Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015292.1 Kokia drynarioides strain JFW-HI SEQ_130337, 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: 338957
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 283 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:261649 original size:3 final size:3
Alignment explanation
Indices: 261641--261678 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
261631 TCTACAGATA
261641 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
261679 ATGTCGAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:262493 original size:14 final size:15
Alignment explanation
Indices: 262474--262502 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
262464 ATTTGTTGAA
262474 GTTATAAAT-TTTAT
1 GTTATAAATATTTAT
262488 GTTATAAATATTTAT
1 GTTATAAATATTTAT
262503 TCAATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
GTTATAAATATTTAT
Found at i:263137 original size:2 final size:2
Alignment explanation
Indices: 263132--263156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
263122 TATATGGTTA
263132 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
263157 AGTTAAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:266615 original size:9 final size:9
Alignment explanation
Indices: 266579--266670 Score: 52
Period size: 9 Copynumber: 10.4 Consensus size: 9
266569 ATATGTGACA
*
266579 AAAAACTAT
1 AAAAATTAT
266588 AAAAA--AT
1 AAAAATTAT
*
266595 AAAAATAAAT
1 AAAAAT-TAT
266605 AAAAATTAT
1 AAAAATTAT
*
266614 -AAAATTTT
1 AAAAATTAT
*
266622 AATAA--A-
1 AAAAATTAT
*
266628 AAAAATTAGA
1 AAAAATTA-T
266638 AAGAAATTAT
1 AA-AAATTAT
*
266648 AAAAATCAT
1 AAAAATTAT
266657 AAAACATTAT
1 AAAA-ATTAT
266667 AAAA
1 AAAA
266671 CTTTTTGAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 19
0.71 0.09 0.21
Matches are distributed among these distances:
6 4 0.06
7 7 0.11
8 8 0.12
9 20 0.31
10 20 0.31
11 6 0.09
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (9 bp):
AAAAATTAT
Found at i:266705 original size:13 final size:13
Alignment explanation
Indices: 266687--266712 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
266677 GAACTTTTAT
266687 AAAAATTATAAAA
1 AAAAATTATAAAA
266700 AAAAATTATAAAA
1 AAAAATTATAAAA
266713 TGCATCAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATTATAAAA
Found at i:266839 original size:17 final size:18
Alignment explanation
Indices: 266819--266852 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
266809 AGGAAAAATG
266819 ATAAAAAATA-AAAATAA
1 ATAAAAAATATAAAATAA
*
266836 ATAAAAATTATAAAATA
1 ATAAAAAATATAAAATA
266853 TTATAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAAAAAATATAAAATAA
Found at i:266855 original size:10 final size:10
Alignment explanation
Indices: 266836--266864 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
266826 ATAAAAATAA
266836 ATAAAA-ATT
1 ATAAAATATT
266845 ATAAAATATT
1 ATAAAATATT
266855 ATAAAATATT
1 ATAAAATATT
266865 TCTTCTAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAAAATATT
Found at i:266940 original size:20 final size:20
Alignment explanation
Indices: 266881--266950 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
266871 AGTACGATAT
*
266881 TTTTTATAATCTT-TTACGA
1 TTTTTATAATTTTCTTACGA
* * **
266900 ATCTTAT-A-TTTCTTAATA
1 TTTTTATAATTTTCTTACGA
266918 TTTTTATAATTTTCTTACGA
1 TTTTTATAATTTTCTTACGA
* *
266938 TTTATAAAATTTT
1 TTTTTATAATTTT
266951 ATATTTTTTC
Statistics
Matches: 37, Mismatches: 11, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
17 2 0.05
18 10 0.27
19 6 0.16
20 19 0.51
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTATAATTTTCTTACGA
Found at i:267019 original size:31 final size:29
Alignment explanation
Indices: 266941--267059 Score: 96
Period size: 30 Copynumber: 4.0 Consensus size: 29
266931 CTTACGATTT
* * *
266941 ATAAAATTTTATATTTTTTCTATATTTCT-
1 ATAAAATTTAATATTTTTTATA-ATTTTTA
* * * *
266970 ATATATTTTATATTTTTTTTCTAATTTTTA
1 ATAAAATTTA-ATATTTTTTATAATTTTTA
* *
267000 ATAAAATTTAAATAATTTTTATAGTTTTTTA
1 ATAAAATTT-AATATTTTTTATA-ATTTTTA
* *
267031 TTAAAATTTAATATTTTTTATAACTTTTA
1 ATAAAATTTAATATTTTTTATAATTTTTA
267060 TTTTTTTTAT
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
29 17 0.24
30 39 0.55
31 15 0.21
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.61
Consensus pattern (29 bp):
ATAAAATTTAATATTTTTTATAATTTTTA
Found at i:267309 original size:90 final size:89
Alignment explanation
Indices: 267147--267314 Score: 250
Period size: 90 Copynumber: 1.9 Consensus size: 89
267137 TTAGGATGGC
* * * *
267147 TCAAGTACCCAATTGAGTGCAAAAAAAAAATAAGAACTTAATTGCTTTTTTTGAAAAAGTTTGAA
1 TCAAGTACCCAATTGAGTGAAAAAAAAAAAAAAAAACTTAATTGCTTTTTTTGAAAAAATTTGAA
267212 GATCTTTTTTACGCATTTTGGTAGT
66 GATC-TTTTTACGCATTTTGGTAGT
*
267237 TCAAGTACTCAATTGAGTGAAAAAAAAAAAAACAAAGACTTAATTG-TTTTTTTGAAAAAATTTG
1 TCAAGTACCCAATTGAGTGAAAAAAAAAAAAA-AAA-ACTTAATTGCTTTTTTTGAAAAAATTTG
267301 AAGA-CTTTTTACGC
64 AAGATCTTTTTACGC
267315 CTTTAAGCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
89 9 0.13
90 30 0.42
91 23 0.32
92 9 0.13
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (89 bp):
TCAAGTACCCAATTGAGTGAAAAAAAAAAAAAAAAACTTAATTGCTTTTTTTGAAAAAATTTGAA
GATCTTTTTACGCATTTTGGTAGT
Found at i:269580 original size:18 final size:19
Alignment explanation
Indices: 269557--269606 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
269547 ACTACTATAT
**
269557 TGGCTCGTTTGAGCA-TAC
1 TGGCTCGTAAGAGCATTAC
269575 TGGCTCGTAAGAGCATTAC
1 TGGCTCGTAAGAGCATTAC
* *
269594 TGGATCGCAAGAG
1 TGGCTCGTAAGAG
269607 ATATTTTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (19 bp):
TGGCTCGTAAGAGCATTAC
Found at i:280835 original size:21 final size:21
Alignment explanation
Indices: 280806--280859 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
280796 GGAGTTTTTA
*
280806 ATATCGGTAGAAGTAAGACTT
1 ATATCGGTAGAAGTAACACTT
* * *
280827 ATTTCGGTAAAAGTTACACTT
1 ATATCGGTAGAAGTAACACTT
*
280848 GTATCGGTAGAA
1 ATATCGGTAGAA
280860 CTTTCCCAAG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (21 bp):
ATATCGGTAGAAGTAACACTT
Found at i:287209 original size:24 final size:25
Alignment explanation
Indices: 287167--287213 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
287157 TCTGATTGTT
* *
287167 TTTTTTTTTTTCTTTTTATGTTTAA
1 TTTTTTTATTTCTTCTTATGTTTAA
287192 TTTTTTTATTT-TTCTTATGTTT
1 TTTTTTTATTTCTTCTTATGTTT
287214 TCATTTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.11, C:0.04, G:0.04, T:0.81
Consensus pattern (25 bp):
TTTTTTTATTTCTTCTTATGTTTAA
Found at i:293041 original size:48 final size:48
Alignment explanation
Indices: 292933--293043 Score: 177
Period size: 48 Copynumber: 2.3 Consensus size: 48
292923 AGAAATAATC
*
292933 TTTCAATTAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTG
* *
292981 TTTCAATTAAACTCTGTTTATTTGTTTCAATTAAACTCTGTTTATTTG
1 TTTCAATCAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTG
* *
293029 TTTGAGTCAAACTCT
1 TTTCAATCAAACTCT
293044 TATTAGTATA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 59 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (48 bp):
TTTCAATCAAACTCTGTTTAATTGTTTCAATTAAACTCTGTTTATTTG
Found at i:293043 original size:24 final size:24
Alignment explanation
Indices: 292933--293031 Score: 189
Period size: 24 Copynumber: 4.1 Consensus size: 24
292923 AGAAATAATC
*
292933 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
292957 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
292981 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
293005 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
293029 TTT
1 TTT
293032 GAGTCAAACT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:294997 original size:24 final size:24
Alignment explanation
Indices: 294969--295043 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
294959 AGAAATAATC
* *
294969 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
*
294993 TTTCAATTAAGCTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
295017 TTTCAATTAAACTTTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
295041 TTT
1 TTT
295044 TAGTCAAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.24, C:0.11, G:0.09, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:295052 original size:24 final size:25
Alignment explanation
Indices: 294977--295059 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 25
294967 TCTTTCAGTT
* * *
294977 AAACTC-TGTTTAATTGTTTCAATT
1 AAACTCTTATTTATTTGTTTCAATC
* * *
295001 AAGCTC-TGTTTATTTGTTTCAATT
1 AAACTCTTATTTATTTGTTTCAATC
* *
295025 AAACT-TTATTTATTTGTTTTAGTC
1 AAACTCTTATTTATTTGTTTCAATC
295049 AAACTCTTATT
1 AAACTCTTATT
295060 AGTATAGATT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
24 45 0.90
25 5 0.10
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (25 bp):
AAACTCTTATTTATTTGTTTCAATC
Found at i:297042 original size:24 final size:24
Alignment explanation
Indices: 296974--297048 Score: 114
Period size: 24 Copynumber: 3.1 Consensus size: 24
296964 AAAAATAATC
* *
296974 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
296998 CTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
297022 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
297046 TTT
1 TTT
297049 GAGTCAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.13, G:0.08, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:307751 original size:10 final size:10
Alignment explanation
Indices: 307725--307770 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
307715 GTTATTTTTT
*
307725 AAAAAAA-TA
1 AAAAAAATTG
307734 AAAAAAATTG
1 AAAAAAATTG
307744 AAAAAAATTG
1 AAAAAAATTG
*
307754 --AAAAATTC
1 AAAAAAATTG
307762 AAAAAAATT
1 AAAAAAATT
307771 AGTACATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
8 7 0.22
9 7 0.22
10 18 0.56
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:307757 original size:18 final size:18
Alignment explanation
Indices: 307736--307770 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
307726 AAAAAATAAA
*
307736 AAAAATTGAAAAAAATTG
1 AAAAATTCAAAAAAATTG
307754 AAAAATTCAAAAAAATT
1 AAAAATTCAAAAAAATT
307771 AGTACATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (18 bp):
AAAAATTCAAAAAAATTG
Found at i:307812 original size:5 final size:5
Alignment explanation
Indices: 307788--307856 Score: 61
Period size: 5 Copynumber: 13.4 Consensus size: 5
307778 TCATTTTCAT
* *
307788 TTTTA GTTTTA GTCTTA TTTTA TTTTAA TTTT- TTTAA TTTTA TTTTAA
1 TTTTA -TTTTA -TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTT-A
*
307836 TTTT- TTTAA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TT
307857 ATGCATTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
4 6 0.11
5 27 0.51
6 20 0.38
ACGTcount: A:0.22, C:0.01, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:307824 original size:9 final size:9
Alignment explanation
Indices: 307810--307848 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
307800 TCTTATTTTA
307810 TTTTAATTT
1 TTTTAATTT
307819 TTTTAATTTT
1 TTTTAA-TTT
307829 ATTTTAATTT
1 -TTTTAATTT
307839 TTTTAATTT
1 TTTTAATTT
307848 T
1 T
307849 ATTTTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 16 0.57
10 6 0.21
11 6 0.21
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTAATTT
Found at i:307829 original size:20 final size:20
Alignment explanation
Indices: 307804--307854 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
307794 TTTTAGTCTT
307804 ATTTTATTTTAATTTTTTTA
1 ATTTTATTTTAATTTTTTTA
307824 ATTTTATTTTAATTTTTTTA
1 ATTTTATTTTAATTTTTTTA
307844 ATTTTATTTTA
1 ATTTTATTTTA
307855 TTATGCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
ATTTTATTTTAATTTTTTTA
Found at i:308827 original size:11 final size:11
Alignment explanation
Indices: 308782--308831 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
308772 TTAGAAAAAG
* *
308782 AAAAAAAGTCA
1 AAAAAAATTGA
308793 AAAAAAA-TGA
1 AAAAAAATTGA
*
308803 AAAGAAAATCGA
1 AAA-AAAATTGA
308815 AAAAAAATTGA
1 AAAAAAATTGA
308826 AAAAAA
1 AAAAAA
308832 GAAAAAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.15
11 24 0.71
12 5 0.15
ACGTcount: A:0.76, C:0.04, G:0.10, T:0.10
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:308836 original size:18 final size:18
Alignment explanation
Indices: 308815--308852 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
308805 AGAAAATCGA
308815 AAAAAAATTGAAAAAAAG
1 AAAAAAATTGAAAAAAAG
*
308833 AAAAAAATTGGAAAAAAG
1 AAAAAAATTGAAAAAAAG
308851 AA
1 AA
308853 GAAGAAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (18 bp):
AAAAAAATTGAAAAAAAG
Found at i:309884 original size:23 final size:25
Alignment explanation
Indices: 309858--309903 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
309848 CCAATTAGAG
309858 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
309881 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
309904 TTGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:311766 original size:29 final size:29
Alignment explanation
Indices: 311724--311783 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
311714 TCCTAAGTAG
311724 ATTGATTTTTAATAATGTGCTTGTGGCAT
1 ATTGATTTTTAATAATGTGCTTGTGGCAT
311753 ATTGATTTTTAATAATGTGCTTGTGGCAT
1 ATTGATTTTTAATAATGTGCTTGTGGCAT
311782 AT
1 AT
311784 GAAATTCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (29 bp):
ATTGATTTTTAATAATGTGCTTGTGGCAT
Found at i:313569 original size:27 final size:27
Alignment explanation
Indices: 313537--313593 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
313527 AAATGTGATT
*
313537 TTTGGATACCCAAGGGCAAAATGGTAA
1 TTTGGACACCCAAGGGCAAAATGGTAA
** * *
313564 TTTGGACACTTAGGGGTAAAATGGTAA
1 TTTGGACACCCAAGGGCAAAATGGTAA
313591 TTT
1 TTT
313594 TGGGAAAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (27 bp):
TTTGGACACCCAAGGGCAAAATGGTAA
Found at i:313639 original size:57 final size:55
Alignment explanation
Indices: 313576--313764 Score: 209
Period size: 57 Copynumber: 3.3 Consensus size: 55
313566 TGGACACTTA
* * *
313576 GGGGT-AAAATGGTAATTTTGGGAAAGATCAGGGTTAAAAAAGAAATTTTAGATGTTC
1 GGGGTAAAAAT-GTAATTTT-GG-AAGTTCAGGGTTAAAAATGGAATTTTAGATGTTC
* * * * * *
313633 GGGGTAAAAATGGAATTTTAGATGTTCGGGGGTAAAAATGGAATTTTAGAAAGTTC
1 GGGGTAAAAATGTAATTTTGGAAGTTCAGGGTTAAAAATGGAATTTTAG-ATGTTC
* * *
313689 GGGGTAAAAATATAATTTTTGGAAGTTTAGGGTTAAAAATGGAATTTTGGATGTTC
1 GGGGTAAAAATGTAA-TTTTGGAAGTTCAGGGTTAAAAATGGAATTTTAGATGTTC
313745 GGGGGTAAAAATGTAATTTT
1 -GGGGTAAAAATGTAATTTT
313765 TGAAAAGTGG
Statistics
Matches: 109, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
55 22 0.20
56 28 0.26
57 54 0.50
58 5 0.05
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (55 bp):
GGGGTAAAAATGTAATTTTGGAAGTTCAGGGTTAAAAATGGAATTTTAGATGTTC
Found at i:313664 original size:28 final size:27
Alignment explanation
Indices: 313610--313764 Score: 166
Period size: 28 Copynumber: 5.6 Consensus size: 27
313600 AGATCAGGGT
* *
313610 TAAAAAAGAAATTTTAGATGTTCGGGG
1 TAAAAATGGAATTTTAGATGTTCGGGG
313637 TAAAAATGGAATTTTAGATGTTCGGGGG
1 TAAAAATGGAATTTTAGATGTTC-GGGG
*
313665 TAAAAATGGAATTTTAGAAAGTTCGGGG
1 TAAAAATGGAATTTTAG-ATGTTCGGGG
** * * * *
313693 TAAAAATATAATTTTTGGAAGTTTAGGGT
1 TAAAAATGGAA-TTTTAGATG-TTCGGGG
*
313722 TAAAAATGGAATTTTGGATGTTCGGGGG
1 TAAAAATGGAATTTTAGATGTTC-GGGG
*
313750 TAAAAATGTAATTTT
1 TAAAAATGGAATTTT
313765 TGAAAAGTGG
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
27 23 0.21
28 62 0.57
29 24 0.22
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (27 bp):
TAAAAATGGAATTTTAGATGTTCGGGG
Found at i:313669 original size:85 final size:86
Alignment explanation
Indices: 313576--313769 Score: 236
Period size: 85 Copynumber: 2.3 Consensus size: 86
313566 TGGACACTTA
* * * *
313576 GGGGT-AAAATGGTAATTTTGGGAAAGATCAGGGTTAAAAA-AGAAATTTTAGATG-TTCGGGGT
1 GGGGTAAAAATGGTAATTTT-AGAAAGATC-GGGGTAAAAATAGAAATTTTAGAAGTTTAGGGGT
313638 AAAAATGGAATTTTAGATGTTCG
64 AAAAATGGAATTTTAGATGTTCG
* * * * *
313661 GGGGTAAAAATGG-AATTTTAGAAAGTTCGGGGTAAAAATATAATTTTTGGAAGTTTAGGGTTAA
1 GGGGTAAAAATGGTAATTTTAGAAAGATCGGGGTAAAAATAGAAATTTTAGAAGTTTAGGGGTAA
*
313725 AAATGGAATTTTGGATGTTCG
66 AAATGGAATTTTAGATGTTCG
*
313746 GGGGTAAAAAT-GTAATTTTTGAAA
1 GGGGTAAAAATGGTAATTTTAGAAA
313770 AGTGGGTGAC
Statistics
Matches: 94, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
83 9 0.10
84 18 0.19
85 60 0.64
86 7 0.07
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (86 bp):
GGGGTAAAAATGGTAATTTTAGAAAGATCGGGGTAAAAATAGAAATTTTAGAAGTTTAGGGGTAA
AAATGGAATTTTAGATGTTCG
Found at i:314846 original size:20 final size:20
Alignment explanation
Indices: 314821--314863 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
314811 TCTCCTTTTT
314821 TTATTAAATA-TTAATATTAA
1 TTATT-AATAGTTAATATTAA
*
314841 TTATTAATAGTTATTATTAA
1 TTATTAATAGTTAATATTAA
314861 TTA
1 TTA
314864 CTGTTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTATTAATAGTTAATATTAA
Found at i:314857 original size:3 final size:3
Alignment explanation
Indices: 314829--314996 Score: 203
Period size: 3 Copynumber: 54.7 Consensus size: 3
314819 TTTTATTAAA
* * * * *
314829 TAT TAA TAT TAAT TAT TAA TAGT TAT TAT TAAT TAC TGT TAT TAA TACT
1 TAT TAT TAT T-AT TAT TAT TA-T TAT TAT T-AT TAT TAT TAT TAT TA-T
* * * *
314878 TAT TAA TAT TAT TAT TAT AAA T-T TGT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
314923 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
314971 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
314997 ATGATACTTA
Statistics
Matches: 142, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.01
3 128 0.90
4 13 0.09
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:320642 original size:85 final size:85
Alignment explanation
Indices: 320534--320701 Score: 207
Period size: 85 Copynumber: 2.0 Consensus size: 85
320524 TTGCTTCATT
* * *
320534 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCG-TCTCAGTGT-TTTAATTCACTTC
1 GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCT-TCA-TGTCTTTAACTCACTTC
320597 TCTGTATCTCATCAGGAAGACG
64 TCTGTATCTCATCAGGAAGACG
* * * * *
320619 GATTTGGTGC-ACTTCTCTATATCTCATCAAGAGGGTGACCGCTTTATTTCTTTGACTCACTTCT
1 GATTTGGT-CTACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATGTCTTTAACTCACTTCT
*
320683 CTGTATCTCGTCAGGAAGA
65 CTGTATCTCATCAGGAAGA
320702 TAGGGGTTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 2 0.03
85 67 0.94
86 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (85 bp):
GATTTGGTCTACTTCTCTATATCTCATCAAGAAGATGACCGCTTCATGTCTTTAACTCACTTCTC
TGTATCTCATCAGGAAGACG
Found at i:320770 original size:209 final size:208
Alignment explanation
Indices: 320468--320955 Score: 717
Period size: 209 Copynumber: 2.3 Consensus size: 208
320458 TCTGATTCAT
* * *
320468 TTCTCTGTATCTCATCAAGAAAATGGGGTTTTAAAGTTTCACTCACACATTGGGTTTT-GCTTCA
1 TTCTCTGTATCTCATCAGGAAGATGGGG-TTTAAAGTTTCACT--CACATT-GATTTTCGCTTCA
* * *
320532 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGTCTCAGTGTTTTAATTCACTTC
62 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCAGTGTTCTAATTCACTTC
* * * *
320597 TCTGTATCTCATCAGGAAGACGGATTTGGTGCACTTCTCTATATCTCATCAAGAGGGTGACCGCT
127 TCTGTATCTCATCAGGAAAACGGATTTGGTGCACTTCTCCATATCTCATCAAGAAGGTAACCGCT
* *
320662 TTATTTCTTTGACTCAC
192 TTATTGCTTTGACCCAC
*
320679 TTCTCTGTATCTCGTCAGGAAGATAGGGGTTTAAAGTTTCACTCACATTGATTTTCGCTTCATTG
1 TTCTCTGTATCTCATCAGGAAGAT-GGGGTTTAAAGTTTCACTCACATTGATTTTCGCTTCATTG
* *
320744 ATTTGGTTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTCTAATTCACTTCTCT
65 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCAGTGTTCTAATTCACTTCTCT
* * *
320809 GTATCTCATCAGGAAAACGGATTTGGTTCACTTCTCCGTATCTCATCAGGAAGGTAACCGCTTTA
130 GTATCTCATCAGGAAAACGGATTTGGTGCACTTCTCCATATCTCATCAAGAAGGTAACCGCTTTA
320874 TTGCTTTGACCCAC
195 TTGCTTTGACCCAC
* * * **
320888 TTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGATTCATTCACATTGAGCTTCGCTTCATTGA
1 TTCTCTGTATCTCATCAGGAAGATGGGGTTTAAAGTTTCACTCACATTGATTTTCGCTTCATTGA
320953 TTT
66 TTT
320956 TGTAACACCC
Statistics
Matches: 251, Mismatches: 24, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
208 44 0.18
209 168 0.67
211 35 0.14
212 4 0.02
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (208 bp):
TTCTCTGTATCTCATCAGGAAGATGGGGTTTAAAGTTTCACTCACATTGATTTTCGCTTCATTGA
TTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCAGTGTTCTAATTCACTTCTCTG
TATCTCATCAGGAAAACGGATTTGGTGCACTTCTCCATATCTCATCAAGAAGGTAACCGCTTTAT
TGCTTTGACCCAC
Found at i:320889 original size:85 final size:85
Alignment explanation
Indices: 320743--320908 Score: 235
Period size: 85 Copynumber: 2.0 Consensus size: 85
320733 TCGCTTCATT
* * **
320743 GATTTGGTTTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTGTTCTAATTCACTTCTC
1 GATTTGGTTCACTTCTCAGTATCTCATCAGGAAGATAACCGCCTCATTGTTCTAACCCACTTCTC
320808 TGTATCTCATCAGGAAAACG
66 TGTATCTCATCAGGAAAACG
* * * * *
320828 GATTTGGTTCACTTCTCCGTATCTCATCAGGAAGGTAACCGCTTTATTGCTT-TGACCCACTTCT
1 GATTTGGTTCACTTCTCAGTATCTCATCAGGAAGATAACCGCCTCATTG-TTCTAACCCACTTCT
320892 CTGTATCTCATCAGGAA
65 CTGTATCTCATCAGGAA
320909 GATGGGGTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 69 0.97
86 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (85 bp):
GATTTGGTTCACTTCTCAGTATCTCATCAGGAAGATAACCGCCTCATTGTTCTAACCCACTTCTC
TGTATCTCATCAGGAAAACG
Found at i:322163 original size:6 final size:6
Alignment explanation
Indices: 322129--322190 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
322119 TAATAGGGAT
* * * *
322129 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
*
322176 TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTT
322191 TGATCACAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 40 0.85
7 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:324273 original size:41 final size:41
Alignment explanation
Indices: 324193--324350 Score: 185
Period size: 41 Copynumber: 3.8 Consensus size: 41
324183 ATTGGAATGG
* * * *
324193 TCTTCAATTTGCCCCTCTTGATTTAAGGGTAAAAAACTAGAA
1 TCTTCAATCTGCCCTTCTTGA-TTAAGAGTAAAAGACTAGAA
* *
324235 TCTTCAATCTGCCTTTCTTGATTAAG-GATAAAAGACTAGTA
1 TCTTCAATCTGCCCTTCTTGATTAAGAG-TAAAAGACTAGAA
* * *
324276 TCTTCAATCTTCCTTTCTTGATTAAGAGTAAAAGA-TTGAAA
1 TCTTCAATCTGCCCTTCTTGATTAAGAGTAAAAGACTAG-AA
*
324317 TCTTCAATCTACCCTTCTTGATTAAGAGTAAAAG
1 TCTTCAATCTGCCCTTCTTGATTAAGAGTAAAAG
324351 TAAATGGACT
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
40 3 0.03
41 81 0.79
42 19 0.18
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (41 bp):
TCTTCAATCTGCCCTTCTTGATTAAGAGTAAAAGACTAGAA
Found at i:330832 original size:82 final size:82
Alignment explanation
Indices: 330690--330842 Score: 254
Period size: 82 Copynumber: 1.9 Consensus size: 82
330680 CACAAAACCA
* *
330690 TTGGATAATCCAACTAGAGCTGGACTCACTTATTGCGGTTTATCCCCTAGGCACTTGGTGCCA-G
1 TTGGATAATCCAACTAGAGCTGGACTCACTTATTGAGGTTTATCCCCTAGGCACTGGGTGCCATG
330754 CAATTGATGGATTTATTG
66 -AATTGATGGATTTATTG
* *
330772 TTGGTTAATCCAACTAGAGCTGGACTCACTTATTGAGGTTTATCCGCTAGGCACTGGGTGCCATG
1 TTGGATAATCCAACTAGAGCTGGACTCACTTATTGAGGTTTATCCCCTAGGCACTGGGTGCCATG
330837 AATTGA
66 AATTGA
330843 CGGAACCATA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
82 65 0.98
83 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (82 bp):
TTGGATAATCCAACTAGAGCTGGACTCACTTATTGAGGTTTATCCCCTAGGCACTGGGTGCCATG
AATTGATGGATTTATTG
Found at i:331360 original size:8 final size:8
Alignment explanation
Indices: 331347--331372 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
331337 ATCAAAGATA
331347 TTGAATCT
1 TTGAATCT
331355 TTGAATCT
1 TTGAATCT
331363 TTGAATCT
1 TTGAATCT
331371 TT
1 TT
331373 AGGTTAATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.54
Consensus pattern (8 bp):
TTGAATCT
Found at i:333406 original size:13 final size:14
Alignment explanation
Indices: 333388--333417 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
333378 GATTTGAGTA
333388 AAATATAGGTTT-G
1 AAATATAGGTTTAG
333401 AAATATAGGTTTAG
1 AAATATAGGTTTAG
333415 AAA
1 AAA
333418 AAAAAACGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (14 bp):
AAATATAGGTTTAG
Found at i:334802 original size:18 final size:18
Alignment explanation
Indices: 334779--334814 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
334769 GTAGGTTTCC
334779 AAAAATGAAAATGGAAAT
1 AAAAATGAAAATGGAAAT
*
334797 AAAAATGGAAATGGAAAT
1 AAAAATGAAAATGGAAAT
334815 TATCCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (18 bp):
AAAAATGAAAATGGAAAT
Found at i:334814 original size:12 final size:12
Alignment explanation
Indices: 334781--334814 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
334771 AGGTTTCCAA
334781 AAATGAAAATGG
1 AAATGAAAATGG
*
334793 AAATAAAAATGG
1 AAATGAAAATGG
*
334805 AAATGGAAAT
1 AAATGAAAAT
334815 TATCCATTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:336985 original size:3 final size:3
Alignment explanation
Indices: 336977--337008 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
336967 TTTAATTTAT
336977 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
337009 GTCGAAACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:338092 original size:28 final size:28
Alignment explanation
Indices: 338061--338122 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
338051 AAAATGAGAT
** *
338061 TTTTGGATGCCCGAGGGTAAAATGGTAA
1 TTTTGGACACCCGAGGGCAAAATGGTAA
* * *
338089 TTTTTGACACTCGGGGGCAAAATGGTAA
1 TTTTGGACACCCGAGGGCAAAATGGTAA
338117 TTTTGG
1 TTTTGG
338123 GAAAGTTAGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.31, T:0.32
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGCAAAATGGTAA
Found at i:338171 original size:60 final size:58
Alignment explanation
Indices: 338087--338269 Score: 192
Period size: 60 Copynumber: 3.1 Consensus size: 58
338077 GTAAAATGGT
* * *
338087 AATTTTT-GACACTCGGGGGCAAAATGGTAATTTTGGGAAAG-TTAGAGGTCAAAAATG
1 AATTTTTAGACATTTGGGGGAAAAATGGTAATTTT-GGAAAGATTAGAGGTCAAAAATG
* * * *
338144 ACATTTTTAGACATTTTGGGGGTAAAATGATAATTTTTGGAAAGTTTAG-GGTTAAAAATG
1 A-ATTTTTAGACA-TTTGGGGGAAAAATGGTAA-TTTTGGAAAGATTAGAGGTCAAAAATG
* * * *
338204 AAATTTTTAGACATTTAGGGGAAAAATAGTAATTTTGGAAGGATTCGAGGTCAAAAATAG
1 -AATTTTTAGACATTTGGGGGAAAAATGGTAATTTTGGAAAGATTAGAGGTCAAAAAT-G
338264 AATTTT
1 AATTTT
338270 GGAAAGTTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
57 1 0.01
58 18 0.17
59 34 0.32
60 43 0.41
61 9 0.09
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.33
Consensus pattern (58 bp):
AATTTTTAGACATTTGGGGGAAAAATGGTAATTTTGGAAAGATTAGAGGTCAAAAATG
Found at i:338200 original size:30 final size:30
Alignment explanation
Indices: 338107--338408 Score: 146
Period size: 30 Copynumber: 10.2 Consensus size: 30
338097 ACTCGGGGGC
* * *
338107 AAAATGGTAATTTTGGGAAAG-TTAGAGGTCA
1 AAAATGATAATTTTTGGAAAGTTTAG-GGT-T
* * * * * *
338138 AAAATGA-CATTTTTAGACATTTTGGGGGT
1 AAAATGATAATTTTTGGAAAGTTTAGGGTT
338167 AAAATGATAATTTTTGGAAAGTTTAGGGTT
1 AAAATGATAATTTTTGGAAAGTTTAGGGTT
* * **
338197 AAAAATGA-AATTTTTAGACA-TTTAGGGGA
1 -AAAATGATAATTTTTGGAAAGTTTAGGGTT
* * * *
338226 AAAAT-AGTAA-TTTTGGAAGGATTCGAGGTC
1 AAAATGA-TAATTTTTGGAAAGTTTAG-GGTT
* *
338256 AAAA--ATAGAATTTTGGAAAGTTTAGGGCTA
1 AAAATGATA-ATTTTTGGAAAGTTTAGGG-TT
* *
338286 AAAATG-GAATTTTTGGAAAATTTAGGGTT
1 AAAATGATAATTTTTGGAAAGTTTAGGGTT
* *
338315 AAAATG-GAA-TTTTGGAAAGTTTAGGGGTA
1 AAAATGATAATTTTTGGAAAGTTTA-GGGTT
* * *
338344 AAAAT-AAAAATTTTGGAAAGTTCGAGGG-T
1 AAAATGATAATTTTTGGAAAGTT-TAGGGTT
* * *
338373 AAAA-AATTAATTTTTGGAAAATTTAGATGTT
1 AAAATGA-TAATTTTTGGAAAGTTTAG-GGTT
338404 AAAAT
1 AAAAT
338409 ATGATTTCTA
Statistics
Matches: 206, Mismatches: 44, Indels: 41
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.00
28 26 0.13
29 51 0.25
30 105 0.51
31 23 0.11
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (30 bp):
AAAATGATAATTTTTGGAAAGTTTAGGGTT
Found at i:338268 original size:59 final size:57
Alignment explanation
Indices: 338102--338387 Score: 188
Period size: 60 Copynumber: 4.8 Consensus size: 57
338092 TTGACACTCG
* *
338102 GGGGCAAAATGGTAATTTTGGGAAAGTTAGAGGTCAAAAATGACATTTTTAGACATTTTG
1 GGGGAAAAAT-GTAATTTT-GGAAAGTTAGAGGTCAAAAATGA-ATTTTTAGACATTTTA
* *
338162 GGGGTAAAATGATAATTTTTGGAAAGTTTAG-GGTTAAAAATGAAATTTTTAGACA-TTTA
1 GGGGAAAAATG-TAA-TTTTGGAAAG-TTAGAGGTCAAAAATG-AATTTTTAGACATTTTA
* * * * *
338221 GGGGAAAAATAGTAATTTTGGAAGGATTCGAGGTCAAAAATAGAA-TTTTGGAAAGTTTA
1 GGGGAAAAAT-GTAATTTTGGAAAG-TTAGAGGTCAAAAAT-GAATTTTTAGACATTTTA
* * * * * * *
338280 GGGCTAAAAATGGAATTTTTGGAAAATTTAG-GGT-TAAAATGGAA-TTTTGGAAAGTTTA
1 GGG-GAAAAATGTAA-TTTTGG-AAAGTTAGAGGTCAAAAAT-GAATTTTTAGACATTTTA
** * * *
338338 GGGGTAAAAATAAAAATTTTGGAAAGTTCGAGGGTAAAAAATTAATTTTT
1 GGGG-AAAAAT-GTAATTTTGGAAAGTTAGA-GGTCAAAAATGAATTTTT
338388 GGAAAATTTA
Statistics
Matches: 185, Mismatches: 24, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
57 6 0.03
58 56 0.30
59 47 0.25
60 65 0.35
61 11 0.06
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (57 bp):
GGGGAAAAATGTAATTTTGGAAAGTTAGAGGTCAAAAATGAATTTTTAGACATTTTA
Found at i:338270 original size:88 final size:88
Alignment explanation
Indices: 338178--338398 Score: 250
Period size: 88 Copynumber: 2.5 Consensus size: 88
338168 AAATGATAAT
* *
338178 TTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAG-ACATTTAGGGGAAAAATAGTAATTTTGG
1 TTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGAAAATTTAGGGGAAAAAT-GGAATTTTGG
* * *
338242 AAGGATTCGAGGTCAAAAAT-AGAA
65 AAAGATTAGAGGT-AAAAATAAAAA
* * * **
338266 TTTTGGAAAGTTTAGGGCTAAAAATGGAATTTTTGGAAAATTTAGGGTTAAAATGGAATTTTGGA
1 TTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGAAAATTTAGGGGAAAAATGGAATTTTGGA
* *
338331 AAGTTTAGGGGTAAAAATAAAAA
66 AAGATTAGAGGTAAAAATAAAAA
* * * *
338354 TTTTGGAAAGTTCGAGGGTAAAAAAT-TAATTTTTGGAAAATTTAG
1 TTTTGGAAAGTT-TAGGGTTAAAAATGAAATTTTTAGAAAATTTAG
338399 ATGTTAAAAT
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
87 6 0.05
88 84 0.74
89 24 0.21
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.33
Consensus pattern (88 bp):
TTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGAAAATTTAGGGGAAAAATGGAATTTTGGA
AAGATTAGAGGTAAAAATAAAAA
Found at i:338376 original size:58 final size:59
Alignment explanation
Indices: 338162--338398 Score: 209
Period size: 58 Copynumber: 4.0 Consensus size: 59
338152 AGACATTTTG
* * * *
338162 GGGGT-AAAAT-GATAATTTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGACA-TTTA
1 GGGGTAAAAATAGA-AA-TTTTGGAAAGTTGAGGGTTAAAAATGGAA-TTTTGGAAAGTTTA
* * * *
338221 GGGG-AAAAATAGTAATTTTGGAAGGATTCGA-GGTCAAAAATAGAATTTTGGAAAGTTTA
1 GGGGTAAAAATAGAAATTTTGGAAAG-TT-GAGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * * *
338280 GGGCTAAAAATGGAATTTTTGGAAAATTTAGGGTT-AAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAAATAGAAATTTTGGAAAGTTGAGGGTTAAAAATGGAATTTTGGAAAGTTTA
* * * *
338338 GGGGTAAAAATAAAAATTTTGGAAAGTTCGAGGGTAAAAAAT-TAATTTTTGGAAAATTTA
1 GGGGTAAAAATAGAAATTTTGGAAAGTT-GAGGGTTAAAAATGGAA-TTTTGGAAAGTTTA
338398 G
1 G
338399 ATGTTAAAAT
Statistics
Matches: 142, Mismatches: 26, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
58 62 0.44
59 43 0.30
60 37 0.26
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (59 bp):
GGGGTAAAAATAGAAATTTTGGAAAGTTGAGGGTTAAAAATGGAATTTTGGAAAGTTTA
Found at i:338386 original size:29 final size:28
Alignment explanation
Indices: 338178--338377 Score: 177
Period size: 30 Copynumber: 6.8 Consensus size: 28
338168 AAATGATAAT
*
338178 TTTTGGAAAGTTTAGGGTTAAAAATGAAA
1 TTTTGGAAAGTTTAGGG-TAAAAATGGAA
* * * *
338207 TTTTTAGACA-TTTAGGGGAAAAATAGTAA
1 -TTTTGGAAAGTTTAGGGTAAAAAT-GGAA
* * * *
338236 TTTTGGAAGGATTCGAGGTCAAAAATAGAA
1 TTTTGGAAAGTTTAG-GGT-AAAAATGGAA
338266 TTTTGGAAAGTTTAGGGCTAAAAATGGAA
1 TTTTGGAAAGTTTAGGG-TAAAAATGGAA
* *
338295 TTTTTGGAAAATTTAGGGTTAAAATGGAA
1 -TTTTGGAAAGTTTAGGGTAAAAATGGAA
**
338324 TTTTGGAAAGTTTAGGGGTAAAAATAAAAA
1 TTTTGGAAAGTTTA-GGGTAAAAAT-GGAA
*
338354 TTTTGGAAAGTTCGAGGGTAAAAA
1 TTTTGGAAAGTT-TAGGGTAAAAA
338378 ATTAATTTTT
Statistics
Matches: 138, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
28 25 0.18
29 43 0.31
30 63 0.46
31 7 0.05
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.32
Consensus pattern (28 bp):
TTTTGGAAAGTTTAGGGTAAAAATGGAA
Found at i:338408 original size:118 final size:119
Alignment explanation
Indices: 338166--338398 Score: 287
Period size: 118 Copynumber: 2.0 Consensus size: 119
338156 ATTTTGGGGG
* * *
338166 TAAAATGATAATTTTTGGAAAGTTTAGGGTTAAAAATGAAATTTTTAGACATTTAGGGGAAAAAT
1 TAAAATGAGAATTTTTGGAAAATTTAGGGTTAAAAATGAAATTTTTAGAAATTTAGGGGAAAAAT
** * * *
338231 AGTAATTTTGGAAGGATTCGAGGTCAAAAATAGAATTTTGGAAAGTTTAGGGCT
66 AAAAATTTTGGAAAGATTCGAGGTAAAAAATAGAATTTTGGAAAATTTAGGGCT
* * *
338285 AAAAATG-GAATTTTTGGAAAATTTAGGGTT-AAAATGGAA-TTTTGGAAAGTTTAGGGGTAAAA
1 TAAAATGAGAATTTTTGGAAAATTTAGGGTTAAAAATGAAATTTTTAGAAA-TTTAGGGG-AAAA
*
338347 ATAAAAATTTTGGAAAG-TTCGAGGGTAAAAAATTA-ATTTTTGGAAAATTTAG
64 ATAAAAATTTTGGAAAGATTCGA-GGTAAAAAA-TAGAATTTTGGAAAATTTAG
338399 ATGTTAAAAT
Statistics
Matches: 98, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
116 7 0.07
117 21 0.21
118 62 0.63
119 8 0.08
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.33
Consensus pattern (119 bp):
TAAAATGAGAATTTTTGGAAAATTTAGGGTTAAAAATGAAATTTTTAGAAATTTAGGGGAAAAAT
AAAAATTTTGGAAAGATTCGAGGTAAAAAATAGAATTTTGGAAAATTTAGGGCT
Done.