACCCAAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
29929 CTTACT-GATGACCCGAAGGATTTAA
1 CTTA-TAGATGACCCGAAGGATTTAA
29954 AAATCAAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
41 20 0.34
42 38 0.64
43 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTATAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGA
Found at i:30088 original size:90 final size:90
Alignment explanation
Indices: 29935--30312 Score: 553
Period size: 90 Copynumber: 4.2 Consensus size: 90
29925 AAGACTTACT
* * * *
29935 GATGACCCGAAGGATTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTT-TTAAAATATCATTTGA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTT-AAATCTCATTTGA
*
29999 AAACATTTTGCACTGAAGGTCTTATG
65 AAACATCTTGCACTGAAGGTCTTATG
* *
30025 GATGACCGGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTTATTTGAA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
* *
30090 AACATCATGTACTGAAGGTCTTATG
66 AACATCTTGCACTGAAGGTCTTATG
* * *
30115 GATGACCCGAAGGACTTATAAATCAATAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
*
30180 AACATCTTGCACTGAAGGTTTTATG
66 AACATCTTGCACTGAAGGTCTTATG
* *
30205 GATGGCCCGAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
1 GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
* *
30270 AACATCCTGCACT-ATAGGTCTTATT
66 AACATCTTGCACTGA-AGGTCTTATG
* *
30295 GATGGCCCGAAAGACTTA
1 GATGACCCGAAGGACTTA
30313 TCATCTTACT
Statistics
Matches: 260, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
89 1 0.00
90 257 0.99
91 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (90 bp):
GATGACCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAATCTCATTTGAA
AACATCTTGCACTGAAGGTCTTATG
Found at i:30367 original size:42 final size:42
Alignment explanation
Indices: 30321--30420 Score: 148
Period size: 42 Copynumber: 2.4 Consensus size: 42
30311 TATCATCTTA
* * **
30321 CTCGAAAGACTTA-TAGATGAGCTGAAGGATTTACGCATCATG
1 CTCGAAAGACTTACT-GATGACCCGAAGGATTTAAACATCATG
30363 CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
1 CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
30405 CTCGAAAGACTTACTG
1 CTCGAAAGACTTACTG
30421 TTGGCCCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
42 52 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
Found at i:30444 original size:42 final size:42
Alignment explanation
Indices: 30321--30444 Score: 142
Period size: 42 Copynumber: 3.0 Consensus size: 42
30311 TATCATCTTA
* ** *
30321 CTCGAAAGACTTA-TAGATGAGCTGAAGGATTTACGCATCATG
1 CTCGAAAGACTTACT-GATGACCCAAAGGATTTACACATCATG
* *
30363 CTCGAAAGACTTACTGATGACCCGAAGGATTTAAACATCATG
1 CTCGAAAGACTTACTGATGACCCAAAGGATTTACACATCATG
* * * *
30405 CTCGAAAGACTTACTGTTGGCCCAAAGGACTTACTCATCA
1 CTCGAAAGACTTACTGATGACCCAAAGGATTTACACATCA
30445 AGAAACCCCC
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
CTCGAAAGACTTACTGATGACCCAAAGGATTTACACATCATG
Found at i:30546 original size:43 final size:43
Alignment explanation
Indices: 30485--30818 Score: 524
Period size: 43 Copynumber: 7.8 Consensus size: 43
30475 GTCACCAAAC
* * * **
30485 AACCCCTACATATCACGTTGGTCCCTCAAGTTTATCATTTAGG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
* *
30528 AACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAAG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
*
30571 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTTATCAAGG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
*
30614 AACCCCTACATATCACGTTGGTCCCTCAAGCTTGTCATCAAGG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
* * *
30657 AACCCCTACATATCACGATAGTCCTTCAAGCTTGTCATTAAGG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
* * *
30700 AACCCTTATATATCACGATGTTCCCTCAAGCTTGTCATCAAGG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
*
30743 AACCCCTACATATTACGATGGTCCCTCAAGCTTGTCATCAAGG
1 AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
30786 AACCCCTACATATCACGATGGTCCCTCAAGCTT
1 AACCCCTACATATCACGATGGTCCCTCAAGCTT
30819 AGTTTCTTAT
Statistics
Matches: 266, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 266 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (43 bp):
AACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGG
Found at i:32451 original size:52 final size:51
Alignment explanation
Indices: 32375--32569 Score: 232
Period size: 52 Copynumber: 3.8 Consensus size: 51
32365 TATCCCAACC
*
32375 TTTTCATGCTGGTGTGAGCCTTCAAGATGCCCCACATGGATTACTTTTGTCT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATTACTTTT-TCT
* *
32427 TTTTTATGCTGATGTGACCCTTCAAGATGCCCCACATGGATTACTTCTTTCT
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATTACTT-TTTCT
** * * * *
32479 TTTTCATATTGATGAGAGCCTTCAAGATACCCCTACATGGATTAATTCTATC-
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCC-ACATGGATTACTT-TTTCT
* * *
32531 TTTTCATGCTTATATGAGCCTTCAAGAT-ACCCACATGGA
1 TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGA
32570 CAATATGGAC
Statistics
Matches: 124, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
50 7 0.06
51 3 0.02
52 96 0.77
53 18 0.15
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.37
Consensus pattern (51 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATGCCCCACATGGATTACTTTTTCT
Found at i:33730 original size:16 final size:16
Alignment explanation
Indices: 33711--33805 Score: 70
Period size: 17 Copynumber: 5.8 Consensus size: 16
33701 AATCTTTCTC
33711 ATTCTTTTTATTAC-TT
1 ATTCTTTTT-TTACTTT
*
33727 ATTCTTTTGTTTTCTTT
1 ATTCTTTT-TTTACTTT
* *
33744 TTTCTTTCTTTTTCTTT
1 ATTCTTT-TTTTACTTT
*
33761 TTTCTTTTTATTAC-TT
1 ATTCTTTTT-TTACTTT
*
33777 ATTCTTTTTTTTCCTTT
1 ATTC-TTTTTTTACTTT
33794 -TTCCTTTTTTTA
1 ATT-CTTTTTTTA
33806 TCCTTTTTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
16 30 0.45
17 35 0.53
18 1 0.02
ACGTcount: A:0.08, C:0.15, G:0.01, T:0.76
Consensus pattern (16 bp):
ATTCTTTTTTTACTTT
Found at i:33750 original size:17 final size:16
Alignment explanation
Indices: 33728--33804 Score: 84
Period size: 17 Copynumber: 4.6 Consensus size: 16
33718 TTATTACTTA
33728 TTCTTTTGTTTTCTTTT
1 TTCTTTT-TTTTCTTTT
33745 TTCTTTCTTTTTCTTTT
1 TTCTTT-TTTTTCTTTT
* *
33762 TTCTTTTTATTAC-TTA
1 TTCTTTTT-TTTCTTTT
33778 TTCTTTTTTTTCCTTTT
1 TTCTTTTTTTT-CTTTT
*
33795 TCCTTTTTTT
1 TTCTTTTTTT
33805 ATCCTTTTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.04
16 13 0.25
17 35 0.69
18 1 0.02
ACGTcount: A:0.04, C:0.16, G:0.01, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTTTCTTTT
Found at i:33768 original size:23 final size:24
Alignment explanation
Indices: 33715--33786 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 24
33705 TTTCTCATTC
33715 TTTTTATTACTTATTCTTTTGTTTTCT
1 TTTTTATTACTTATTC--TT-TTTTCT
* * *
33742 TTTTTCTTTCTTTTTCTTTTTTC-
1 TTTTTATTACTTATTCTTTTTTCT
33765 TTTTTATTACTTATTCTTTTTT
1 TTTTTATTACTTATTCTTTTTT
33787 TTCCTTTTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
23 19 0.49
24 5 0.13
25 2 0.05
27 13 0.33
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.78
Consensus pattern (24 bp):
TTTTTATTACTTATTCTTTTTTCT
Found at i:33771 original size:50 final size:50
Alignment explanation
Indices: 33712--33813 Score: 154
Period size: 50 Copynumber: 2.0 Consensus size: 50
33702 ATCTTTCTCA
* *
33712 TTCTTTTTATTACTTATTCTTTTGTTTT-CTTTTTTCTTTCTTTT-TCTTTT
1 TTCTTTTTATTACTTATTCTTTT-TTTTCCTTTTTCCTTT-TTTTATCCTTT
33762 TTCTTTTTATTACTTATTCTTTTTTTTCCTTTTTCCTTTTTTTATCCTTT
1 TTCTTTTTATTACTTATTCTTTTTTTTCCTTTTTCCTTTTTTTATCCTTT
33812 TT
1 TT
33814 GAGTGTAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
49 8 0.17
50 40 0.83
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (50 bp):
TTCTTTTTATTACTTATTCTTTTTTTTCCTTTTTCCTTTTTTTATCCTTT
Found at i:33812 original size:17 final size:17
Alignment explanation
Indices: 33730--33813 Score: 75
Period size: 17 Copynumber: 4.9 Consensus size: 17
33720 ATTACTTATT
*
33730 CTTTTGTTTT-CTTTTTT
1 CTTTT-TTTTCCTTTTTC
*
33747 CTTTCTTTTT-CTTTTTT
1 CTTT-TTTTTCCTTTTTC
* * *
33764 CTTTTTATTACTTATT-
1 CTTTTTTTTCCTTTTTC
33780 CTTTTTTTTCCTTTTTC
1 CTTTTTTTTCCTTTTTC
33797 CTTTTTTTATCCTTTTT
1 CTTTTTTT-TCCTTTTT
33814 GAGTGTAGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
16 17 0.29
17 32 0.55
18 9 0.16
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.77
Consensus pattern (17 bp):
CTTTTTTTTCCTTTTTC
Found at i:40051 original size:16 final size:16
Alignment explanation
Indices: 40030--40074 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
40020 ACTTTTTGTC
40030 ATTTTAAATAAAATTA
1 ATTTTAAATAAAATTA
40046 ATTTTAAATAAAATTA
1 ATTTTAAATAAAATTA
*
40062 ATTTTAATTAAAA
1 ATTTTAAATAAAA
40075 CAACAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTAAATAAAATTA
Found at i:43737 original size:32 final size:32
Alignment explanation
Indices: 43701--43786 Score: 97
Period size: 32 Copynumber: 2.7 Consensus size: 32
43691 TTTCTACTAA
* *
43701 GCATTTTCTAAATGCAACACTGA-TACTCTTGT
1 GCATTTTCTGAATGCAACACTGACTA-TATTGT
43733 GCATTATT-TGAATGCATAC-CTGACTATATTGT
1 GCATT-TTCTGAATGCA-ACACTGACTATATTGT
*
43765 GCATTATCTGAATGCAACACTG
1 GCATTTTCTGAATGCAACACTG
43787 GCTCTGCTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
31 3 0.07
32 37 0.80
33 6 0.13
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (32 bp):
GCATTTTCTGAATGCAACACTGACTATATTGT
Found at i:47750 original size:34 final size:33
Alignment explanation
Indices: 47712--47890 Score: 95
Period size: 34 Copynumber: 5.4 Consensus size: 33
47702 CTCCAACCAG
47712 ATATATTTTAATATTCAAATTTAAATAGATAATA
1 ATATATTTTAATATTCAAATTTAAATAGAT-ATA
*
47746 ATATATTTTAAT-TTGAAATATTTAAA-AGATATA
1 ATATATTTTAATATT-CAA-ATTTAAATAGATATA
* * * ** **
47779 GGTACATTTTACTATTCAAACATAAA-A-AGGT-
1 -ATATATTTTAATATTCAAATTTAAATAGATATA
* *
47810 AT-TATTTTAAT-TTAAAATATTTAATAGGATATA
1 ATATATTTTAATATTCAAAT-TTAAATA-GATATA
* *
47843 AT-TATCCATTAATATTCAAAGTTAAATAGATAATAA
1 ATATAT--TTTAATATTCAAATTTAAATAGAT-AT-A
*
47879 ATACATTTTAAT
1 ATATATTTTAAT
47891 TTGACATATT
Statistics
Matches: 106, Mismatches: 24, Indels: 29
0.67 0.15 0.18
Matches are distributed among these distances:
28 5 0.05
29 10 0.09
30 2 0.02
32 4 0.04
33 16 0.15
34 32 0.30
35 27 0.25
36 8 0.08
37 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.42
Consensus pattern (33 bp):
ATATATTTTAATATTCAAATTTAAATAGATATA
Found at i:52798 original size:96 final size:96
Alignment explanation
Indices: 52634--52861 Score: 456
Period size: 96 Copynumber: 2.4 Consensus size: 96
52624 TCTATTTGGG
52634 TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGACGATGGACAGACGATGTGATTACTAGGTT
1 TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGACGATGGACAGACGATGTGATTACTAGGTT
52699 TCATGGGGGTAGCGACGGTTAAGACGCTGGT
66 TCATGGGGGTAGCGACGGTTAAGACGCTGGT
52730 TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGACGATGGACAGACGATGTGATTACTAGGTT
1 TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGACGATGGACAGACGATGTGATTACTAGGTT
52795 TCATGGGGGTAGCGACGGTTAAGACGCTGGT
66 TCATGGGGGTAGCGACGGTTAAGACGCTGGT
52826 TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGA
1 TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGA
52862 TATATATATA
Statistics
Matches: 132, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 132 1.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (96 bp):
TGGAAGAAGCTCCTCGTTGGGTCATACACCAATCGACGATGGACAGACGATGTGATTACTAGGTT
TCATGGGGGTAGCGACGGTTAAGACGCTGGT
Found at i:52868 original size:2 final size:2
Alignment explanation
Indices: 52861--52891 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52851 ACACCAATCG
52861 AT AT AT 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 AT AT AT A
52892 GGCTGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53037 original size:30 final size:29
Alignment explanation
Indices: 52988--53064 Score: 127
Period size: 30 Copynumber: 2.6 Consensus size: 29
52978 CTACAATTCG
*
52988 AATGAAGGTCGTCGGTGGTCTGGGCGACC
1 AATGAAGGTCGCCGGTGGTCTGGGCGACC
53017 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
1 AATGAAGGTCGCC-GGTGGTCTGGGCGACC
53047 AATGAAGGTCGCCAGGTG
1 AATGAAGGTCGCC-GGTG
53065 ATCTATGGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 12 0.27
30 33 0.73
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.18
Consensus pattern (29 bp):
AATGAAGGTCGCCGGTGGTCTGGGCGACC
Found at i:53268 original size:50 final size:50
Alignment explanation
Indices: 53205--53306 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
53195 TTTATCCTAT
53205 TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
*
53255 TTTAGTATGTATTTATTTTAAAATTGATTATTGGGATATCTTGTTTTGTA
1 TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
53305 TT
1 TT
53307 CAATAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (50 bp):
TTTAGTATGTATTTATTTTAAAATTGATTATTGAGATATCTTGTTTTGTA
Found at i:54012 original size:2 final size:2
Alignment explanation
Indices: 54005--54032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
53995 AAATTCAGCC
54005 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
54033 ATTCTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54184 original size:24 final size:24
Alignment explanation
Indices: 54152--54221 Score: 74
Period size: 24 Copynumber: 2.8 Consensus size: 24
54142 TAATAGTATT
54152 TTTATTTTTAATATAATTTTAATA
1 TTTATTTTTAATATAATTTTAATA
54176 TTTATTTTT--TATAATTTTTTAATA
1 TTTATTTTTAATATAA--TTTTAATA
54200 TTTAAATTTTTAA-ATAAATTTT
1 TTT--ATTTTTAATAT-AATTTT
54222 CATTTTTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
22 5 0.13
24 20 0.51
26 10 0.26
27 2 0.05
28 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTATTTTTAATATAATTTTAATA
Found at i:54207 original size:16 final size:17
Alignment explanation
Indices: 54183--54215 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54173 ATATTTATTT
*
54183 TTTATAATTTTTTAATA
1 TTTATAATTTTTAAATA
54200 TTTA-AATTTTTAAATA
1 TTTATAATTTTTAAATA
54216 AATTTTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATAATTTTTAAATA
Found at i:61965 original size:25 final size:24
Alignment explanation
Indices: 61918--61967 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
61908 ATTTATATAC
* *
61918 TTTTTAATAAAATTTATATATAAT
1 TTTTTAATAAAATTTAAAGATAAT
*
61942 TTTTTTATAAAATTTAAAAGATAAT
1 TTTTTAATAAAATTT-AAAGATAAT
61967 T
1 T
61968 GGGTAGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTTAATAAAATTTAAAGATAAT
Found at i:64904 original size:3 final size:3
Alignment explanation
Indices: 64896--64938 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
64886 TCACCATTGG
64896 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
64939 GATGATGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:66601 original size:28 final size:29
Alignment explanation
Indices: 66541--66671 Score: 198
Period size: 29 Copynumber: 4.7 Consensus size: 29
66531 ACCCGACCCA
66541 GTGACATTCTGGGAATTTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
66570 GTGACATTCTGAGAATTTTTGTGAAAAA-
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
66598 GTGACATTCTGGGAA-TTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
* *
66626 GTGACATTCTGGGATTTTTTGTGAAAAAA
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
66655 ATGA-ATT-TGGGAATTTT
1 GTGACATTCTGGGAATTTT
66672 CGAATGTGGA
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
27 21 0.22
28 31 0.33
29 42 0.45
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (29 bp):
GTGACATTCTGGGAATTTTTGTGAAAAAG
Found at i:66632 original size:56 final size:57
Alignment explanation
Indices: 66540--66671 Score: 207
Period size: 56 Copynumber: 2.4 Consensus size: 57
66530 GACCCGACCC
66540 AGTGACATTCTGGGAATTTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTG-AAAA
1 AGTGACATTCTGGGAA-TTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTGAAAAA
* *
66597 AGTGACATTCTGGGAATTTTGTGAAAAAGGTGACATTCTGGGATTTTTTGTGAAAAA
1 AGTGACATTCTGGGAATTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTGAAAAA
*
66654 AATGA-ATT-TGGGAATTTT
1 AGTGACATTCTGGGAATTTT
66672 CGAATGTGGA
Statistics
Matches: 71, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
55 10 0.14
56 37 0.52
57 24 0.34
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (57 bp):
AGTGACATTCTGGGAATTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTGAAAAA
Found at i:74038 original size:28 final size:29
Alignment explanation
Indices: 73983--74039 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
73973 GACCGACCCA
*
73983 GTGACATTCTGGGAATTTTTGTGTAAAAG
1 GTGACATTCTAGGAATTTTTGTGTAAAAG
* * *
74012 GTGACATTCTATGATTTTTTGTGAAAAA
1 GTGACATTCTAGGAATTTTTGTGTAAAA
74040 ATGACAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
GTGACATTCTAGGAATTTTTGTGTAAAAG
Found at i:74044 original size:28 final size:29
Alignment explanation
Indices: 73984--74058 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
73974 ACCGACCCAG
* **
73984 TGACATTCTGGGAATTTTTGTGTAAAAGG
1 TGACATTCTAGGAATTTTTGTGTAAAAAA
* *
74013 TGACATTCTATGATTTTTTGTG-AAAAAA
1 TGACATTCTAGGAATTTTTGTGTAAAAAA
*
74041 TGACAATT-TGGGAATTTT
1 TGAC-ATTCTAGGAATTTT
74059 CGAATGTGGA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (29 bp):
TGACATTCTAGGAATTTTTGTGTAAAAAA
Found at i:75044 original size:23 final size:23
Alignment explanation
Indices: 75013--75064 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
75003 CTTAGAGTAA
75013 GCCCAACGGACCTAAGGATACAG
1 GCCCAACGGACCTAAGGATACAG
*
75036 GCCCTACGGACCTAAGGATACAG
1 GCCCAACGGACCTAAGGATACAG
75059 GCCCAA
1 GCCCAA
75065 AAGCTTATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.25, T:0.10
Consensus pattern (23 bp):
GCCCAACGGACCTAAGGATACAG
Found at i:77974 original size:24 final size:24
Alignment explanation
Indices: 77929--77974 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
77919 AAAGGGGTCG
* *
77929 AAAAAAAATAAAGATATGATATAT
1 AAAAAAAATAAAGAAATAATATAT
* *
77953 AAAATAAATAAATAAATAATAT
1 AAAAAAAATAAAGAAATAATAT
77975 TGTCGATTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAAAAATAAAGAAATAATATAT
Found at i:95197 original size:10 final size:10
Alignment explanation
Indices: 95181--95325 Score: 50
Period size: 10 Copynumber: 13.8 Consensus size: 10
95171 AAATGAAAAT
95181 GAAAAAAGAA
1 GAAAAAAGAA
*
95191 TAAAAAAGAA
1 GAAAAAAGAA
*
95201 GAAAAGAAAAA
1 GAAAA-AAGAA
* *
95212 TGAAAAATGAT
1 -GAAAAAAGAA
*
95223 GAAAAAA-AT
1 GAAAAAAGAA
*
95232 G--AAAAGGA
1 GAAAAAAGAA
*
95240 -AAAAAAGGA
1 GAAAAAAGAA
95249 GAAAAATAGAAAA
1 GAAAAA-AG--AA
*
95262 TGGGAAAATAGAA
1 ---GAAAAAAGAA
95275 GAAAAAAGAAAA
1 GAAAAAAG--AA
*
95287 GAAAAAATGAT
1 GAAAAAA-GAA
95298 GAAAAAAGAA
1 GAAAAAAGAA
95308 -AAAGAAA-AA
1 GAAA-AAAGAA
95317 GAAATAAAG
1 GAAA-AAAG
95326 GGGGGTTCAA
Statistics
Matches: 102, Mismatches: 15, Indels: 35
0.67 0.10 0.23
Matches are distributed among these distances:
7 4 0.04
9 15 0.15
10 42 0.41
11 16 0.16
12 14 0.14
13 4 0.04
15 2 0.02
16 5 0.05
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (10 bp):
GAAAAAAGAA
Found at i:95216 original size:32 final size:32
Alignment explanation
Indices: 95176--95243 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
95166 ATAAAAAATG
95176 AAAATGAAAAAAGAAT-AAAAAAGAAGAAAA-GA
1 AAAATGAAAAAAG-ATGAAAAAA-AAGAAAAGGA
* *
95208 AAAATGAAAAATGATGAAAAAAATGAAAAGGA
1 AAAATGAAAAAAGATGAAAAAAAAGAAAAGGA
95240 AAAA
1 AAAA
95244 AAGGAGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.25
32 24 0.75
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (32 bp):
AAAATGAAAAAAGATGAAAAAAAAGAAAAGGA
Found at i:95230 original size:25 final size:23
Alignment explanation
Indices: 95202--95316 Score: 90
Period size: 25 Copynumber: 4.7 Consensus size: 23
95192 AAAAAAGAAG
95202 AAAAGAAAAATGAAAAATGATGAAA
1 AAAAGAAAAA-GAAAAATGATG-AA
* *
95227 AAAATGAAAAGGAAAAAAAGGA-GAA
1 AAAA-GAAAA--AGAAAAATGATGAA
* * *
95252 AAATAGAAAATGGGAAAATAGAAGAA
1 AAA-AGAAAA-AGAAAAAT-GATGAA
95278 AAAAG-AAAAGAAAAAATGATGAA
1 AAAAGAAAAAG-AAAAATGATGAA
95301 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
95317 GAAATAAAGG
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
23 16 0.22
24 17 0.24
25 18 0.25
26 13 0.18
27 7 0.10
28 1 0.01
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (23 bp):
AAAAGAAAAAGAAAAATGATGAA
Found at i:95236 original size:7 final size:7
Alignment explanation
Indices: 95153--95221 Score: 51
Period size: 7 Copynumber: 10.3 Consensus size: 7
95143 TTCGCTTGAA
95153 GAAAAAT
1 GAAAAAT
95160 GATAAAAT
1 GA-AAAAT
*
95168 AAAAAAT
1 GAAAAAT
95175 G-AAAAT
1 GAAAAAT
*
95181 GAAAAAA
1 GAAAAAT
95188 GAATAAA-
1 GAA-AAAT
95195 -AAAGAA-
1 GAAA-AAT
95201 G-AAAA-
1 GAAAAAT
95206 GAAAAAT
1 GAAAAAT
95213 GAAAAAT
1 GAAAAAT
95220 GA
1 GA
95222 TGAAAAAAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
5 4 0.08
6 16 0.31
7 23 0.44
8 9 0.17
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:96276 original size:8 final size:8
Alignment explanation
Indices: 96263--96287 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
96253 AAACGCATCA
96263 AATTGCAT
1 AATTGCAT
96271 AATTGCAT
1 AATTGCAT
96279 AATTGCAT
1 AATTGCAT
96287 A
1 A
96288 CATTTTAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (8 bp):
AATTGCAT
Found at i:96671 original size:37 final size:37
Alignment explanation
Indices: 96612--96687 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
96602 AAACAATTTA
*
96612 ATCTTAAGTCTTCACGGAAGAGTAGTGAAGCAAA-TC
1 ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
96648 ATCTATAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
1 ATCT-TAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
96686 AT
1 AT
96688 TTTATGAAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 4 0.11
37 29 0.78
38 4 0.11
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (37 bp):
ATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAACTC
Found at i:96757 original size:55 final size:55
Alignment explanation
Indices: 96698--97012 Score: 352
Period size: 55 Copynumber: 5.7 Consensus size: 55
96688 TTTATGAAGA
96698 TCGAGTCCTATACTCTCTGATA-GAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGA-ACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * *
96753 TCGAGTTCTATACTCTCTGATA-GAAGAGGGAGC-GAGCCCATTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGA-ACGAATAGGGAGCGGA-CCCGTTTGTTGAAGATTGT
* * * * * *
96808 TTGAGTTCTATACTCTCTGAAGGAATAGAGTGTGGACCCGTTT-TATGAAGATTGT
1 TCGAGTCCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGT-TGAAGATTGT
* * * ** *
96863 TCGAGTTCTATACTCCCTGAACGAATAGGGAGCGTACTTGTTTATTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* * * * *
96918 TCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGCTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
* *
96973 TCGAGTCTTATACTCTCTGAAGGAAT-GAGGAGCGGACCCG
1 TCGAGTCCTATACTCTCTGAACGAATAG-GGAGCGGACCCG
97013 CCATCATTCG
Statistics
Matches: 224, Mismatches: 30, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
54 5 0.02
55 216 0.96
56 3 0.01
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (55 bp):
TCGAGTCCTATACTCTCTGAACGAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:96987 original size:165 final size:165
Alignment explanation
Indices: 96698--96998 Score: 414
Period size: 165 Copynumber: 1.8 Consensus size: 165
96688 TTTATGAAGA
* *
96698 TCGAGTCCTATACTCTCTGATAGAATAGGGAGCGGACCCGTTTGTTGAAGATTGTTCGAGTTCTA
1 TCGAGTCCTATACTCCCTGATAGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTCTA
* * * *
96763 TACTCTCTGATAGAAGAGGGAGCGAGCCCATTTGTTGAAGATTGTTTGAGTTCTATACTCTCTGA
66 TACTCCCTGATAGAAGAGGGAGCGAGCACATTTGCTGAAGATTGTTCGAGTTCTATACTCTCTGA
96828 AGGAATAGAGTGTGGACCCGTTTTATGAAGATTGT
131 AGGAATAGAGTGTGGACCCGTTTTATGAAGATTGT
* * **
96863 TCGAGTTCTATACTCCCTGA-ACGAATAGGGAGCGTACTTGTTTATTGAAGATTGTTCGAG-TCT
1 TCGAGTCCTATACTCCCTGATA-GAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTC-
* *
96926 TATACTCCCTGA-ACGAATAGGGAGC-AGACACGTTTGCTGAAGATTGTTCGAG-TCTTATACTC
64 TATACTCCCTGATA-GAAGAGGGAGCGAG-CACATTTGCTGAAGATTGTTCGAGTTC-TATACTC
96988 TCTGAAGGAAT
126 TCTGAAGGAAT
96999 GAGGAGCGGA
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
164 8 0.07
165 111 0.93
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (165 bp):
TCGAGTCCTATACTCCCTGATAGAATAGGGAGCGGACCCGTTTATTGAAGATTGTTCGAGTTCTA
TACTCCCTGATAGAAGAGGGAGCGAGCACATTTGCTGAAGATTGTTCGAGTTCTATACTCTCTGA
AGGAATAGAGTGTGGACCCGTTTTATGAAGATTGT
Found at i:100302 original size:15 final size:15
Alignment explanation
Indices: 100282--100312 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
100272 TTAACTCAAT
100282 TTCATAAATTTAATC
1 TTCATAAATTTAATC
100297 TTCATAAATTTAATC
1 TTCATAAATTTAATC
100312 T
1 T
100313 CTAATTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (15 bp):
TTCATAAATTTAATC
Found at i:100504 original size:41 final size:41
Alignment explanation
Indices: 100455--100537 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
100445 AAAAATTCAC
* * *
100455 ATAACATTTTA-AGTTGTAACCTGAAATGTTACCAAAAACAT
1 ATAACATTTTAGA-TTGCAACCTAAAATATTACCAAAAACAT
*
100496 ATAACATTTTAGATTGCAACCTAAAATATTACCAAAATCAT
1 ATAACATTTTAGATTGCAACCTAAAATATTACCAAAAACAT
100537 A
1 A
100538 AAAAATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.97
42 1 0.03
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.31
Consensus pattern (41 bp):
ATAACATTTTAGATTGCAACCTAAAATATTACCAAAAACAT
Found at i:107721 original size:4 final size:4
Alignment explanation
Indices: 107712--107742 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
107702 CTTCTTCTTT
*
107712 TTCC TTCC TTCC TTCC TTCC TTCC TTTC TTC
1 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTC
107743 TTCTTCTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (4 bp):
TTCC
Found at i:122680 original size:7 final size:7
Alignment explanation
Indices: 122662--122690 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
122652 TTCAACAAAT
122662 ATATAT-
1 ATATATG
122668 ATATATG
1 ATATATG
122675 ATATATG
1 ATATATG
122682 ATATATG
1 ATATATG
122689 AT
1 AT
122691 TATAGTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (7 bp):
ATATATG
Found at i:122687 original size:14 final size:13
Alignment explanation
Indices: 122662--122694 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
122652 TTCAACAAAT
122662 ATATATATATATG
1 ATATATATATATG
122675 ATATATGATATATG
1 ATATAT-ATATATG
122689 AT-TATA
1 ATATATA
122695 GTAAACCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 9 0.47
14 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (13 bp):
ATATATATATATG
Done.