Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005645.1 Hibiscus syriacus cultivar Beakdansim tig00013163_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: 65510
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.32
Found at i:145 original size:18 final size:18
Alignment explanation
Indices: 118--161 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
108 ATATATTGGG
*
118 AATGCAAAGTAGAATAGA
1 AATGCCAAGTAGAATAGA
*
136 TATGCCAAGTAGAATAGA
1 AATGCCAAGTAGAATAGA
154 AATGCCAA
1 AATGCCAA
162 ATCAGACGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.50, C:0.11, G:0.20, T:0.18
Consensus pattern (18 bp):
AATGCCAAGTAGAATAGA
Found at i:1830 original size:69 final size:71
Alignment explanation
Indices: 1747--1887 Score: 196
Period size: 73 Copynumber: 2.0 Consensus size: 71
1737 AAGAAACATT
* * *
1747 TTGCTCTTCCATAAACCCCACGTCTAT-AAG-AAGAATCCCCACAAATTAACCATGCTTTTCCTA
1 TTGCTCTTCCATAAACCCCACGTCTATAAAGAAAGAATCCCCAAAAATCAACCATGCTTTTCCCA
1810 AATGGG
66 AATGGG
* * *
1816 TTGCTCTTCTATAAACCCCATGTCTATAAGAAGAAAGAATCCCCAAAAATCAGCCATGCTTTTCC
1 TTGCTCTTCCATAAACCCCACGTCTAT-A-AAGAAAGAATCCCCAAAAATCAACCATGCTTTTCC
1881 CAAATGG
64 CAAATGG
1888 ATAAATCGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 25 0.40
72 3 0.05
73 34 0.55
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (71 bp):
TTGCTCTTCCATAAACCCCACGTCTATAAAGAAAGAATCCCCAAAAATCAACCATGCTTTTCCCA
AATGGG
Found at i:4085 original size:2 final size:2
Alignment explanation
Indices: 4078--4105 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4068 CATTCTTCAA
4078 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
4106 TAAATATGTC
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):
AT
Found at i:6093 original size:22 final size:22
Alignment explanation
Indices: 6065--6185 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 22
6055 ATGAATTTCT
*
6065 TTAGCACTGGTACGAAAGTGCA
1 TTAGCACTGATACGAAAGTGCA
*
6087 TTAGCACTAATAC-ATAAGTGCA
1 TTAGCACTGATACGA-AAGTGCA
*
6109 TTAGCATTGATACAGAAA-TGCA
1 TTAGCACTGATAC-GAAAGTGCA
* * *
6131 TCAACATTGATAC-AGAAGTGCA
1 TTAGCACTGATACGA-AAGTGCA
* * * * *
6153 TTATCATTGATACTAAATTGCC
1 TTAGCACTGATACGAAAGTGCA
*
6175 TTAGCATTGAT
1 TTAGCACTGAT
6186 TGAAATATAT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
20 1 0.01
21 3 0.04
22 74 0.90
23 3 0.04
24 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (22 bp):
TTAGCACTGATACGAAAGTGCA
Found at i:6183 original size:44 final size:44
Alignment explanation
Indices: 6065--6185 Score: 120
Period size: 44 Copynumber: 2.8 Consensus size: 44
6055 ATGAATTTCT
* * * * *
6065 TTAGCACTGGTAC-GAAAGTGCATTAGCACTAATACATAAGTGCA
1 TTAGCATTGATACAGAAA-TGCATTAGCATTGATACAGAAGTGCA
* *
6109 TTAGCATTGATACAGAAATGCATCAACATTGATACAGAAGTGCA
1 TTAGCATTGATACAGAAATGCATTAGCATTGATACAGAAGTGCA
* * *
6153 TTATCATTGATACTA-AATTGCCTTAGCATTGAT
1 TTAGCATTGATAC-AGAAATGCATTAGCATTGAT
6186 TGAAATATAT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
44 58 0.92
45 5 0.08
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (44 bp):
TTAGCATTGATACAGAAATGCATTAGCATTGATACAGAAGTGCA
Found at i:8246 original size:17 final size:19
Alignment explanation
Indices: 8211--8250 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
8201 GAAGAAATAA
8211 AGAGAATGAAGAAGAAAGG
1 AGAGAATGAAGAAGAAAGG
8230 AGAGAATATGAAGAAGGAAAG
1 AGAG-A-ATGAAGAA-GAAAG
8251 AAGAACCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 1 0.06
21 8 0.44
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.35, T:0.07
Consensus pattern (19 bp):
AGAGAATGAAGAAGAAAGG
Found at i:9700 original size:18 final size:18
Alignment explanation
Indices: 9677--9712 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
9667 CTAATAAGAT
9677 CATCCAATTATCTAAATG
1 CATCCAATTATCTAAATG
9695 CATCCAATTATCTAAATG
1 CATCCAATTATCTAAATG
9713 ATCATCCAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (18 bp):
CATCCAATTATCTAAATG
Found at i:10323 original size:20 final size:21
Alignment explanation
Indices: 10300--10339 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
10290 TTTATCATTA
10300 TTTATATTTTT-AAATTAAAT
1 TTTATATTTTTAAAATTAAAT
10320 TTTATATTTTTAAAATTAAA
1 TTTATATTTTTAAAATTAAA
10340 CTATTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTATATTTTTAAAATTAAAT
Found at i:10842 original size:33 final size:32
Alignment explanation
Indices: 10800--10864 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 32
10790 TCCGATTTGC
10800 CCAAATGCCATCTTCAGTTCAATATATTTTCTA
1 CCAAATGCCATCTTCAGTTCAATAT-TTTTCTA
*
10833 CCAAATGCCATCTTCAGTTTAATATTTTTCTA
1 CCAAATGCCATCTTCAGTTCAATATTTTTCTA
10865 TTTAAAATGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 7 0.23
33 24 0.77
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (32 bp):
CCAAATGCCATCTTCAGTTCAATATTTTTCTA
Found at i:11518 original size:17 final size:17
Alignment explanation
Indices: 11496--11534 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
11486 ATCCCTTGAA
11496 ATTTTAAATTATTATAT
1 ATTTTAAATTATTATAT
* * *
11513 ATTTTAATTTTTTTTAT
1 ATTTTAAATTATTATAT
11530 ATTTT
1 ATTTT
11535 TTATTGATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTAAATTATTATAT
Found at i:14009 original size:15 final size:14
Alignment explanation
Indices: 13972--14014 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
13962 TGATTAATGG
13972 AAATAAGAAATGAA
1 AAATAAGAAATGAA
*
13986 ATA-AAGAAATGAA
1 AAATAAGAAATGAA
13999 AGAATAAGAAATGAA
1 A-AATAAGAAATGAA
14014 A
1 A
14015 TGGATAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (14 bp):
AAATAAGAAATGAA
Found at i:14582 original size:19 final size:21
Alignment explanation
Indices: 14539--14590 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
14529 GAAACCCCTT
14539 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
14560 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
14579 TGAAGATACATG
1 TGAAAATACATG
14591 CTCTTGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:16857 original size:21 final size:21
Alignment explanation
Indices: 16824--16865 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
16814 CTTTAATTGC
* *
16824 ATTGTCTTTAATTTTCTATTTT
1 ATTGTCTTCAATTCTC-ATTTT
16846 ATTG-CTTCAATTCTCATTTT
1 ATTGTCTTCAATTCTCATTTT
16866 CAAATGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.19, C:0.14, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTGTCTTCAATTCTCATTTT
Found at i:17673 original size:19 final size:19
Alignment explanation
Indices: 17649--17687 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17639 AGGTAATGAA
17649 AAATGATG-AAAGCAAAAGG
1 AAATGATGAAAAG-AAAAGG
17668 AAATGATGAAAAGAAAAGG
1 AAATGATGAAAAGAAAAGG
17687 A
1 A
17688 TGAAGATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.62, C:0.03, G:0.26, T:0.10
Consensus pattern (19 bp):
AAATGATGAAAAGAAAAGG
Found at i:18097 original size:15 final size:15
Alignment explanation
Indices: 18077--18105 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18067 GATTAATGGA
18077 AATAAGAAATGAAAG
1 AATAAGAAATGAAAG
18092 AATAAGAAATGAAA
1 AATAAGAAATGAAA
18106 TGGATAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
AATAAGAAATGAAAG
Found at i:19645 original size:2 final size:2
Alignment explanation
Indices: 19638--19682 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
19628 TAAAACATAC
19638 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
19680 AT A
1 AT A
19683 CACCCCCATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19869 original size:24 final size:24
Alignment explanation
Indices: 19842--19913 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
19832 AAACGGAGAT
19842 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
19866 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
19890 ATCAGAAA-CAAGAACAAAATTCAG
1 ATCAGAAATCAA-AACAGAATTCAG
19914 GTAATGTATC
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.05
24 38 0.95
ACGTcount: A:0.53, C:0.18, G:0.14, T:0.15
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:19913 original size:48 final size:48
Alignment explanation
Indices: 19842--19933 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
19832 AAACGGAGAT
* *
19842 ATCAGAAATCAAAACAGAATTCAGATCA-GATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAAAATTCAGATAATG-TATCAGAACAGAATCCAG
*
19890 ATCAGAAA-CAAGAACAAAATTCAGGTAATGTATCAGAACAGAAT
1 ATCAGAAATCAA-AACAAAATTCAGATAATGTATCAGAACAGAAT
19934 TCAAGTCGGA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
47 3 0.08
48 35 0.90
49 1 0.03
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.17
Consensus pattern (48 bp):
ATCAGAAATCAAAACAAAATTCAGATAATGTATCAGAACAGAATCCAG
Found at i:24443 original size:24 final size:24
Alignment explanation
Indices: 24416--24463 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
24406 AAACGGAGAT
24416 ATCAGAAATCAAAACAAAATTCAG
1 ATCAGAAATCAAAACAAAATTCAG
* * *
24440 ATCAGATATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAAAATTCAG
24464 GTAATGTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.52, C:0.17, G:0.12, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAAAATTCAG
Found at i:26976 original size:18 final size:18
Alignment explanation
Indices: 26970--27043 Score: 139
Period size: 18 Copynumber: 4.1 Consensus size: 18
26960 GGTCAACGGA
26970 TCGGGTCAACGGGTTGGG
1 TCGGGTCAACGGGTTGGG
26988 TCGGGTCAACGGGTTGGG
1 TCGGGTCAACGGGTTGGG
27006 TCGGGTCAACGGGTTGGG
1 TCGGGTCAACGGGTTGGG
*
27024 TCGGGTCAACGGGTCGGG
1 TCGGGTCAACGGGTTGGG
27042 TC
1 TC
27044 TGGTTGTGAC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.11, C:0.19, G:0.49, T:0.22
Consensus pattern (18 bp):
TCGGGTCAACGGGTTGGG
Found at i:27025 original size:13 final size:13
Alignment explanation
Indices: 26947--26989 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
26937 GCCGGTTAAC
26947 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
26960 GGTCAACGGATCG
1 GGTCAACGGGTCG
*
26973 GGTCAACGGGTTG
1 GGTCAACGGGTCG
26986 GGTC
1 GGTC
26990 GGGTCAACGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:31091 original size:61 final size:60
Alignment explanation
Indices: 31025--31194 Score: 134
Period size: 61 Copynumber: 2.8 Consensus size: 60
31015 TTCTCATCCG
* *
31025 TGTTGAAGAGATCTGGTCACTTTCAGATGAATTATTTGTTGAAGATGACGCTGC-TCTTTC
1 TGTTGAAGAGATCTGGTCA-TTTCAGATGAATTATTTGTTGAAGATGACGCTGCTTATTTA
* * * * * *
31085 TCGTTGAGGAAAT-TGGGTCAATTTGGAAAT-AATT-TGGTGTTGAAGATGACTCTGCTTATTTA
1 T-GTTGAAGAGATCT-GGTC-ATTT-CAGATGAATTAT-TTGTTGAAGATGACGCTGCTTATTTA
* * *
31147 TTTTGAATAGATCTGGTTGATTTCAGATGAATTGA-TTGTTGAAGATGA
1 TGTTGAAGAGATCTGG-TCATTTCAGATGAATT-ATTTGTTGAAGATGA
31195 TGATGTTCCT
Statistics
Matches: 83, Mismatches: 16, Indels: 21
0.69 0.13 0.17
Matches are distributed among these distances:
60 6 0.07
61 66 0.80
62 11 0.13
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.39
Consensus pattern (60 bp):
TGTTGAAGAGATCTGGTCATTTCAGATGAATTATTTGTTGAAGATGACGCTGCTTATTTA
Found at i:31153 original size:122 final size:122
Alignment explanation
Indices: 30927--31245 Score: 347
Period size: 122 Copynumber: 2.6 Consensus size: 122
30917 TTATATTTTG
* * * * * *
30927 AGATAAATTATTTGTTGAATATGACAATGATCCTTCTCATTGAGAAAATCGGGTCAATCTGGAAA
1 AGATGAATTATTTGTTGAAGATGACGATGATCTTTCTCGTTGAGGAAATCGGGTCAATCTGGAAA
* * * * *
30992 TAATTTTGTGTTGAATATGGCTCTTCTCATCCGTGTTGAAGAGATCTGG-TCACTTTC
66 TAATTTGGTGTTGAAGATGACTCTGCTCATCCATGTTGAAGAGATCTGGTTCA-TTTC
* * * *
31049 AGATGAATTATTTGTTGAAGATGACGCTGCTCTTTCTCGTTGAGGAAATTGGGTCAATTTGGAAA
1 AGATGAATTATTTGTTGAAGATGACGATGATCTTTCTCGTTGAGGAAATCGGGTCAATCTGGAAA
* ** * * *
31114 TAATTTGGTGTTGAAGATGACTCTGCTTATTTATTTTGAATAGATCTGGTTGATTTC
66 TAATTTGGTGTTGAAGATGACTCTGCTCATCCATGTTGAAGAGATCTGGTTCATTTC
* * * * *
31171 AGATGAATTGA-TTGTTGAAGATGATGATGTTCCTTTGT-GTTGAGGAAATCGGGTAAATCTAGA
1 AGATGAATT-ATTTGTTGAAGATGACGATGAT-CTTTCTCGTTGAGGAAATCGGGTCAATCTGGA
*
31234 GATAATTTGGTG
64 AATAATTTGGTG
31246 ACAACACAAT
Statistics
Matches: 164, Mismatches: 30, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
122 156 0.95
123 8 0.05
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (122 bp):
AGATGAATTATTTGTTGAAGATGACGATGATCTTTCTCGTTGAGGAAATCGGGTCAATCTGGAAA
TAATTTGGTGTTGAAGATGACTCTGCTCATCCATGTTGAAGAGATCTGGTTCATTTC
Found at i:31796 original size:220 final size:220
Alignment explanation
Indices: 31167--31974 Score: 1004
Period size: 220 Copynumber: 3.7 Consensus size: 220
31157 ATCTGGTTGA
* * * * * *
31167 TTTCAGATGAATTGATTGTTGAAGATGATGATGTTCCTT-TGTGTTGAGGAAATCGGGTAAATCT
1 TTTCAGGTAAATTGTTTGCTGAAGATGACGATGTTCCTTCT-TGTTGAGGAAATCGGGTCAATCT
* * * * *
31231 AGAGATAATTTGGTGACAACACAATCCCTTCACGTTGAGGAAGTCTGATTATCTGAGGATGACAC
65 AGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATTATCTGAGGATGACAA
* *
31296 TGCTCCTTCGCGTTGAGGAGATCAGGTCAATCTGGAGATAATTTGATGTTGAAAATGACACTACT
130 TGCTCCTTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCT
* * *
31361 CATCTGTGTTGAAGAGATCTGGTTAT
195 CATCCGTGTTGAAGAGATATGGTAAT
*
31387 TTTCAGGTAAATTGTTTTGCTGAAGATGACG-TCGTTCCTTCTTGTTGAGGAAATTGGGTCAATC
1 TTTCAGGTAAATTG-TTTGCTGAAGATGACGAT-GTTCCTTCTTGTTGAGGAAATCGGGTCAATC
* * * * ** * * * * *
31451 T-G-GA-GA--TGGTGACAAAATGGCTCCTTCGCGTTGAGGAAGTCTGATTATATAAGGACGACA
64 TAGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATTATCTGAGGATGACA
* * * * * *
31511 ATTCTTCTTCGCTTTGAGGAGATCGGGTCAATCTAGAGATAATTTGTTGTTGAGAATGACACTGC
129 ATGCTCCTTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGC
*
31576 TCATCCATGTTGAAGAGATATGGTAAT
194 TCATCCGTGTTGAAGAGATATGGTAAT
* *
31603 TTTCAAGTAAATTGTTTGCT-AGAGATGACGATGTTCCTTCTTGTTGAGGAAATCGGGTCAATGT
1 TTTCAGGTAAATTGTTTGCTGA-AGATGACGATGTTCCTTCTTGTTGAGGAAATCGGGTCAATCT
* * *
31667 AGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGAAAGTCTGTTTATCTGAGGATGACAC
65 AGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATTATCTGAGGATGACAA
** * * *
31732 TGCTCCTTCATGTTGAGGAGATCAGATCAATCTAGAGATAATTTGATGTTAAAAATGGCACTGCT
130 TGCTCCTTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCT
* * **
31797 CATCCGTGTTAAATAGATATGGTCGT
195 CATCCGTGTTGAAGAGATATGGTAAT
* *
31823 TTTCAGGTAAATTTTTTGCTGAAGAAGAC-ATTGTTCCTTCTTGTTGAGGAAATCGGGTCAATCT
1 TTTCAGGTAAATTGTTTGCTGAAGATGACGA-TGTTCCTTCTTGTTGAGGAAATCGGGTCAATCT
* * * *
31887 GGAGATAATTTGGAGACAACACGGTTCCTTCGCATTGAGGAAGTCTGATTGTCTGAGGATGACAA
65 AGAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATTATCTGAGGATGACAA
*
31952 TGCTCATTCGCGTTGAGGAGATC
130 TGCTCCTTCGCGTTGAGGAGATC
31975 TAGTCATAGT
Statistics
Matches: 498, Mismatches: 78, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
214 1 0.00
215 44 0.09
216 138 0.28
217 2 0.00
218 2 0.00
219 3 0.01
220 265 0.53
221 42 0.08
222 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (220 bp):
TTTCAGGTAAATTGTTTGCTGAAGATGACGATGTTCCTTCTTGTTGAGGAAATCGGGTCAATCTA
GAGATAATTTGGAGACAACACGATTCCTTCACATTGAGGAAGTCTGATTATCTGAGGATGACAAT
GCTCCTTCGCGTTGAGGAGATCAGGTCAATCTAGAGATAATTTGATGTTGAAAATGACACTGCTC
ATCCGTGTTGAAGAGATATGGTAAT
Found at i:32300 original size:103 final size:103
Alignment explanation
Indices: 32177--32366 Score: 301
Period size: 103 Copynumber: 1.8 Consensus size: 103
32167 TTGAGTTTCA
* * *
32177 AGGGAAAACTATCTCAAGCGAGGCGAAATTGGTTTTTAAGAAAATAATCAT-AGGTGAGATCAAT
1 AGGGAAAACTATCTCAAGCGAGACGAAATTAGTTTTTAAGAAAACAATC-TCAGGTGAGATCAAT
*
32241 TTTGTTTCAAGTTAAACAATTTCCAATTTTTTTGTTTTG
65 TTTGTTTCAAGTGAAACAATTTCCAATTTTTTTGTTTTG
* * *
32280 AGGGAAAACTATCTCAAGCGAGATGAAATTAGTTTTTAGGAAAACAATCTCAGGTGATATCAATT
1 AGGGAAAACTATCTCAAGCGAGACGAAATTAGTTTTTAAGAAAACAATCTCAGGTGAGATCAATT
32345 TTGTTTCAAGTGAAACAATTTC
66 TTGTTTCAAGTGAAACAATTTC
32367 AAACTTTGCA
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 1 0.01
103 78 0.99
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (103 bp):
AGGGAAAACTATCTCAAGCGAGACGAAATTAGTTTTTAAGAAAACAATCTCAGGTGAGATCAATT
TTGTTTCAAGTGAAACAATTTCCAATTTTTTTGTTTTG
Found at i:38545 original size:2 final size:2
Alignment explanation
Indices: 38538--38572 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
38528 ATAGTTATGA
38538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38573 GATCATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41292 original size:35 final size:36
Alignment explanation
Indices: 41246--41341 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 36
41236 GGCATTCATG
* *
41246 GAGTATCGATACCTGGAGGGT-AGTATCGATACCAC
1 GAGTATCGATACCTAGAAGGTCAGTATCGATACCAC
* *
41281 GAGTATCGATA-CTATAAGGTCAGTATTGATACCAC
1 GAGTATCGATACCTAGAAGGTCAGTATCGATACCAC
* *
41316 GAGAATCGATA-CTATAAGGTCAGTAT
1 GAGTATCGATACCTAGAAGGTCAGTAT
41342 TGGTTCCAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 6 0.11
35 49 0.89
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (36 bp):
GAGTATCGATACCTAGAAGGTCAGTATCGATACCAC
Found at i:41342 original size:35 final size:35
Alignment explanation
Indices: 41267--41343 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
41257 CCTGGAGGGT
* *
41267 AGTATCGATACCACGAGTATCGATACTATAAGGTC
1 AGTATTGATACCACGAGAATCGATACTATAAGGTC
41302 AGTATTGATACCACGAGAATCGATACTATAAGGTC
1 AGTATTGATACCACGAGAATCGATACTATAAGGTC
41337 AGTATTG
1 AGTATTG
41344 GTTCCAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (35 bp):
AGTATTGATACCACGAGAATCGATACTATAAGGTC
Found at i:41556 original size:54 final size:54
Alignment explanation
Indices: 41469--41634 Score: 264
Period size: 54 Copynumber: 3.1 Consensus size: 54
41459 ATTTTTCTTT
41469 TATCATAAGAAATTAAGGATCGAATTATAATACTTGGAATATATGATTGTGTAGA
1 TATC-TAAGAAATTAAGGATCGAATTATAATACTTGGAATATATGATTGTGTAGA
*
41524 TATCTAAGAAATTAATGATCGAATTATAATACTTGGAAGTATA--ATTGTGTAGA
1 TATCTAAGAAATTAAGGATCGAATTATAATACTTGGAA-TATATGATTGTGTAGA
* * *
41577 TATCTAAGAAATTAAGGATCAAATTATAATGCTTGGAATGTATGATTGTGTAGA
1 TATCTAAGAAATTAAGGATCGAATTATAATACTTGGAATATATGATTGTGTAGA
41631 TATC
1 TATC
41635 GAGCACACGT
Statistics
Matches: 103, Mismatches: 5, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
52 3 0.03
53 45 0.44
54 47 0.46
55 8 0.08
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (54 bp):
TATCTAAGAAATTAAGGATCGAATTATAATACTTGGAATATATGATTGTGTAGA
Found at i:42133 original size:22 final size:22
Alignment explanation
Indices: 42105--42149 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
42095 AGTCGAGGGT
*
42105 TACATAGGTCCTTCGGGACATA
1 TACATAGGTCCTTCGAGACATA
42127 TACATAGGTCCTTCGAGACATA
1 TACATAGGTCCTTCGAGACATA
42149 T
1 T
42150 TTCACATGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (22 bp):
TACATAGGTCCTTCGAGACATA
Found at i:45973 original size:24 final size:23
Alignment explanation
Indices: 45934--45978 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
45924 ATCAGCAAAG
*
45934 AAATTGAAGCACTCAAAAGAATA
1 AAATTGAAGAACTCAAAAGAATA
45957 AAATTGCAAGAACTCAAAAGAA
1 AAATTG-AAGAACTCAAAAGAA
45979 AAAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.58, C:0.13, G:0.13, T:0.16
Consensus pattern (23 bp):
AAATTGAAGAACTCAAAAGAATA
Found at i:50139 original size:25 final size:25
Alignment explanation
Indices: 50101--50149 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
50091 ACAAAGTAAG
50101 TCGTCAGAAGATTACTGACGGAAAT
1 TCGTCAGAAGATTACTGACGGAAAT
* *
50126 TCGTCAGTATATTACTGACGGAAA
1 TCGTCAGAAGATTACTGACGGAAA
50150 AATTAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (25 bp):
TCGTCAGAAGATTACTGACGGAAAT
Found at i:51139 original size:31 final size:31
Alignment explanation
Indices: 51104--51171 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
51094 AATCTGTCAG
**
51104 AAATTTGTGACAGGTCCACATATTTTATCAC
1 AAATTTGTGACAGGTCCACATATTCCATCAC
**
51135 AAATTTGTGATGGGTCCACATATTCCATCAC
1 AAATTTGTGACAGGTCCACATATTCCATCAC
51166 AAATTT
1 AAATTT
51172 AAAAAATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (31 bp):
AAATTTGTGACAGGTCCACATATTCCATCAC
Found at i:51380 original size:18 final size:19
Alignment explanation
Indices: 51342--51380 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
51332 TTTTAAGATT
*
51342 TTATATTCGATTTCAAATA
1 TTATATTCGAATTCAAATA
*
51361 TTATATTC-AATTCAATTA
1 TTATATTCGAATTCAAATA
51379 TT
1 TT
51381 CGAATATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.51
Consensus pattern (19 bp):
TTATATTCGAATTCAAATA
Found at i:52274 original size:23 final size:23
Alignment explanation
Indices: 52247--52292 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
52237 ATTCAACAAA
52247 ACATCAGATAATATTAAAAAACT
1 ACATCAGATAATATTAAAAAACT
*
52270 ACATCATATAATATTAAAAAACT
1 ACATCAGATAATATTAAAAAACT
52293 TGAAGTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
ACATCAGATAATATTAAAAAACT
Found at i:56496 original size:14 final size:15
Alignment explanation
Indices: 56469--56499 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
56459 GATACTTAAA
56469 TTAATAATTTTTTAT
1 TTAATAATTTTTTAT
56484 TTAATAA-TTTTTAT
1 TTAATAATTTTTTAT
56498 TT
1 TT
56500 TTATTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTAATAATTTTTTAT
Found at i:57695 original size:47 final size:48
Alignment explanation
Indices: 57642--57740 Score: 121
Period size: 47 Copynumber: 2.1 Consensus size: 48
57632 GTTGAACAAA
* *
57642 ATTTCCGAC-GAAATCATTGTCCCATCATAAATTAAATTGATAT-TTTT
1 ATTTCCGACTG-AATCATTATCCCATCACAAATTAAATTGATATATTTT
* * * *
57689 ATTTCCGACTGAATGATTATTCTATCACAAATTAAATTGGTATATTTT
1 ATTTCCGACTGAATCATTATCCCATCACAAATTAAATTGATATATTTT
57737 ATTT
1 ATTT
57741 AAAGTTGAAC
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
47 35 0.80
48 9 0.20
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (48 bp):
ATTTCCGACTGAATCATTATCCCATCACAAATTAAATTGATATATTTT
Found at i:57704 original size:112 final size:112
Alignment explanation
Indices: 57572--57797 Score: 380
Period size: 112 Copynumber: 2.0 Consensus size: 112
57562 AATGTATATT
*
57572 TTTTTATTTCCGACGGAATGACTATTCCATCATAAATTAAATTGGTATATTTTAATTAAAGTTGA
1 TTTTTATTTCCGACGGAATGACTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTGA
57637 ACAAAATTTCCGACGAAATCATTGTCCCATCATAAATTAAATTGATA
66 ACAAAATTTCCGACGAAATCATTGTCCCATCATAAATTAAATTGATA
* * * *
57684 TTTTTATTTCCGACTGAATGATTATTCTATCACAAATTAAATTGGTATATTTTATTTAAAGTTGA
1 TTTTTATTTCCGACGGAATGACTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTGA
* * *
57749 ACATAATTTCCGATGGAATCATTGTCCCATCATAAATTAAATTGATA
66 ACAAAATTTCCGACGAAATCATTGTCCCATCATAAATTAAATTGATA
57796 TT
1 TT
57798 GTTTTTATTG
Statistics
Matches: 106, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (112 bp):
TTTTTATTTCCGACGGAATGACTATTCCATCACAAATTAAATTGGTATATTTTAATTAAAGTTGA
ACAAAATTTCCGACGAAATCATTGTCCCATCATAAATTAAATTGATA
Found at i:58144 original size:26 final size:25
Alignment explanation
Indices: 58097--58145 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
58087 CAGGTTTCAG
* * *
58097 TCGGATACTGTCAGGTCGGGTAATA
1 TCGGATACGGTCAAGTCAGGTAATA
58122 TCGGATACAGGTCAAGTCAGGTAA
1 TCGGATAC-GGTCAAGTCAGGTAA
58146 ATTTGATGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (25 bp):
TCGGATACGGTCAAGTCAGGTAATA
Found at i:59241 original size:216 final size:216
Alignment explanation
Indices: 58538--59435 Score: 1298
Period size: 216 Copynumber: 4.2 Consensus size: 216
58528 ATTTTATGAA
* * * *
58538 AAATACAACTTTAAGAACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAA-TAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
*
58602 AC-A-ACACATTGATGAGGGATC-AATATAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCTAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
58664 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGAAATAA
131 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGAAATAA
58729 GTATGGGCCAATTTCAT-ATGC
196 GTATGGGCCAATTTC-TGATGC
* * * * *
58750 AAGTATAATTTTAAGGACTAAATTGAACAAATATAAAATAAAAAATAAAAAATTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* * * *
58815 ATAACACACATTGATGAGGGATCATAT-TGAAATAATTTTAAATTGTGAGGTTTAAATTAATGC-
66 ACAACACACATTGATGAGGGATCAAATCT-AAATAATTTTAAATTGTGAGGTTGAAATTAATACA
* *
58878 AAAAAGTACTAAATTATACCAATTTAAAAAGTTATGGACCAATT-AAAAATATAAATAA-ATAAT
130 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGA-AAT
58941 AAGTATGGGCCAATTT-TAGATGC
194 AAGTATGGGCCAATTTCT-GATGC
* * **
58964 AAA-AAAAATTTAAGGACTAAATTGAACAAATATGAAATTACAAATTCAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
* *
59028 ACAACACACATTGATGAGGGATCAAATCTAAATGATTTTAAATTGTGAGGTAGAAATTAATACAA
66 ACAACACACATTGATGAGGGATCAAATCTAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
** * *
59093 AAAAGTACTAAATTATATTCATATAAAAAGTTATGGGCCAATTAAAAAATATAAGTAAGAAATAA
131 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGAAATAA
59158 GTATGGGCCAATTTCTGATGC
196 GTATGGGCCAATTTCTGATGC
* *
59179 AAATATAATTTTAAGGACTAAATTAAATAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
** *
59244 ACAATGCACATTGATGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAC
66 ACAACACACATTGATGAGGGATCAAATCTAAATAATTTTAAATTGTGAGGTTGAAATTAATACA-
* *
59309 AAAAA-TACTAAATTATACCCATTTAAAAAGTTATGAGCCAATTAAAAAATATAAATAAGTAATA
130 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGAAATA
* **
59373 AGTATGGGTCAATTTGAGATGC
195 AGTATGGGCCAATTTCTGATGC
* * * * *
59395 AAATATAGTTTTAAAGACTAAATTGAATACATATAAAATTA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTA
59436 AAAGACTTTA
Statistics
Matches: 610, Mismatches: 61, Indels: 26
0.88 0.09 0.04
Matches are distributed among these distances:
212 53 0.09
213 113 0.19
214 80 0.13
215 101 0.17
216 258 0.42
217 5 0.01
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (216 bp):
AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
ACAACACACATTGATGAGGGATCAAATCTAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGAAATAA
GTATGGGCCAATTTCTGATGC
Found at i:59570 original size:13 final size:13
Alignment explanation
Indices: 59554--59664 Score: 58
Period size: 13 Copynumber: 8.9 Consensus size: 13
59544 TAATATAAGT
59554 TATATATATATAC
1 TATATATATATAC
*
59567 TATAT-T-TATAT
1 TATATATATATAC
* *
59578 TATAAACTATATAA
1 TATATA-TATATAC
59592 T-TAT-TATA-AGC
1 TATATATATATA-C
*
59603 TATATATA-A-AT
1 TATATATATATAC
*
59614 TATGT-TATATGAC
1 TATATATATAT-AC
*
59627 TATATATATAAAC
1 TATATATATATAC
* *
59640 TATGTATATAAAC
1 TATATATATATAC
*
59653 TATATATGTATA
1 TATATATATATA
59665 AACTATAAAA
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
10 3 0.04
11 18 0.24
12 6 0.08
13 38 0.51
14 9 0.12
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (13 bp):
TATATATATATAC
Found at i:59615 original size:18 final size:18
Alignment explanation
Indices: 59554--59616 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
59544 TAATATAAGT
*
59554 TATATA-TATATACTATA
1 TATATATTATAAACTATA
*
59571 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
*
59589 TA-ATTATTATAAGCTATA
1 TATA-TATTATAAACTATA
*
59607 TATAAATTAT
1 TATATATTAT
59617 GTTATATGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.16
18 31 0.82
19 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:59658 original size:28 final size:26
Alignment explanation
Indices: 59603--59670 Score: 84
Period size: 26 Copynumber: 2.5 Consensus size: 26
59593 TATTATAAGC
* *
59603 TATATATAAATTATGTTATATGACTA
1 TATATATAAACTATGTTATATAACTA
59629 TATATATAAACTATG-TATATAAACTA
1 TATATATAAACTATGTTATAT-AACTA
59655 TATATGTATAAACTAT
1 TATA--TATAAACTAT
59671 AAAATAGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 5 0.14
26 22 0.59
28 10 0.27
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (26 bp):
TATATATAAACTATGTTATATAACTA
Found at i:59671 original size:15 final size:14
Alignment explanation
Indices: 59573--59671 Score: 68
Period size: 13 Copynumber: 7.1 Consensus size: 14
59563 ATACTATATT
59573 TATATTATAAACTA
1 TATATTATAAACTA
59587 TATAATTATTATAAGC--
1 TAT-ATTA-TA-AA-CTA
59603 TATA-TATAAA-T-
1 TATATTATAAACTA
* *
59614 TATGTTATATGACTA
1 TATATTATA-AACTA
59629 TATA-TATAAACTA
1 TATATTATAAACTA
*
59642 TGTA-TATAAACTA
1 TATATTATAAACTA
59655 TATATGTATAAACTA
1 TATAT-TATAAACTA
59670 TA
1 TA
59672 AAATAGTTTA
Statistics
Matches: 68, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
11 3 0.04
12 6 0.09
13 22 0.32
14 10 0.15
15 19 0.28
16 5 0.07
17 2 0.03
18 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.42
Consensus pattern (14 bp):
TATATTATAAACTA
Found at i:60050 original size:21 final size:21
Alignment explanation
Indices: 60026--60065 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
60016 ATAAACTAAT
60026 ATATATAACCTATAT-TATATG
1 ATATATAA-CTATATATATATG
60047 ATATATAACTATATATATA
1 ATATATAACTATATATATA
60066 AACCTATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
ATATATAACTATATATATATG
Found at i:60388 original size:5 final size:6
Alignment explanation
Indices: 60343--60481 Score: 71
Period size: 6 Copynumber: 23.7 Consensus size: 6
60333 CATATAATTT
* * * *
60343 ATATTA ATATTA ATTTTA AGACT- ATATTT ATA-TA ATATTA AT-TTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA
* * *
60388 AAATT- ATAATA TATATTA CTA-TA ATA-TA ATAATTAA TATATTA ATATTA
1 ATATTA ATATTA -ATATTA ATATTA ATATTA AT-ATT-A -ATATTA ATATTA
* * *
60437 AT-TT- ATAATA ATTATTA ATATTA ATTATAA ATATT- TTATTA ATAT
1 ATATTA ATATTA A-TATTA ATATTA A-TATTA ATATTA ATATTA ATAT
60482 AATTTTATAG
Statistics
Matches: 100, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
4 2 0.02
5 29 0.29
6 46 0.46
7 17 0.17
8 4 0.04
9 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:60402 original size:28 final size:28
Alignment explanation
Indices: 60282--60446 Score: 99
Period size: 31 Copynumber: 5.8 Consensus size: 28
60272 AAACTATACT
* *
60282 TATTAATATTAATTATATTAACTATATTATA
1 TATTAATATTAATT-TA--AAATATAATATA
* * * *
60313 AACTACTATATAATTTATAACATATAATTTA
1 TATTAATAT-TAATTTA-AA-ATATAATATA
* *
60344 TATTAATATTAATTTTAAGACTAT-ATTTA
1 TATTAATATTAA-TTTAA-AATATAATATA
60373 TA-TAATATTAATTTAAAATTATAATATA
1 TATTAATATTAATTTAAAA-TATAATATA
* *
60401 TATTACTA-TAATATAATAAT-T-A-ATA
1 TATTAATATTAATTTAA-AATATAATATA
*
60426 TATTAATATTAATTTATAATA
1 TATTAATATTAATTTAAAATA
60447 ATTATTAATA
Statistics
Matches: 107, Mismatches: 17, Indels: 25
0.72 0.11 0.17
Matches are distributed among these distances:
25 13 0.12
26 8 0.07
27 9 0.08
28 23 0.21
29 13 0.12
30 10 0.09
31 26 0.24
32 5 0.05
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTAATATTAATTTAAAATATAATATA
Found at i:60456 original size:23 final size:23
Alignment explanation
Indices: 60368--60486 Score: 90
Period size: 23 Copynumber: 5.2 Consensus size: 23
60358 TTAAGACTAT
60368 ATTTAT-ATAA-TATTAAT-TTAA
1 ATTTATAATAATTATTAATATT-A
* *
60389 AATTATAAT-ATATATTACTA-TA
1 ATTTATAATAAT-TATTAATATTA
*
60411 ATATAATAATTAATATATTAATATTA
1 AT-TTATAA-TAAT-TATTAATATTA
60437 ATTTATAATAATTATTAATATTA
1 ATTTATAATAATTATTAATATTA
*
60460 A-TTATAAATATTTTATTAATA-TA
1 ATTTAT-AATA-ATTATTAATATTA
60483 ATTT
1 ATTT
60487 TATAGGGATG
Statistics
Matches: 80, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
21 6 0.08
22 8 0.10
23 31 0.39
24 16 0.20
25 15 0.19
26 4 0.05
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTTATAATAATTATTAATATTA
Found at i:60461 original size:13 final size:13
Alignment explanation
Indices: 60414--60485 Score: 66
Period size: 13 Copynumber: 5.8 Consensus size: 13
60404 TACTATAATA
60414 TAATAATTAATATAT
1 TAAT-ATTAAT-TAT
60429 TAATATTAA-T-T
1 TAATATTAATTAT
*
60440 T-ATAATAATTAT
1 TAATATTAATTAT
60452 TAATATTAATTAT
1 TAATATTAATTAT
*
60465 AAATATT--TTAT
1 TAATATTAATTAT
60476 TAATA-TAATT
1 TAATATTAATT
60486 TTATAGGGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
10 7 0.15
11 11 0.23
12 5 0.10
13 16 0.33
14 5 0.10
15 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATATTAATTAT
Found at i:63797 original size:24 final size:23
Alignment explanation
Indices: 63770--63816 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
63760 CCTCCCTTGC
63770 ACTTTA-TAGTTTTCCTTCTTATGG
1 ACTTTACTA-TTTTCCTT-TTATGG
63794 ACTTTATCTATTTTCCTTTTATG
1 ACTTTA-CTATTTTCCTTTTATG
63817 TTTCAGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 8 0.38
26 2 0.10
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (23 bp):
ACTTTACTATTTTCCTTTTATGG
Found at i:64801 original size:181 final size:181
Alignment explanation
Indices: 64518--65174 Score: 910
Period size: 182 Copynumber: 3.6 Consensus size: 181
64508 CGATACAAAT
* * * * *
64518 AAAAAATGTATCGTTACAT-ACAATATTACAGGT-AAAATATGAC-AAATCGGTCTCGAAATGAC
1 AAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
* * *
64580 AAAACCGGTAAACGATATCGGATATGTTGAAAGTGTCGATAATTTAATATAAATATCGACACTTT
66 AAAACCGGTAAACAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
* * *
64645 TGGAATTTAAAAAACAAGAAGTTATAACGCCTATAAAGTGTCGATACTTTA
131 TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
* ***
64696 AAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAACATATCTCAAAAATGA
1 AAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTC-AAAATGA
* * *
64761 CAAAACCGGTAAA-AAAACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGAAATTT
65 CAAAACCGGTAAACAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACA-CT
64825 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
129 TTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
* * *
64878 AAAAAATGTATCAATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTCCCAAAATGAC
1 AAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
* **
64943 AAATCCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
66 AAAACCGGTAAA-CAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
65008 TCT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTA
130 T-TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
** * * *
65060 TGAAAATGTATCGATCCATAATAATATAACAGCTAAAAATATGACAAAACCGGTCTTAAAATGAC
1 AAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
* * * * * *
65125 AAAACTGGTAAAGAGCTACTGAATATGTTGAAAGTGTCGATACTTTAATA
66 AAAACCGGTAAACA-ATACCGGATATGTTGAAAGTGTCGATAATTTAATA
65175 AGTACGTGTA
Statistics
Matches: 423, Mismatches: 47, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
178 17 0.04
179 12 0.03
180 10 0.02
181 69 0.16
182 270 0.64
183 45 0.11
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (181 bp):
AAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGAC
AAAACCGGTAAACAATACCGGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTT
TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTA
Done.