Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011494.1 Kokia drynarioides strain JFW-HI SEQ_126479, 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: 307715
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 42 characters in sequence are not A, C, G, or T
Found at i:14706 original size:21 final size:21
Alignment explanation
Indices: 14663--14716 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
14653 GGAGTTTTTA
*
14663 GTATCGGTAGAAGCATGTCGT
1 GTATCGGTAGAAGCATATCGT
*
14684 GTATCGGTAGAAGTTATAT-GT
1 GTATCGGTAGAAG-CATATCGT
*
14705 GTATTGGTAGAA
1 GTATCGGTAGAA
14717 CTAGCACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.90
22 3 0.10
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATATCGT
Found at i:18872 original size:36 final size:36
Alignment explanation
Indices: 18832--18955 Score: 117
Period size: 36 Copynumber: 3.4 Consensus size: 36
18822 TGTGTTTGCA
* * *
18832 TACGTCTCGGTTAGAGTGTATTGCTATGGAAGTTCT
1 TACGTCTCGATTAGAGTGTAATGCTAAGGAAGTTCT
* **
18868 TACGTCTC-AGTTAGAGCGTAATGCTAAATAA-TTGCT
1 TACGTCTCGA-TTAGAGTGTAATGCTAAGGAAGTT-CT
* ** *
18904 TATGTCTCGATTAGAGTGTAATAATAAGGAAGTGCT
1 TACGTCTCGATTAGAGTGTAATGCTAAGGAAGTTCT
*
18940 TATGTCTCGATTAGAG
1 TACGTCTCGATTAGAG
18956 CATAAGGCCA
Statistics
Matches: 71, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
35 2 0.03
36 67 0.94
37 2 0.03
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (36 bp):
TACGTCTCGATTAGAGTGTAATGCTAAGGAAGTTCT
Found at i:23800 original size:15 final size:16
Alignment explanation
Indices: 23780--23819 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
23770 ATTAATTCAT
23780 AATTTAAATTAT-TAA
1 AATTTAAATTATATAA
*
23795 AATTT-AAGTATATAA
1 AATTTAAATTATATAA
23810 AATTTAAATT
1 AATTTAAATT
23820 CAATATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
AATTTAAATTATATAA
Found at i:24072 original size:3 final size:3
Alignment explanation
Indices: 24064--24089 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24054 CCCCAACCCC
24064 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
24090 ATTATCGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:24915 original size:18 final size:19
Alignment explanation
Indices: 24894--24931 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
24884 CTATAATAAT
*
24894 ATAAATTTTAATTTT-AAA
1 ATAAAATTTAATTTTGAAA
24912 ATAAAATTTAATTTTGAAA
1 ATAAAATTTAATTTTGAAA
24931 A
1 A
24932 GCAAAAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATAAAATTTAATTTTGAAA
Found at i:40788 original size:35 final size:35
Alignment explanation
Indices: 40742--40811 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
40732 GATGCTAATT
40742 TTCCTAAAGACCTTGATAGAAGAAGATCTATCACA
1 TTCCTAAAGACCTTGATAGAAGAAGATCTATCACA
*
40777 TTCCTAGAGACCTTGATAGAAGAAGATCTATCACA
1 TTCCTAAAGACCTTGATAGAAGAAGATCTATCACA
40812 GGGTATCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.26
Consensus pattern (35 bp):
TTCCTAAAGACCTTGATAGAAGAAGATCTATCACA
Found at i:46393 original size:24 final size:24
Alignment explanation
Indices: 46366--46429 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 24
46356 TTATGTTAAA
* *
46366 AAAATTTTAGATAAATTAAAATGT
1 AAAATTTCACATAAATTAAAATGT
* *
46390 AAAATTTCACTTAAATTAAAATTT
1 AAAATTTCACATAAATTAAAATGT
*
46414 AAAATTTCACTTAAAT
1 AAAATTTCACATAAAT
46430 ATATTAATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (24 bp):
AAAATTTCACATAAATTAAAATGT
Found at i:48299 original size:11 final size:11
Alignment explanation
Indices: 48276--48310 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
48266 TTGTGAAGAC
48276 AATAAAAATAAA
1 AATAAAAA-AAA
48288 AATAAAAAAAA
1 AATAAAAAAAA
*
48299 AAGAAAAAAAA
1 AATAAAAAAAA
48310 A
1 A
48311 GTTGATGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.64
12 8 0.36
ACGTcount: A:0.89, C:0.00, G:0.03, T:0.09
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:51278 original size:18 final size:18
Alignment explanation
Indices: 51257--51304 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
51247 ATGAGAAGAG
* * *
51257 AGAAAAATAAAGGGAAAA
1 AGAAAAAGAAAAGAAAAA
*
51275 AGAAAAGGAAAAGAAAAA
1 AGAAAAAGAAAAGAAAAA
51293 AGAAAAAGAAAA
1 AGAAAAAGAAAA
51305 AAATTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAAAAAGAAAAGAAAAA
Found at i:51281 original size:13 final size:12
Alignment explanation
Indices: 51258--51304 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
51248 TGAGAAGAGA
* *
51258 GAAAAATAAAGG
1 GAAAAAGAAAAG
51270 GAAAAAGAAAAG
1 GAAAAAGAAAAG
*
51282 G-AAAAGAAAAAA
1 GAAAAAG-AAAAG
51294 GAAAAAGAAAA
1 GAAAAAGAAAA
51305 AAATTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 5 0.17
12 20 0.67
13 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (12 bp):
GAAAAAGAAAAG
Found at i:51305 original size:13 final size:13
Alignment explanation
Indices: 51277--51306 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
51267 AGGGAAAAAG
*
51277 AAAAGGAAAAGAA
1 AAAAGAAAAAGAA
51290 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
51303 AAAA
1 AAAA
51307 ATTAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:52383 original size:80 final size:80
Alignment explanation
Indices: 52289--52438 Score: 219
Period size: 80 Copynumber: 1.9 Consensus size: 80
52279 TACAAATTCG
* * * * *
52289 TCCCTTAAAGTTAATTTAATTTCAATTCAAAAGCGCACGTTGGGATTGAAATTGCTTGGTGTACA
1 TCCCTTAAAGTTAATTCAATTTAAATTCAAAAGCGCACATTGCGATTGAAATTGCTTGGCGTACA
52354 GTTGGGACTAAATTA
66 GTTGGGACTAAATTA
* ** *
52369 TCCCTTAAAGTTAATTCAATTTAAATTCAAAATCGTGCATTGCGATTGAAATTGTTTGGCGTACA
1 TCCCTTAAAGTTAATTCAATTTAAATTCAAAAGCGCACATTGCGATTGAAATTGCTTGGCGTACA
52434 GTTGG
66 GTTGG
52439 AAAGTCGAGT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
80 61 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (80 bp):
TCCCTTAAAGTTAATTCAATTTAAATTCAAAAGCGCACATTGCGATTGAAATTGCTTGGCGTACA
GTTGGGACTAAATTA
Found at i:66643 original size:29 final size:32
Alignment explanation
Indices: 66617--66687 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 32
66607 TCCGAAGAAT
66617 ATTTCAGAGGTACGTAGCTTCCTAAGATTAGTTG
1 ATTTCAGAGGTACGTAGCTTCCTAAGA-TAG-TG
* *
66651 GTTTCTGAGGTACGTAGCTTCCTAAGATTAGCTG
1 ATTTCAGAGGTACGTAGCTTCCTAAGA-TAG-TG
66685 ATT
1 ATT
66688 ATTACTGTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (32 bp):
ATTTCAGAGGTACGTAGCTTCCTAAGATAGTG
Found at i:70146 original size:89 final size:89
Alignment explanation
Indices: 69987--70160 Score: 226
Period size: 89 Copynumber: 2.0 Consensus size: 89
69977 TGGATTACAT
* * * * * *
69987 GCCCTACGATGGCTAAGATTTATGCTTGATTTGCATATTCTCGTTAGCTTAGTATGAACGACATC
1 GCCCTACGATGGCTAAAATTTATACTTGATTTGCATATTATCATCAGCTTAGTATGAAAGACATC
* *
70052 GTTAGGGAACAATTGTATGTATAG
66 ATTAGGGAACAATTATATGTATAG
*
70076 GCCCTACGATGGTTAAAATTTATACTTGATTTGCATATTATCATCAGCTTAGTGA-GAGAAG-CA
1 GCCCTACGATGGCTAAAATTTATACTTGATTTGCATATTATCATCAGCTTAGT-ATGA-AAGACA
*
70139 TCATTAGGGAACAGTTATATGT
64 TCATTAGGGAACAATTATATGT
70161 GCAGATACCG
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
89 70 0.96
90 3 0.04
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (89 bp):
GCCCTACGATGGCTAAAATTTATACTTGATTTGCATATTATCATCAGCTTAGTATGAAAGACATC
ATTAGGGAACAATTATATGTATAG
Found at i:81193 original size:21 final size:21
Alignment explanation
Indices: 81163--81206 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
81153 TGGTTTGAAA
* *
81163 GACAAGAAGAGGAAGCACAAG
1 GACAAAAAGAAGAAGCACAAG
*
81184 GACAAAAAGAAGAAGCATAAG
1 GACAAAAAGAAGAAGCACAAG
81205 GA
1 GA
81207 GGAAGGAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.11, G:0.30, T:0.02
Consensus pattern (21 bp):
GACAAAAAGAAGAAGCACAAG
Found at i:84279 original size:37 final size:37
Alignment explanation
Indices: 84220--84384 Score: 215
Period size: 37 Copynumber: 4.5 Consensus size: 37
84210 GCTCTTGGAT
* *
84220 CACCGGCACGAAGCCTACTAGGCACATAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
* * *
84257 CACTGGCACAAAGCCTGTTAGGCACATAGCCCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
*
84294 CACCGGCACAAAGCTTGCTAGGCACATAGCCTGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
* * *
84331 CACCGACACAAAGCCTACTAGGCTCATAG-CTCGAATA
1 CACCGGCACAAAGCCTGCTAGGCACATAGCCT-GAATA
* *
84368 CACCGACAAAAAGCCTG
1 CACCGGCACAAAGCCTG
84385 AATATTGTGC
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
36 2 0.02
37 110 0.98
ACGTcount: A:0.34, C:0.32, G:0.20, T:0.15
Consensus pattern (37 bp):
CACCGGCACAAAGCCTGCTAGGCACATAGCCTGAATA
Found at i:87730 original size:3 final size:3
Alignment explanation
Indices: 87722--87760 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
87712 TTTCATTTTA
87722 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
87761 CATAGACTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:88526 original size:18 final size:17
Alignment explanation
Indices: 88500--88533 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
88490 TAAGTTTATA
*
88500 ATATTTTATGTTATTTTT
1 ATATATTATG-TATTTTT
88518 ATATATTATGTATTTT
1 ATATATTATGTATTTT
88534 AAAACACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
ATATATTATGTATTTTT
Found at i:90162 original size:30 final size:31
Alignment explanation
Indices: 90128--90199 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
90118 CAATTTGGTT
90128 ATTGAACTATTCAAAA-GTTTTATTTAAGTC
1 ATTGAACTATTCAAAATGTTTTATTTAAGTC
* * *
90158 ATTGAACTATTTAAAATTTTTTGTTTAAGTC
1 ATTGAACTATTCAAAATGTTTTATTTAAGTC
* *
90189 ACTGGACTATT
1 ATTGAACTATT
90200 ATCTTTTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 15 0.42
31 21 0.58
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTCAAAATGTTTTATTTAAGTC
Found at i:93203 original size:25 final size:26
Alignment explanation
Indices: 93160--93208 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
93150 ACTCAATTTG
93160 AATTTTTTTCGAATCAAATCGAGTAA
1 AATTTTTTTCGAATCAAATCGAGTAA
* *
93186 AATTTTTTT-GAGTGAAATCGAGT
1 AATTTTTTTCGAATCAAATCGAGT
93209 TAACAAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (26 bp):
AATTTTTTTCGAATCAAATCGAGTAA
Found at i:97634 original size:15 final size:15
Alignment explanation
Indices: 97591--97677 Score: 61
Period size: 15 Copynumber: 5.9 Consensus size: 15
97581 ACTTTCGGAT
*
97591 AGTTCACATATAAAAC
1 AGTTCACACAT-AAAC
* *
97607 AATTCTCACATAAAC
1 AGTTCACACATAAAC
*
97622 AGTTCACATAT-AAC
1 AGTTCACACATAAAC
* *
97636 AATTCGCACATAAAC
1 AGTTCACACATAAAC
* * *
97651 AGATCGCATAT-AAC
1 AGTTCACACATAAAC
*
97665 ATTTCACACATAA
1 AGTTCACACATAA
97678 TTGGTTCGCA
Statistics
Matches: 53, Mismatches: 16, Indels: 5
0.72 0.22 0.07
Matches are distributed among these distances:
14 21 0.40
15 24 0.45
16 8 0.15
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (15 bp):
AGTTCACACATAAAC
Found at i:97646 original size:29 final size:29
Alignment explanation
Indices: 97591--97677 Score: 111
Period size: 29 Copynumber: 2.9 Consensus size: 29
97581 ACTTTCGGAT
*
97591 AGTTCACATATAAAACAATTCTCACATAAAC
1 AGTTCACATAT--AACAATTCACACATAAAC
*
97622 AGTTCACATATAACAATTCGCACATAAAC
1 AGTTCACATATAACAATTCACACATAAAC
* * *
97651 AGATCGCATATAACATTTCACACATAA
1 AGTTCACATATAACAATTCACACATAA
97678 TTGGTTCGCA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 40 0.78
31 11 0.22
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (29 bp):
AGTTCACATATAACAATTCACACATAAAC
Found at i:97648 original size:14 final size:14
Alignment explanation
Indices: 97604--97677 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
97594 TCACATATAA
*
97604 AACAATTCTCACAT
1 AACAATTCACACAT
* *
97618 AAACAGTTCACATAT
1 -AACAATTCACACAT
*
97633 AACAATTCGCACAT
1 AACAATTCACACAT
* *
97647 AAACAGA-TCGCATAT
1 -AACA-ATTCACACAT
*
97662 AACATTTCACACAT
1 AACAATTCACACAT
97676 AA
1 AA
97678 TTGGTTCGCA
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
14 23 0.50
15 22 0.48
16 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.24
Consensus pattern (14 bp):
AACAATTCACACAT
Found at i:97686 original size:29 final size:29
Alignment explanation
Indices: 97604--97717 Score: 84
Period size: 29 Copynumber: 3.9 Consensus size: 29
97594 TCACATATAA
* * ** * *
97604 AACAATTCTCACATAAACAGTTCACATAT
1 AACAGTTCACACATAATTAGTTCGCATAC
* * ** * *
97633 AACAATTCGCACATAAACAGATCGCATAT
1 AACAGTTCACACATAATTAGTTCGCATAC
* *
97662 AACATTTCACACATAATTGGTTCGCATAC
1 AACAGTTCACACATAATTAGTTCGCATAC
* *
97691 AATAGTTCACATATAATTAGTTCGCAT
1 AACAGTTCACACATAATTAGTTCGCAT
97718 GCATATTAGC
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (29 bp):
AACAGTTCACACATAATTAGTTCGCATAC
Found at i:97713 original size:15 final size:15
Alignment explanation
Indices: 97667--97713 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
97657 CATATAACAT
* *
97667 TTCACACATAATTGG
1 TTCACATATAATTAG
* *
97682 TTCGCATACAA-TAG
1 TTCACATATAATTAG
97696 TTCACATATAATTAG
1 TTCACATATAATTAG
97711 TTC
1 TTC
97714 GCATGCATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (15 bp):
TTCACATATAATTAG
Found at i:98042 original size:126 final size:128
Alignment explanation
Indices: 97816--98081 Score: 333
Period size: 126 Copynumber: 2.1 Consensus size: 128
97806 AAATCTCCTG
* * * *
97816 AAACATTGCCTGTAAGTGAAGCACGAATGCTCACACTCTTCGAAAACACTTCCTATAAGTGAAGC
1 AAACACTGCCTGTAAGTGAAGCACAAATGCTCACACTCTTCAAAAACACTTCCTATAACTGAAGC
* * * ***
97881 ATGAATGCTCGCACTCTTCGAAAACACTGCTTGTAAGTGC-AC-GAATACTTGCACTCTTTGA
66 ACGAATGCTCGCACTCTCCGAAAACACTGCCTGTAAGTGCAACAGAATACTTGCACTCTCCAA
** * *
97942 AAACACTGCCTGTAAGTGCAA-CACAAATGCTCGTACTTTTCAAAAACACTGT-CTGTAACTGAA
1 AAACACTGCCTGTAAGTG-AAGCACAAATGCTCACACTCTTCAAAAACACT-TCCTATAACTGAA
* *
98005 GCACGAATGCTTGCACTCTCCGAAAACATTGCCTGTAAGTGCAACATGAATACTTGCACTCTCCA
64 GCACGAATGCTCGCACTCTCCGAAAACACTGCCTGTAAGTGCAACA-GAATACTTGCACTCTCCA
98070 A
128 A
98071 AAACACTGCCT
1 AAACACTGCCT
98082 TCTCCTCCAT
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
126 87 0.73
127 5 0.04
129 27 0.23
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (128 bp):
AAACACTGCCTGTAAGTGAAGCACAAATGCTCACACTCTTCAAAAACACTTCCTATAACTGAAGC
ACGAATGCTCGCACTCTCCGAAAACACTGCCTGTAAGTGCAACAGAATACTTGCACTCTCCAA
Found at i:98081 original size:43 final size:43
Alignment explanation
Indices: 97816--98081 Score: 272
Period size: 43 Copynumber: 6.3 Consensus size: 43
97806 AAATCTCCTG
* *
97816 AAACATTGCCTGTAAGTGAAGCACGAATGCTCACACTCTTCGA
1 AAACACTGCCTGTAAGTGAAGCACGAATGCTCGCACTCTTCGA
* * *
97859 AAACACTTCCTATAAGTGAAGCATGAATGCTCGCACTCTTCGA
1 AAACACTGCCTGTAAGTGAAGCACGAATGCTCGCACTCTTCGA
* * * *
97902 AAACACTGCTTGTAAGT---GCACGAATACTTGCACTCTTTGA
1 AAACACTGCCTGTAAGTGAAGCACGAATGCTCGCACTCTTCGA
* * * *
97942 AAACACTGCCTGTAAGTGCAA-CACAAATGCTCGTACTTTTCAA
1 AAACACTGCCTGTAAGTG-AAGCACGAATGCTCGCACTCTTCGA
* * * *
97985 AAACACTGTCTGTAACTGAAGCACGAATGCTTGCACTCTCCGA
1 AAACACTGCCTGTAAGTGAAGCACGAATGCTCGCACTCTTCGA
* * * * * *
98028 AAACATTGCCTGTAAGTGCAA-CATGAATACTTGCACTCTCCAA
1 AAACACTGCCTGTAAGTG-AAGCACGAATGCTCGCACTCTTCGA
98071 AAACACTGCCT
1 AAACACTGCCT
98082 TCTCCTCCAT
Statistics
Matches: 182, Mismatches: 35, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
40 35 0.19
42 2 0.01
43 143 0.79
44 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACACTGCCTGTAAGTGAAGCACGAATGCTCGCACTCTTCGA
Found at i:98353 original size:24 final size:25
Alignment explanation
Indices: 98303--98367 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 25
98293 ATAAAGCTCA
98303 CAATGCATAGTTCAC-AGAAACTCG
1 CAATGCATAGTTCACAAGAAACTCG
* * *
98327 CAATGCACAGTTCACAAG-AGCTTG
1 CAATGCATAGTTCACAAGAAACTCG
*
98351 CAATGCATAATTCACAA
1 CAATGCATAGTTCACAA
98368 TGGTTATACT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 33 0.94
25 2 0.06
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (25 bp):
CAATGCATAGTTCACAAGAAACTCG
Found at i:98789 original size:21 final size:21
Alignment explanation
Indices: 98763--98824 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
98753 TAAGAGCTCA
*
98763 CACAACATATGAAAGTGTTCG
1 CACAACATATAAAAGTGTTCG
*
98784 CACAACATCTAAAAGTGTTCG
1 CACAACATATAAAAGTGTTCG
* *
98805 CATAACATATAAAAGAGTTC
1 CACAACATATAAAAGTGTTC
98825 ACATATGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (21 bp):
CACAACATATAAAAGTGTTCG
Found at i:98829 original size:21 final size:21
Alignment explanation
Indices: 98754--98827 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
98744 ATTCGTACGT
* *
98754 AAGAGCTCACACAACATATGA
1 AAGAGTTCACACAACATATAA
* * *
98775 AAGTGTTCGCACAACATCTAA
1 AAGAGTTCACACAACATATAA
* * *
98796 AAGTGTTCGCATAACATATAA
1 AAGAGTTCACACAACATATAA
98817 AAGAGTTCACA
1 AAGAGTTCACA
98828 TATGAATGTA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (21 bp):
AAGAGTTCACACAACATATAA
Found at i:103572 original size:16 final size:15
Alignment explanation
Indices: 103533--103588 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
103523 AGGAAATGTG
* *
103533 TAAAAAAAAAAAACA
1 TAAAATAAATAAACA
*
103548 TAAATATAAATAGACA
1 TAAA-ATAAATAAACA
*
103564 TGAAAATAAATAAAGA
1 T-AAAATAAATAAACA
103580 TAAAATAAA
1 TAAAATAAA
103589 AATAAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 12 0.35
16 19 0.56
17 3 0.09
ACGTcount: A:0.73, C:0.04, G:0.05, T:0.18
Consensus pattern (15 bp):
TAAAATAAATAAACA
Found at i:103587 original size:11 final size:10
Alignment explanation
Indices: 103533--103600 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
103523 AGGAAATGTG
103533 TAAAAA-AAA
1 TAAAAATAAA
103542 -AAAACATAAA
1 TAAAA-ATAAA
*
103552 TATAAATAGACA
1 TAAAAATA-A-A
*
103564 TGAAAATAAA
1 TAAAAATAAA
*
103574 TAAAGATAAAA
1 TAAAAAT-AAA
103585 TAAAAATAAA
1 TAAAAATAAA
103595 TAAAAA
1 TAAAAA
103601 ATTATACAAG
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
8 4 0.09
9 1 0.02
10 21 0.45
11 14 0.30
12 7 0.15
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:104208 original size:31 final size:30
Alignment explanation
Indices: 104173--104249 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
104163 TTTTTTAAAG
*
104173 ATCAAAACTTTTATTTCAAAATAATTAAAAA
1 ATCAAAA-TTTTATTTCAAAATAACTAAAAA
* ** *
104204 ATCAAAATTTTGTTTTTGAAATGACTAAAAA
1 ATCAAAATTTT-ATTTCAAAATAACTAAAAA
*
104235 AACAAAATTTTATTT
1 ATCAAAATTTTATTT
104250 TTAAAAATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (30 bp):
ATCAAAATTTTATTTCAAAATAACTAAAAA
Found at i:104428 original size:26 final size:24
Alignment explanation
Indices: 104381--104429 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
104371 GGATAGATTT
*
104381 TATTTTTAAAAAATCTAAACTTTC
1 TATTTTTAAAAAATCAAAACTTTC
104405 TATTTTTAAAAAGAATCAAAACTTT
1 TATTTTT-AAAA-AATCAAAACTTT
104430 TCCCAAGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (24 bp):
TATTTTTAAAAAATCAAAACTTTC
Found at i:104770 original size:3 final size:3
Alignment explanation
Indices: 104762--104796 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
104752 CATGAAACCT
104762 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
104797 GTAGTAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:105815 original size:28 final size:28
Alignment explanation
Indices: 105775--105831 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
105765 ATGAAAATAT
*
105775 GATATTTGTTACTATTTCACCGAACCAC
1 GATATTTGTTACTATTTCACCAAACCAC
105803 GATATTTGTTACTATTTCACCAAACCAC
1 GATATTTGTTACTATTTCACCAAACCAC
105831 G
1 G
105832 TGTTTACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.35
Consensus pattern (28 bp):
GATATTTGTTACTATTTCACCAAACCAC
Found at i:110251 original size:17 final size:17
Alignment explanation
Indices: 110213--110266 Score: 81
Period size: 17 Copynumber: 3.1 Consensus size: 17
110203 ATTTTTTCAA
*
110213 AAACCTTAAACCCTAAAC
1 AAACCTTAAACCCT-AAT
*
110231 AAACCTAAAACCCTAAT
1 AAACCTTAAACCCTAAT
110248 AAACCTTAAACCCTAAT
1 AAACCTTAAACCCTAAT
110265 AA
1 AA
110267 TAAAATCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 20 0.61
18 13 0.39
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.19
Consensus pattern (17 bp):
AAACCTTAAACCCTAAT
Found at i:110380 original size:42 final size:42
Alignment explanation
Indices: 110332--110464 Score: 130
Period size: 41 Copynumber: 3.2 Consensus size: 42
110322 ATAAAACCCT
* *
110332 AAACCCTAATTTAATTAACCCTAAATCCTAATTAAACAATTA
1 AAACCCTAATTTAATTAACCTTAAAACCTAATTAAACAATTA
* * ** * *
110374 AAACCCTAA-TT-ATAAACATTTAAAAAATAAATACAAC-CTT-
1 AAACCCTAATTTAATTAAC-CTTAAAACCTAATTA-AACAATTA
* *
110414 AAACCCTAATCTAATTAACCTTAAACCCTAATTAAACAATTA
1 AAACCCTAATTTAATTAACCTTAAAACCTAATTAAACAATTA
110456 AAACCCTAA
1 AAACCCTAA
110465 AAAGCATGAG
Statistics
Matches: 69, Mismatches: 16, Indels: 12
0.71 0.16 0.12
Matches are distributed among these distances:
40 17 0.25
41 26 0.38
42 26 0.38
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (42 bp):
AAACCCTAATTTAATTAACCTTAAAACCTAATTAAACAATTA
Found at i:110417 original size:82 final size:81
Alignment explanation
Indices: 110304--110464 Score: 250
Period size: 82 Copynumber: 2.0 Consensus size: 81
110294 AATCTAATCA
* * *
110304 ATAAACACTTAAAATTAAATAAAACCCTAAACCCTAATTTAATTAACCCTAAATCCTAATTAAAC
1 ATAAACACTTAAAAATAAATAAAACCCTAAACCCTAATCTAATTAACCCTAAACCCTAATTAAAC
110369 AATTAAAACCCTAATT
66 AATTAAAACCCTAATT
* * * *
110385 ATAAACATTTAAAAAATAAATACAACCTTAAACCCTAATCTAATTAACCTTAAACCCTAATTAAA
1 ATAAACACTT-AAAAATAAATAAAACCCTAAACCCTAATCTAATTAACCCTAAACCCTAATTAAA
110450 CAATTAAAACCCTAA
65 CAATTAAAACCCTAA
110465 AAAGCATGAG
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
81 9 0.12
82 63 0.88
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (81 bp):
ATAAACACTTAAAAATAAATAAAACCCTAAACCCTAATCTAATTAACCCTAAACCCTAATTAAAC
AATTAAAACCCTAATT
Found at i:110438 original size:41 final size:41
Alignment explanation
Indices: 110297--110438 Score: 98
Period size: 41 Copynumber: 3.5 Consensus size: 41
110287 TCCTAATAAT
* *
110297 CTAATC-AATAAACACTT-AAAATTAAATAAAACCCTAAACC
1 CTAATCTAATAAACACTTAAAAAATAAAT-AAACCTTAAACC
* * * *** * *
110337 CTAATTTAATTAAC-CCTAAATCCTAATTAAACAATTAAAACC
1 CTAATCTAATAAACACTTAAAAAATAAATAAAC-CTT-AAACC
*
110379 CTAAT-T-ATAAACATTTAAAAAATAAATACAACCTTAAACC
1 CTAATCTAATAAACACTTAAAAAATAAATA-AACCTTAAACC
*
110419 CTAATCTAATTAAC-CTTAAA
1 CTAATCTAATAAACACTTAAA
110439 CCCTAATTAA
Statistics
Matches: 75, Mismatches: 19, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
40 26 0.35
41 31 0.41
42 18 0.24
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.28
Consensus pattern (41 bp):
CTAATCTAATAAACACTTAAAAAATAAATAAACCTTAAACC
Found at i:111018 original size:21 final size:23
Alignment explanation
Indices: 110975--111021 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
110965 AATTAAATTT
*
110975 TTTATTTTTAATAATTTAGTAAA
1 TTTATTTTCAATAATTTAGTAAA
*
110998 TTTA-TTTCAATATTTTA-TAAA
1 TTTATTTTCAATAATTTAGTAAA
111019 TTT
1 TTT
111022 TAAGAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTATTTTCAATAATTTAGTAAA
Found at i:111372 original size:29 final size:29
Alignment explanation
Indices: 111317--111375 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
111307 AAACAAATGA
*
111317 TTTTAAAATTATTTCTTAAAATATAAAAT
1 TTTTAAAATTATATCTTAAAATATAAAAT
111346 TTTTAAAATTA-AT-TTAAAATTATTAAAAT
1 TTTTAAAATTATATCTTAAAA-TA-TAAAAT
111375 T
1 T
111376 ATTTTTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 6 0.22
28 3 0.11
29 18 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTAAAATTATATCTTAAAATATAAAAT
Found at i:111376 original size:9 final size:9
Alignment explanation
Indices: 111332--111378 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
111322 AAATTATTTC
111332 TTAAAA-TA
1 TTAAAATTA
*
111340 -TAAAATTT
1 TTAAAATTA
111348 TTAAAATTAA
1 TTAAAATT-A
111358 TTTAAAATTA
1 -TTAAAATTA
111368 TTAAAATTA
1 TTAAAATTA
111377 TT
1 TT
111379 TTTTTTGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 5 0.15
8 1 0.03
9 18 0.55
10 1 0.03
11 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:112451 original size:9 final size:9
Alignment explanation
Indices: 112437--112461 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
112427 TTAAAAAAAT
112437 AATTTTAAA
1 AATTTTAAA
112446 AATTTTAAA
1 AATTTTAAA
112455 AATTTTA
1 AATTTTA
112462 TATTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
AATTTTAAA
Found at i:112459 original size:40 final size:39
Alignment explanation
Indices: 112400--112484 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 39
112390 AAATTGTAAA
* *
112400 TTAAAATTATTTAATAATTTTATTATTTTAAAAAAATAATT
1 TTAAAAATATTTAAAAATTTTA-TATTTT-AAAAAATAATT
* *
112441 TTAAAAAT-TTTAAAAATTTTATATTTTCAAAAATGATT
1 TTAAAAATATTTAAAAATTTTATATTTTAAAAAATAATT
112479 TTAAAA
1 TTAAAA
112485 TCATTTGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 15 0.38
39 6 0.15
40 12 0.30
41 7 0.17
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
TTAAAAATATTTAAAAATTTTATATTTTAAAAAATAATT
Found at i:116365 original size:20 final size:20
Alignment explanation
Indices: 116342--116379 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
116332 TTGACCGTTA
116342 GATTTAATGGATGACCATTG
1 GATTTAATGGATGACCATTG
* *
116362 GATTTAATTGTTGACCAT
1 GATTTAATGGATGACCAT
116380 CAAGTCCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (20 bp):
GATTTAATGGATGACCATTG
Found at i:116924 original size:76 final size:76
Alignment explanation
Indices: 116668--116921 Score: 358
Period size: 76 Copynumber: 3.4 Consensus size: 76
116658 ATTTTCCCAG
* * *
116668 ATTTTCTCAAACTTTCTTTCTTTCCAAACACCCATGACTTTTTATTTTCTCAGACTTTCCCTTCA
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATGACTTTTTATTTTCTTAGACTTTCCCTTCA
116733 TTCCTTCATGA
66 TTCCTTCATGA
* * * *
116744 ATTTTCTTAGA----CTGTCTTTCCAAACACCCGTGACTTTTTATTCTC-TA-ACTTTCCCTTCA
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATGACTTTTTATTTTCTTAGACTTTCCCTTCA
116803 TTCCTTCATGA
66 TTCCTTCATGA
* * * *
116814 ATTTTCTCAGACTTTCTGTCTTTTCAAACACCTATGCCTTTTTATTTTCTTAGACTTTCCCTTCA
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATGACTTTTTATTTTCTTAGACTTTCCCTTCA
116879 TTCCTTCATGA
66 TTCCTTCATGA
*
116890 ATTTTCTCAGACTTTCTCTGTTTCCAAACACC
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACC
116922 TATTTTCGTG
Statistics
Matches: 157, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
70 33 0.21
71 1 0.01
72 31 0.20
74 29 0.18
75 2 0.01
76 61 0.39
ACGTcount: A:0.20, C:0.28, G:0.06, T:0.46
Consensus pattern (76 bp):
ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATGACTTTTTATTTTCTTAGACTTTCCCTTCA
TTCCTTCATGA
Found at i:117581 original size:76 final size:78
Alignment explanation
Indices: 117488--117674 Score: 299
Period size: 76 Copynumber: 2.4 Consensus size: 78
117478 CTCAAGAAAA
*
117488 TGGGTGTTTGGAAAGAGAGAAAGTCTAAGAAAATTCATGAAGGAATGAAGGGATAGTCAGAGAAA
1 TGGGTGTTTGGAAAGAGAGAAAGTCTAAGAAAATTCATGAAGGAATGAAGGGAAAGTCAGAGAAA
117553 AT-AAAAAGTT-G
66 ATAAAAAAGTTAG
* * * *
117564 TGGGTGTTTGGAAAGAGAAAAATTCTAAGAAAATTCATGAAGGAATGAATGGAAAGTCTGAGAAA
1 TGGGTGTTTGGAAAGAGAGAAAGTCTAAGAAAATTCATGAAGGAATGAAGGGAAAGTCAGAGAAA
117629 ATAAAAAAGTTAG
66 ATAAAAAAGTTAG
*
117642 -GGGTGTTTGGAAAGAGAGAAAGTCTGAGAAAAT
1 TGGGTGTTTGGAAAGAGAGAAAGTCTAAGAAAAT
117675 CTGAGAAAAT
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
76 62 0.61
77 38 0.38
78 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.29, T:0.22
Consensus pattern (78 bp):
TGGGTGTTTGGAAAGAGAGAAAGTCTAAGAAAATTCATGAAGGAATGAAGGGAAAGTCAGAGAAA
ATAAAAAAGTTAG
Found at i:131381 original size:50 final size:50
Alignment explanation
Indices: 131299--131407 Score: 139
Period size: 50 Copynumber: 2.2 Consensus size: 50
131289 ATATTTTACC
* * *
131299 CCTAAAGCTGTGGAGGTGCAGATTGAAACCGCAATGACAAATCTCATACA
1 CCTAAAGCTGTAGAGGTACAGAATGAAACCGCAATGACAAATCTCATACA
* * * *
131349 CCTAAAGCTGTAGATGG-ACAGAATGAAGCCGCAATGGCAAATCTTATTCA
1 CCTAAAGCTGTAGA-GGTACAGAATGAAACCGCAATGACAAATCTCATACA
131399 CCTAAAGCT
1 CCTAAAGCT
131408 ATAAAGGAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 49 0.96
51 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGTACAGAATGAAACCGCAATGACAAATCTCATACA
Found at i:131426 original size:50 final size:50
Alignment explanation
Indices: 131317--131426 Score: 132
Period size: 50 Copynumber: 2.2 Consensus size: 50
131307 TGTGGAGGTG
* * *
131317 CAGATTGAAACCGCAATGACAAATCTCATACACCTAAAGCTGTAGATGGA
1 CAGATTGAAGCCGCAATGACAAATCTCATACACCTAAAGCTATAGAAGGA
* * * *
131367 CAGAATGAAGCCGCAATGGCAAATCTTATTCACCTAAAGCTATA-AAGGA
1 CAGATTGAAGCCGCAATGACAAATCTCATACACCTAAAGCTATAGAAGGA
*
131416 GTAGATTGAAG
1 -CAGATTGAAG
131427 TCACAAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
49 4 0.08
50 46 0.92
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (50 bp):
CAGATTGAAGCCGCAATGACAAATCTCATACACCTAAAGCTATAGAAGGA
Found at i:131537 original size:40 final size:39
Alignment explanation
Indices: 131471--131595 Score: 110
Period size: 40 Copynumber: 3.2 Consensus size: 39
131461 ATGAAGTGAA
* *
131471 CCAATCTCTTACCCTAA-CTAGAGGGCAAATTGAAGACCAT
1 CCAATCTCTTACCCCAATC-AAAGGGC-AATTGAAGACCAT
* * ** * *
131511 CCGATCTCTTACCCCGATCATGGGGCATATTGAAAACTAT
1 CCAATCTCTTACCCCAATCAAAGGGCA-ATTGAAGACCAT
* *
131551 CCAATCTTTTACCCTAATCAAAGGGC-ATTGAAGACCAT
1 CCAATCTCTTACCCCAATCAAAGGGCAATTGAAGACCAT
*
131589 CTAATCT
1 CCAATCT
131596 TTTAGCCTGA
Statistics
Matches: 67, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
38 16 0.24
39 1 0.01
40 49 0.73
41 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (39 bp):
CCAATCTCTTACCCCAATCAAAGGGCAATTGAAGACCAT
Found at i:131934 original size:29 final size:29
Alignment explanation
Indices: 131894--131958 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
131884 TTTTCCCTTG
* * * *
131894 TATATATGTCTGTTTCCTTAATTTATATA
1 TATATATATCTGTCTCCCTAACTTATATA
*
131923 TATATATATCTGTCTCCCTAACTTATGTA
1 TATATATATCTGTCTCCCTAACTTATATA
131952 TATATAT
1 TATATAT
131959 GGTTAATCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (29 bp):
TATATATATCTGTCTCCCTAACTTATATA
Found at i:142364 original size:19 final size:19
Alignment explanation
Indices: 142342--142381 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
142332 ATCAACAAAA
142342 AAGTCAACAGTCAATGGTC
1 AAGTCAACAGTCAATGGTC
* * *
142361 AAGTTAACGGTCAATTGTC
1 AAGTCAACAGTCAATGGTC
142380 AA
1 AA
142382 CGGTTAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (19 bp):
AAGTCAACAGTCAATGGTC
Found at i:143084 original size:26 final size:26
Alignment explanation
Indices: 143041--143091 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
143031 TCTAGAAATG
*
143041 TCGCTGCATAAACATGTCCATAATTA
1 TCGCTGCATAAACATGTCCAGAATTA
* *
143067 TCGCTGCATGAACGTGTCCAGAATT
1 TCGCTGCATAAACATGTCCAGAATT
143092 GCGCCCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (26 bp):
TCGCTGCATAAACATGTCCAGAATTA
Found at i:143919 original size:16 final size:16
Alignment explanation
Indices: 143898--143928 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
143888 TTGTGGATCC
143898 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
143914 CATTTTACCTTTATT
1 CATTTTACCTTTATT
143929 TTTACATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:148832 original size:61 final size:60
Alignment explanation
Indices: 148704--148982 Score: 436
Period size: 61 Copynumber: 4.6 Consensus size: 60
148694 GTTTTACTCG
* * *
148704 CATTTACA-ACTCACGATGACACAAAGTCATCGGACC-CTTGTTCGTATTGGAACTCATTT
1 CATTTA-ATACTCACGATGACATATAGTCATCGGACCTCTTGTTCGTATAGGAACTCATTT
* * * * *
148763 CATTTAATACTCACGATGACATATATTCATCGAACCTATTGTTCCATATAGGAACACATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTT-CGTATAGGAACTCATTT
148824 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGCTTCGTATAGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTG-TTCGTATAGGAACTCATTT
148885 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCCGTATAGGAACTCATTT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTT-CGTATAGGAACTCATTT
148946 CATTTAATACTCACGATGACATATAGTCATCGGACCT
1 CATTTAATACTCACGATGACATATAGTCATCGGACCT
148983 TCAATCCATC
Statistics
Matches: 202, Mismatches: 13, Indels: 8
0.91 0.06 0.04
Matches are distributed among these distances:
58 1 0.00
59 30 0.15
60 7 0.03
61 162 0.80
62 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (60 bp):
CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTGTTCGTATAGGAACTCATTT
Found at i:149024 original size:51 final size:51
Alignment explanation
Indices: 148953--149086 Score: 189
Period size: 51 Copynumber: 2.6 Consensus size: 51
148943 TTTCATTTAA
* *
148953 TACTCACGATGACA-TATAGTCATCGGACCTTCAATCCATCATGGATTCATT
1 TACTCACGATGACACT-TAGTCATCGGACCTTCAATCCATAAAGGATTCATT
* *
149004 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTCAATCCATAAAGGATTCATT
* *
149055 TACTCTCGATGGCACTTAGTCATCGGATCCTT
1 TACTCACGATGACACTTAGTCATCGGA-CCTT
149087 TCGTTTATAG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
51 70 0.93
52 5 0.07
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTCAATCCATAAAGGATTCATT
Found at i:151516 original size:28 final size:25
Alignment explanation
Indices: 151448--151513 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 25
151438 CAAAAAAATC
*
151448 ATAAATAAAAAATAGAAAAAGTGTTT
1 ATAAA-AAAAAATAGAAAAAGAGTTT
151474 ATAAAAAGAAAATAGAAAAAAGAGATTTT
1 ATAAAAA-AAAATAG-AAAAAGAG--TTT
151503 CATAAAAAAAA
1 -ATAAAAAAAA
151514 TAGTAGTTCC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
25 2 0.06
26 12 0.35
27 7 0.21
29 6 0.18
30 7 0.21
ACGTcount: A:0.67, C:0.02, G:0.11, T:0.21
Consensus pattern (25 bp):
ATAAAAAAAAATAGAAAAAGAGTTT
Found at i:158417 original size:16 final size:16
Alignment explanation
Indices: 158392--158456 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 16
158382 CGGTGTATTC
158392 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
*
158408 AGGCTTTGTG-CTAGTGTATT
1 AGGCTATGTGCCTA--G---T
158428 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
*
158445 AGGCTTTGTGCC
1 AGGCTATGTGCC
158457 GGTGTATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
15 3 0.08
16 20 0.51
17 2 0.05
20 2 0.05
21 9 0.23
22 3 0.08
ACGTcount: A:0.15, C:0.18, G:0.31, T:0.35
Consensus pattern (16 bp):
AGGCTATGTGCCTAGT
Found at i:158477 original size:21 final size:21
Alignment explanation
Indices: 158382--158514 Score: 80
Period size: 21 Copynumber: 7.0 Consensus size: 21
158372 AGCTTTATGT
158382 CGGTGTATTCAGGCTATGTGC
1 CGGTGTATTCAGGCTATGTGC
* *
158403 C----TAGT-AGGCTTTGTGC
1 CGGTGTATTCAGGCTATGTGC
**
158419 TAGTGTATTCAGGCTATGTGC
1 CGGTGTATTCAGGCTATGTGC
* *
158440 C----TAGT-AGGCTTTGTGC
1 CGGTGTATTCAGGCTATGTGC
*
158456 CGGTGTATTCAAGCTATGTGC
1 CGGTGTATTCAGGCTATGTGC
* *
158477 C----TATT-AGGCTTTGTGT
1 CGGTGTATTCAGGCTATGTGC
158493 CGGTGTATTCAGGCTATGTGC
1 CGGTGTATTCAGGCTATGTGC
158514 C
1 C
158515 TAGTAGGCTT
Statistics
Matches: 81, Mismatches: 16, Indels: 30
0.64 0.13 0.24
Matches are distributed among these distances:
16 30 0.37
17 10 0.12
20 10 0.12
21 31 0.38
ACGTcount: A:0.15, C:0.18, G:0.30, T:0.37
Consensus pattern (21 bp):
CGGTGTATTCAGGCTATGTGC
Found at i:158488 original size:111 final size:111
Alignment explanation
Indices: 158351--158566 Score: 369
Period size: 111 Copynumber: 1.9 Consensus size: 111
158341 TGCATCTAAA
*
158351 ATTCAGGCTATGTGCCTAGTAAGCTTTATGTCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTTG
1 ATTCAAGCTATGTGCCTAGTAAGCTTTATGTCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTTG
*
158416 TGCTAGTGTATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGT
66 TGCTAGTGTATTCAGGCTATGTACCTAGTAGGCTTTGTGCCGGTGT
* * *
158462 ATTCAAGCTATGTGCCTATTAGGCTTTGTGTCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTTG
1 ATTCAAGCTATGTGCCTAGTAAGCTTTATGTCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTTG
* *
158527 TGCTAGTGTTTTCAGTCTATGTACCTAGTAGGCTTTGTGC
66 TGCTAGTGTATTCAGGCTATGTACCTAGTAGGCTTTGTGC
158567 TAGTAATCCA
Statistics
Matches: 98, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 98 1.00
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.38
Consensus pattern (111 bp):
ATTCAAGCTATGTGCCTAGTAAGCTTTATGTCGGTGTATTCAGGCTATGTGCCTAGTAGGCTTTG
TGCTAGTGTATTCAGGCTATGTACCTAGTAGGCTTTGTGCCGGTGT
Found at i:158567 original size:37 final size:37
Alignment explanation
Indices: 158351--158570 Score: 309
Period size: 37 Copynumber: 5.9 Consensus size: 37
158341 TGCATCTAAA
* * *
158351 ATTCAGGCTATGTGCCTAGTAAGCTTTATG-TCGGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCT-AGTGT
158388 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGTGT
**
158425 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGTGT
* * *
158462 ATTCAAGCTATGTGCCTATTAGGCTTTGTG-TCGGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCT-AGTGT
158499 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGTGT
1 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGTGT
* * *
158536 TTTCAGTCTATGTACCTAGTAGGCTTTGTGCTAGT
1 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGT
158571 AATCCAAGAA
Statistics
Matches: 166, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
37 164 0.99
38 2 0.01
ACGTcount: A:0.16, C:0.17, G:0.28, T:0.39
Consensus pattern (37 bp):
ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCTAGTGT
Found at i:165735 original size:16 final size:16
Alignment explanation
Indices: 165710--165811 Score: 51
Period size: 16 Copynumber: 5.8 Consensus size: 16
165700 TCTAAAATTC
165710 AGGCTATGTGCCTAGT
1 AGGCTATGTGCCTAGT
* *
165726 AGGCTTTGTGCCGGTGTATT
1 AGGCTATGTGCC----TAGT
165746 CAGGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
* * *
165763 TGGCTTTGTGCCAGTGTATT
1 AGGCTATGTGCC----TAGT
*
165783 CAAGCTATGTGCCTAGT
1 -AGGCTATGTGCCTAGT
*
165800 AGGCTTTGTGCC
1 AGGCTATGTGCC
165812 AGTGTTTTCA
Statistics
Matches: 63, Mismatches: 13, Indels: 20
0.66 0.14 0.21
Matches are distributed among these distances:
16 31 0.49
17 6 0.10
20 6 0.10
21 20 0.32
ACGTcount: A:0.15, C:0.20, G:0.30, T:0.35
Consensus pattern (16 bp):
AGGCTATGTGCCTAGT
Found at i:165756 original size:37 final size:37
Alignment explanation
Indices: 165706--165847 Score: 230
Period size: 37 Copynumber: 3.8 Consensus size: 37
165696 TGCATCTAAA
* *
165706 ATTCAGGCTATGTGCCTAGTAGGCTTTGTGCCGGTGT
1 ATTCAAGCTATGTGCCTAGTAGGCTTTGTGCCAGTGT
* *
165743 ATTCAGGCTATGTGCCTAGTTGGCTTTGTGCCAGTGT
1 ATTCAAGCTATGTGCCTAGTAGGCTTTGTGCCAGTGT
165780 ATTCAAGCTATGTGCCTAGTAGGCTTTGTGCCAGTGT
1 ATTCAAGCTATGTGCCTAGTAGGCTTTGTGCCAGTGT
* *
165817 TTTCAAGCTATGTACCTAGTAGGCTTTGTGC
1 ATTCAAGCTATGTGCCTAGTAGGCTTTGTGC
165848 TAGTAGTCCA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (37 bp):
ATTCAAGCTATGTGCCTAGTAGGCTTTGTGCCAGTGT
Found at i:166510 original size:23 final size:21
Alignment explanation
Indices: 166483--166532 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
166473 ATTTAGACTG
*
166483 TCGGTAGGATTATGGAAATAGTA
1 TCGGTAGGATTA-AGAAAT-GTA
*
166506 TCGGTA-GATTAAGAGATGTA
1 TCGGTAGGATTAAGAAATGTA
166526 TCGGTAG
1 TCGGTAG
166533 AAAAATGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 4 0.17
22 5 0.21
23 6 0.25
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGGTAGGATTAAGAAATGTA
Found at i:174309 original size:17 final size:17
Alignment explanation
Indices: 174287--174348 Score: 106
Period size: 17 Copynumber: 3.6 Consensus size: 17
174277 CAGTAAAATA
174287 CAATGACAATGGGAATG
1 CAATGACAATGGGAATG
174304 CAATGACAATGGGAATG
1 CAATGACAATGGGAATG
* *
174321 CAATGACAGTAGGAATG
1 CAATGACAATGGGAATG
174338 CAATGACAATG
1 CAATGACAATG
174349 CTTACTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.42, C:0.13, G:0.27, T:0.18
Consensus pattern (17 bp):
CAATGACAATGGGAATG
Found at i:203271 original size:22 final size:21
Alignment explanation
Indices: 203222--203271 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
203212 ATCTTGTTTG
203222 TTTATTTTATTTTTTTATCAT
1 TTTATTTTATTTTTTTATCAT
** * *
203243 TAAATTTTATGTTTTTTCTCTT
1 TTTATTTTAT-TTTTTTATCAT
203265 TTTATTT
1 TTTATTT
203272 AACTACATGA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTATTTTATTTTTTTATCAT
Found at i:203337 original size:21 final size:20
Alignment explanation
Indices: 203313--203362 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
203303 ATTATGTTTG
*
203313 ATATTTTTATAATTTCATTTC
1 ATATATTTATAATTT-ATTTC
*
203334 ATATATTTATTATTTATTT-
1 ATATATTTATAATTTATTTC
*
203353 ATTTATTTAT
1 ATATATTTAT
203363 TGGTTATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 4 0.15
21 13 0.50
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (20 bp):
ATATATTTATAATTTATTTC
Found at i:203423 original size:22 final size:20
Alignment explanation
Indices: 203396--203445 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
203386 ACATTCTCAC
203396 TTTTATTTAATTTTATTTATT
1 TTTTATTT-ATTTTATTTATT
*
203417 GTTTTATGTATTTTATTTATT
1 -TTTTATTTATTTTATTTATT
*
203438 TGTTATTT
1 TTTTATTT
203446 TTATGCTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTTATTTATTTTATTTATT
Found at i:203431 original size:21 final size:22
Alignment explanation
Indices: 203396--203437 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
203386 ACATTCTCAC
*
203396 TTTTATTTAATTTTATTTATTG
1 TTTTATGTAATTTTATTTATTG
203418 TTTTATGT-ATTTTATTTATT
1 TTTTATGTAATTTTATTTATT
203438 TGTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTATGTAATTTTATTTATTG
Found at i:203434 original size:26 final size:28
Alignment explanation
Indices: 203399--203462 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
203389 TTCTCACTTT
*
203399 TATTTAATTTTATTTATT-GTTTTATG-
1 TATTTTATTTTATTTATTAGTTTTATGC
* *
203425 TATTTTA-TTTATTTGTTATTTTTATGC
1 TATTTTATTTTATTTATTAGTTTTATGC
203452 TATTTATATTT
1 TATTT-TATTT
203463 GTACGTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 9 0.29
26 13 0.42
27 5 0.16
28 2 0.06
29 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (28 bp):
TATTTTATTTTATTTATTAGTTTTATGC
Found at i:203713 original size:22 final size:23
Alignment explanation
Indices: 203687--203738 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
203677 CTCCTATTTA
203687 TTATTTTATTGTATT-A-TTAAT
1 TTATTTTATTGTATTCATTTAAT
*
203708 TGTATTTAATTGTATTCATTTAAT
1 T-TATTTTATTGTATTCATTTAAT
203732 TTATTTT
1 TTATTTT
203739 TTTCATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 13 0.50
23 6 0.23
24 6 0.23
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.65
Consensus pattern (23 bp):
TTATTTTATTGTATTCATTTAAT
Found at i:208467 original size:50 final size:50
Alignment explanation
Indices: 208375--208824 Score: 562
Period size: 50 Copynumber: 9.0 Consensus size: 50
208365 GGAACGACAC
* * *
208375 CAAATCTTATACCCCTAAAGCTGTAAAGGGGCAAATTAAAGCTACAAAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
* *
208425 CAAATCTTACACCCCTAAAGCTGTAGAGAGGCAGATTGAAGCTACAAAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
** ** * *
208475 TGAATCTTATACCTGTAAAGTTGTAGAGGGGCATATTGAAGCTACAAAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
* *
208525 CGAATCTTATACCCCCTAAAGCTGTAGA-GGGCAGATTAAAGCTACAAAAG
1 CAAATCTTATA-CCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
* * * * * *
208575 AAAATATTATACCCCTAAAGTTGTAAAGTGGTAGATTGAAGCTACAAAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
* * * * *
208625 TAAATCTTATACCCCTAAAGCTATAGAGGGGCGGATTAAAGCTACAAAAA
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
** * *
208675 TGAATCTTATACACCTAAAGCTGTAGAGGGG-AAATTGAAGCTACAAAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
** * *
208724 TGAATCTTATACCCCTAAAGCTGTAGAGGGGAAGATTGAAGCTACAGAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
* * *
208774 AAAATCATATACCCCTAAAGCTATAGAGGGGCAGATTGAAGCTACAAAAG
1 CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
208824 C
1 C
208825 TACAGAAGCA
Statistics
Matches: 343, Mismatches: 54, Indels: 6
0.85 0.13 0.01
Matches are distributed among these distances:
49 58 0.17
50 272 0.79
51 13 0.04
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (50 bp):
CAAATCTTATACCCCTAAAGCTGTAGAGGGGCAGATTGAAGCTACAAAAG
Found at i:210028 original size:17 final size:17
Alignment explanation
Indices: 210008--210045 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
209998 TAATTTTAGC
210008 ATTTAATTTTTATT-TTT
1 ATTTAATTTTT-TTGTTT
210025 ATTT-ATTTTTTTGTTT
1 ATTTAATTTTTTTGTTT
210041 ATTTA
1 ATTTA
210046 TCTAGATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.11
16 13 0.68
17 4 0.21
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTAATTTTTTTGTTT
Found at i:210272 original size:22 final size:22
Alignment explanation
Indices: 210247--210360 Score: 74
Period size: 22 Copynumber: 5.1 Consensus size: 22
210237 TTTCATATAA
210247 TTATTGTTTATTTATT-TTTTAT
1 TTATT-TTTATTTATTCTTTTAT
**
210269 TTATTTATTGGTTATTCATTTT-T
1 TTATTT-TTATTTATTC-TTTTAT
* * *
210292 TTGTTATTTACATTCTTGCTTTTAT
1 TTATT-TTTA-TTTATT-CTTTTAT
* *
210317 TTAATTTTATTTATTGTTTTAT
1 TTATTTTTATTTATTCTTTTAT
*
210339 GTATTTTT-TTTATT-TTTTAT
1 TTATTTTTATTTATTCTTTTAT
210359 TT
1 TT
210361 TTTATACTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
20 7 0.10
21 7 0.10
22 24 0.34
23 11 0.15
24 17 0.24
25 5 0.07
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.73
Consensus pattern (22 bp):
TTATTTTTATTTATTCTTTTAT
Found at i:210277 original size:26 final size:26
Alignment explanation
Indices: 210247--210301 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
210237 TTTCATATAA
* *
210247 TTATTGTTTATTTATTTTTTAT-TTAT
1 TTATTGGTTATTCATTTTTT-TGTTAT
210273 TTATTGGTTATTCATTTTTTTGTTAT
1 TTATTGGTTATTCATTTTTTTGTTAT
210299 TTA
1 TTA
210302 CATTCTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (26 bp):
TTATTGGTTATTCATTTTTTTGTTAT
Found at i:210338 original size:12 final size:11
Alignment explanation
Indices: 210311--210360 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 11
210301 ACATTCTTGC
*
210311 TTTTATTTA-A
1 TTTTATTTATT
210321 TTTTATTTATT
1 TTTTATTTATT
*
210332 GTTTTATGTA-T
1 -TTTTATTTATT
210343 TTTT-TTTATT
1 TTTTATTTATT
210353 TTTTATTT
1 TTTTATTT
210361 TTTATACTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
9 3 0.09
10 18 0.55
11 4 0.12
12 8 0.24
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTATTTATT
Found at i:210350 original size:21 final size:21
Alignment explanation
Indices: 210311--210358 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
210301 ACATTCTTGC
*
210311 TTTTATTTAATTTTATTTATT
1 TTTTATGTAATTTTATTTATT
*
210332 GTTTTATGT-ATTTTTTTTATT
1 -TTTTATGTAATTTTATTTATT
210353 TTTTAT
1 TTTTAT
210359 TTTTTATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 11 0.46
22 7 0.29
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (21 bp):
TTTTATGTAATTTTATTTATT
Found at i:210657 original size:18 final size:17
Alignment explanation
Indices: 210622--210672 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
210612 TGTTATTAAT
*
210622 TGTATTTAATTGTATTCA
1 TGTATTT-ATTTTATTCA
*
210640 TTTAATTTATTTTATTCA
1 TGT-ATTTATTTTATTCA
*
210658 TGTATTTTTTTTATT
1 TGTATTTATTTTATT
210673 TTGTCGTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 11 0.39
18 13 0.46
19 4 0.14
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (17 bp):
TGTATTTATTTTATTCA
Found at i:213372 original size:17 final size:17
Alignment explanation
Indices: 213350--213383 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
213340 CTTTAATGAG
213350 GGTTTAAAGGAGTTAGA
1 GGTTTAAAGGAGTTAGA
213367 GGTTTAAAGGAGTTAGA
1 GGTTTAAAGGAGTTAGA
213384 CATTCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (17 bp):
GGTTTAAAGGAGTTAGA
Found at i:221179 original size:20 final size:19
Alignment explanation
Indices: 221156--221221 Score: 87
Period size: 20 Copynumber: 3.3 Consensus size: 19
221146 AGGCATGATT
221156 GTGCAATCAGAGGCACCAAA
1 GTGCAAT-AGAGGCACCAAA
*
221176 GTGCAAATAGAGACACCAAA
1 GTGC-AATAGAGGCACCAAA
*
221196 GTGTGAATAGAGGCACCAAA
1 GTG-CAATAGAGGCACCAAA
221216 GTGCAA
1 GTGCAA
221222 ACCTATACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 2 0.05
20 35 0.88
21 3 0.08
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (19 bp):
GTGCAATAGAGGCACCAAA
Found at i:233313 original size:14 final size:14
Alignment explanation
Indices: 233279--233322 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
233269 ATTTTATATG
**
233279 GAATTTTGAATTAAA
1 GAATTTT-AATTATT
*
233294 GAATTTTAGTTATT
1 GAATTTTAATTATT
233308 GAATTTTAATTATT
1 GAATTTTAATTATT
233322 G
1 G
233323 TATAGATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
14 18 0.72
15 7 0.28
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
GAATTTTAATTATT
Found at i:234749 original size:195 final size:193
Alignment explanation
Indices: 234362--234798 Score: 463
Period size: 195 Copynumber: 2.2 Consensus size: 193
234352 CGATGGCTGG
* * * * * *
234362 GGTACCGTATATGTTGGAGTCCTCGACAGCTCGTGTGAGCAGTATCGTGAGTCAGGAAATGAGAA
1 GGTACCGCATATGTTCGAGTCCTAGACAGCTCGTGTGAGCAGCATCGTGACTCA-GAAATAAGAA
* * *
234427 AAGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATTTATGCATAAGTGCATATTCTCA
65 AAGAATCCAAGAACGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGTGCATACTCTCA
** * * * *
234492 ACAGCTCGTATGAGCAGCATTGTTAGGGAATAGATATATGCACAGATACCGTATCGATGGCTAA
130 ACAGCTCGTATGAGCAGCACCGTTAGGGAACAGATATATGCACAGACACCGTACCAATGGCTAA
*
234556 GGTACCGCATATGTTACGAGTCCTAGACAGCTTGTGTGAGCAGCATCGTGACTC-GAAA-AAGAA
1 GGTACCGCATATGTT-CGAGTCCTAGACAGCTCGTGTGAGCAGCATCGTGACTCAGAAATAAGAA
* * * * *
234619 ATATGGATCCTA-AACGGATTACAGGCCCTACGATGGTTGGGA-CTATGCTTTA-TGCATACTCT
65 A-A-GAATCCAAGAACGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGTGCATACTCT
* * * * *
234681 CGACAGCTCGTGTGAGTAGCACCGTTAGGGAACAG-TTTATGGTACAAACAGGCACCGTACCAAT
128 CAACAGCTCGTATGAGCAGCACCGTTAGGGAACAGATATAT-G--C--ACAGACACCGTACCAAT
*
234745 GGCTAG
188 GGCTAA
* * * *
234751 GGTATCGCATATGTTTCGAGTCCTGGACAGCTCGTGCGAGTAGCATCG
1 GGTACCGCATATG-TTCGAGTCCTAGACAGCTCGTGTGAGCAGCATCG
234799 AGTACTGGAA
Statistics
Matches: 202, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
190 4 0.02
191 39 0.19
192 12 0.06
193 34 0.17
194 20 0.10
195 91 0.45
196 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (193 bp):
GGTACCGCATATGTTCGAGTCCTAGACAGCTCGTGTGAGCAGCATCGTGACTCAGAAATAAGAAA
AGAATCCAAGAACGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGTGCATACTCTCAA
CAGCTCGTATGAGCAGCACCGTTAGGGAACAGATATATGCACAGACACCGTACCAATGGCTAA
Found at i:236308 original size:20 final size:20
Alignment explanation
Indices: 236283--236321 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
236273 AAAGTCTAGG
236283 GAGTACATGCCATATAAACA
1 GAGTACATGCCATATAAACA
*
236303 GAGTACATGTCATATAAAC
1 GAGTACATGCCATATAAAC
236322 CTGTGATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (20 bp):
GAGTACATGCCATATAAACA
Found at i:243606 original size:21 final size:21
Alignment explanation
Indices: 243558--243609 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
243548 GGAGTTTTTA
243558 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
* * *
243579 GTTTCGGTAGAGGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACAT
243600 GTATCGGTAG
1 GTATCGGTAG
243610 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACAT
Found at i:252028 original size:6 final size:6
Alignment explanation
Indices: 252017--252044 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
252007 GTTGGTTAGA
252017 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
252045 TAGAAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:255083 original size:158 final size:158
Alignment explanation
Indices: 254792--255224 Score: 553
Period size: 158 Copynumber: 2.7 Consensus size: 158
254782 TAATCATATA
* *
254792 TGCTCACACGAGCTGTGGGTCGAGATGTGAGGCTATACGATGCTGCTCACACGAGCTGTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
* * * * * *** *
254857 TCTGCAACAAATGTC-GGACCTCAGCCATCGATAAGATATCTAAGACCAGTGCCTATATAACCTA
66 TCCGCAACAAATG-CAGGTCCTCAGCCATCGGTAAGACATCCAAGACCAACACCCATATAACCTA
*
254921 TAATGCTCTCACAAGCTATGAAATGGGTC
130 TAATGCTCACACAAGCTATGAAATGGGTC
* * * * * * *
254950 TGCTCACACAAGCTGTGGGTCAAGATGTTAGGCTACGCGATGTTGCTCAGACGAGTTTTGGAGAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
* * * * *
255015 TCCGTAACCAATGCAGGTCCTCAGCCATCGGTAGGACATCCAAGACCAACACCCATATAACTTGT
66 TCCGCAACAAATGCAGGTCCTCAGCCATCGGTAAGACATCCAAGACCAACACCCATATAACCTAT
* *
255080 AATGCTCACACGAGCTGTGAAATGGGTC
131 AATGCTCACACAAGCTATGAAATGGGTC
* * * * *
255108 TGCTCACACGAGCTATGGGTCGGGATGTTAGGATACACGATGCTGCTCACACAAGCTGTGGAAAA
1 TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
* *
255173 TCCGCAACAAATGCAAGTCCTCAACCATCGGTAAGACATCCAAGACCAACAC
66 TCCGCAACAAATGCAGGTCCTCAGCCATCGGTAAGACATCCAAGACCAACAC
255225 TCGAAACTGT
Statistics
Matches: 231, Mismatches: 43, Indels: 2
0.84 0.16 0.01
Matches are distributed among these distances:
157 1 0.00
158 230 1.00
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.22
Consensus pattern (158 bp):
TGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTACACGATGCTGCTCACACGAGCTGTGGAGAA
TCCGCAACAAATGCAGGTCCTCAGCCATCGGTAAGACATCCAAGACCAACACCCATATAACCTAT
AATGCTCACACAAGCTATGAAATGGGTC
Found at i:256138 original size:21 final size:20
Alignment explanation
Indices: 256110--256148 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
256100 ACTTCTCTCG
256110 TTTCTTT-ATCTAAATAATAA
1 TTTCTTTAAT-TAAATAATAA
256130 TTTCATTTAATTAAATAAT
1 TTTC-TTTAATTAAATAAT
256149 TCAAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTCTTTAATTAAATAATAA
Found at i:256607 original size:88 final size:88
Alignment explanation
Indices: 256515--256691 Score: 273
Period size: 88 Copynumber: 2.0 Consensus size: 88
256505 ATTCCTCATT
* * *
256515 TTTACTTTAATTTACCAAATTTACAAAATTTAATTCTTACTACTTGAAGTCGACAATTTAATTTA
1 TTTACTTTAATTTACCAAATTTACAAAATTTAATTCTTACTACTTGAAATCAACAATTTAATTCA
*
256580 CAAATTTAGTCTCTTTTCATTTC
66 CAAATTTAGTCTATTTTCATTTC
* * ** *
256603 TTTACTTTAATTTATCAAATTTATAAAATTTGGTTCTTAGTACTTGAAATCAACAATTTAATTCA
1 TTTACTTTAATTTACCAAATTTACAAAATTTAATTCTTACTACTTGAAATCAACAATTTAATTCA
256668 CAAATTTAGTCTATTTTCATTTC
66 CAAATTTAGTCTATTTTCATTTC
256691 T
1 T
256692 ATTTCAAAAT
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 80 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.47
Consensus pattern (88 bp):
TTTACTTTAATTTACCAAATTTACAAAATTTAATTCTTACTACTTGAAATCAACAATTTAATTCA
CAAATTTAGTCTATTTTCATTTC
Found at i:257489 original size:25 final size:26
Alignment explanation
Indices: 257460--257511 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
257450 TGAATTGATG
257460 TTTGTTGTTGCT-TT-TTGCTGATTTT
1 TTTGTTGTTGCTATTGTTGCT-ATTTT
257485 TTTGTTGTTGCTATTGTTGCTATTTT
1 TTTGTTGTTGCTATTGTTGCTATTTT
257511 T
1 T
257512 AGAGGGAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.48
26 8 0.32
27 5 0.20
ACGTcount: A:0.06, C:0.08, G:0.19, T:0.67
Consensus pattern (26 bp):
TTTGTTGTTGCTATTGTTGCTATTTT
Found at i:260291 original size:24 final size:24
Alignment explanation
Indices: 260240--260291 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
260230 TTCTTCAGCC
*
260240 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATGCTAATAAATACA
* * *
260264 AAATATATTATGTTAATAAATACT
1 AAATAAATTATGCTAATAAATACA
260288 AAAT
1 AAAT
260292 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATAAATTATGCTAATAAATACA
Found at i:264032 original size:18 final size:18
Alignment explanation
Indices: 264009--264064 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
263999 AGAACCCCAT
*
264009 CTGGAGAAATCACTAGGC
1 CTGGAGTAATCACTAGGC
*
264027 CTGGAGTAATCACTAGGT
1 CTGGAGTAATCACTAGGC
*
264045 CGGGAGTAATCACTAGGC
1 CTGGAGTAATCACTAGGC
264063 CT
1 CT
264065 ATTACCCCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (18 bp):
CTGGAGTAATCACTAGGC
Found at i:268214 original size:15 final size:14
Alignment explanation
Indices: 268198--268237 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
268188 AACTTTTTTA
268198 AAAAATATATATTT
1 AAAAATATATATTT
*
268212 -AAAATTTAT-TTT
1 AAAAATATATATTT
268224 AAAAATATATATTT
1 AAAAATATATATTT
268238 TATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAAATATATATTT
Found at i:268238 original size:15 final size:15
Alignment explanation
Indices: 268193--268239 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
268183 GTGACAACTT
268193 TTTTAAAAA-ATATA
1 TTTTAAAAATATATA
268207 TATTT-AAAAT-T-TA
1 T-TTTAAAAATATATA
268220 TTTTAAAAATATATA
1 TTTTAAAAATATATA
268235 TTTTA
1 TTTTA
268240 TTATATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.11
13 8 0.29
14 7 0.25
15 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAAAAATATATA
Found at i:268700 original size:30 final size:30
Alignment explanation
Indices: 268645--268701 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
268635 AGGAATCGAA
*
268645 ATTAAATTATTTATAATTTTATTTTAAAAT
1 ATTAAATTATTTATAATTATATTTTAAAAT
268675 ATTAAATTAAATTT-TAATTAT-TTTTAA
1 ATTAAATT--ATTTATAATTATATTTTAA
268702 GAGGAGTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
30 14 0.58
31 6 0.25
32 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATTAAATTATTTATAATTATATTTTAAAAT
Found at i:268871 original size:6 final size:6
Alignment explanation
Indices: 268860--268902 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
268850 TTTAGAGGTT
268860 GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG G
1 GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG GGCAGG G
268903 TCATTGTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.16, C:0.16, G:0.67, T:0.00
Consensus pattern (6 bp):
GGCAGG
Found at i:269590 original size:16 final size:16
Alignment explanation
Indices: 269569--269602 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
269559 TACGTAGTTT
269569 TTTTTTCTTTACTTTC
1 TTTTTTCTTTACTTTC
269585 TTTTTTCTTTACTTTC
1 TTTTTTCTTTACTTTC
269601 TT
1 TT
269603 ATTTATCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCTTTACTTTC
Found at i:270631 original size:18 final size:18
Alignment explanation
Indices: 270608--270643 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
270598 CAGCAAATGA
* *
270608 TTTTAAAATTATTAAATT
1 TTTTAAAAATATAAAATT
270626 TTTTAAAAATATAAAATT
1 TTTTAAAAATATAAAATT
270644 ATTAAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTAAAAATATAAAATT
Found at i:270640 original size:17 final size:18
Alignment explanation
Indices: 270608--270650 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
270598 CAGCAAATGA
* *
270608 TTTTAAAATTATTAAATT
1 TTTTAAAAATATTAAAAT
270626 TTTTAAAAATA-TAAAAT
1 TTTTAAAAATATTAAAAT
*
270643 TATTAAAA
1 TTTTAAAA
270651 TCATCATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTTAAAAATATTAAAAT
Found at i:274795 original size:15 final size:15
Alignment explanation
Indices: 274775--274808 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
274765 TAAAGAATTT
274775 GAATGGAGAAAGAGA
1 GAATGGAGAAAGAGA
*
274790 GAATGGAGAAGGAGA
1 GAATGGAGAAAGAGA
274805 GAAT
1 GAAT
274809 TTGGGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.41, T:0.09
Consensus pattern (15 bp):
GAATGGAGAAAGAGA
Found at i:275780 original size:21 final size:21
Alignment explanation
Indices: 275754--275798 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
275744 CTAATGAAAT
275754 CCATTTTCTTCAGTTTTCTCA
1 CCATTTTCTTCAGTTTTCTCA
*
275775 CCATTTTCTTTAGTTTTCTCA
1 CCATTTTCTTCAGTTTTCTCA
275796 CCA
1 CCA
275799 ATCAAACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.16, C:0.29, G:0.04, T:0.51
Consensus pattern (21 bp):
CCATTTTCTTCAGTTTTCTCA
Found at i:281023 original size:20 final size:20
Alignment explanation
Indices: 281000--281047 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
280990 ACAGAGCTAT
* * *
281000 CGATACTTGCATGAAGGTAC
1 CGATACTTACATAAAAGTAC
281020 CGATACTTACATAAAAGTAC
1 CGATACTTACATAAAAGTAC
*
281040 TGATACTT
1 CGATACTT
281048 TGATCTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (20 bp):
CGATACTTACATAAAAGTAC
Found at i:285270 original size:94 final size:94
Alignment explanation
Indices: 285095--285276 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 94
285085 ACCAACAATT
* * * *
285095 TCATTTAGTCCTTCACCCTCGACTTCTTCAGGGACCTCAGCCTCAAATTGCTCTCTAAAGCTTTC
1 TCATTTAGTCCTTCACCCACAACTTCTTCAAGGACCTCAGCCTCAAACTGCTCTCTAAAGCTTTC
* * *
285160 ACTTTCGGTCTTATCAAGGACTGCCACTA
66 ACTTTCAGCCTCATCAAGGACTGCCACTA
* *
285189 TCATTTAGTCCTTCACCCACAACTTTTTCAAGGACCTCAGCCTCAAACT-CTTCTCTAGAGCTTT
1 TCATTTAGTCCTTCACCCACAACTTCTTCAAGGACCTCAGCCTCAAACTGC-TCTCTAAAGCTTT
* *
285253 CACTTTTAGCCTCATCAAGTACTG
65 CACTTTCAGCCTCATCAAGGACTG
285277 TTTCCTTAGC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
93 1 0.01
94 75 0.99
ACGTcount: A:0.23, C:0.32, G:0.12, T:0.34
Consensus pattern (94 bp):
TCATTTAGTCCTTCACCCACAACTTCTTCAAGGACCTCAGCCTCAAACTGCTCTCTAAAGCTTTC
ACTTTCAGCCTCATCAAGGACTGCCACTA
Found at i:285533 original size:33 final size:33
Alignment explanation
Indices: 285496--285565 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
285486 GCAACATCAA
*
285496 CACCCTCCTCACCTAAACCTTTAACACCCTCAC
1 CACCCTCCTCACCTAAACCTTCAACACCCTCAC
* *
285529 CACCCTCTTCACCTAAACCTTCAACACCCTTAC
1 CACCCTCCTCACCTAAACCTTCAACACCCTCAC
285562 CACC
1 CACC
285566 TTTACTGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.51, G:0.00, T:0.21
Consensus pattern (33 bp):
CACCCTCCTCACCTAAACCTTCAACACCCTCAC
Found at i:285577 original size:24 final size:24
Alignment explanation
Indices: 285550--285619 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
285540 CCTAAACCTT
* *
285550 CAACACCCTTACCACCTTTACTGC
1 CAACACCCTCACCACCTTTACTAC
* * *
285574 CAACAACCTCACCACCTTCACCAC
1 CAACACCCTCACCACCTTTACTAC
**
285598 CCTCACCCTCACCACCTTTACT
1 CAACACCCTCACCACCTTTACT
285620 TTCAATAACC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.26, C:0.51, G:0.01, T:0.21
Consensus pattern (24 bp):
CAACACCCTCACCACCTTTACTAC
Found at i:285652 original size:48 final size:48
Alignment explanation
Indices: 285553--285652 Score: 119
Period size: 48 Copynumber: 2.1 Consensus size: 48
285543 AAACCTTCAA
* * *
285553 CACCCTTACCACCTTTACTGCCAACAACCTCACCACCTTCACCACCCT
1 CACCCTCACCACCTTTACTGCCAACAACCTCAACACCTTCACCACCAT
** * * **
285601 CACCCTCACCACCTTTACTTTCAATAACCTTAACACCTTCATTACCAT
1 CACCCTCACCACCTTTACTGCCAACAACCTCAACACCTTCACCACCAT
285649 CACC
1 CACC
285653 AAAACCATCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.27, C:0.47, G:0.01, T:0.25
Consensus pattern (48 bp):
CACCCTCACCACCTTTACTGCCAACAACCTCAACACCTTCACCACCAT
Found at i:286544 original size:30 final size:30
Alignment explanation
Indices: 286471--286548 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
286461 AATCCTTAAA
*
286471 ACCCTAAACAAAAATCACCAAAATCAATTT
1 ACCCTAAACAAAAATCCCCAAAATCAATTT
286501 ACCCTAAACAAAAATCCCCAAAATCGAA-TT
1 ACCCTAAACAAAAATCCCCAAAATC-AATTT
286531 ACCCT-AACAAAAAATCCC
1 ACCCTAAAC-AAAAATCCC
286549 GAAACTAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
29 3 0.07
30 40 0.89
31 2 0.04
ACGTcount: A:0.51, C:0.31, G:0.01, T:0.17
Consensus pattern (30 bp):
ACCCTAAACAAAAATCCCCAAAATCAATTT
Found at i:287162 original size:17 final size:17
Alignment explanation
Indices: 287136--287184 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
287126 ATTAAATAAG
*
287136 AAATATTAAATATATAT
1 AAATAATAAATATATAT
*
287153 AAATAATAAAAATGA-AT
1 AAATAATAAATAT-ATAT
*
287170 AAATAAAAAATATAT
1 AAATAATAAATATAT
287185 TACAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AAATAATAAATATATAT
Found at i:301217 original size:18 final size:16
Alignment explanation
Indices: 301194--301232 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 16
301184 CTATTTTCAC
301194 ATTTTATTTTAAGTGTTT
1 ATTTTATTTTAA-T-TTT
301212 ATTTTATTTTAATTTT
1 ATTTTATTTTAATTTT
301228 ATTTT
1 ATTTT
301233 TGTTCAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
17 1 0.05
18 12 0.57
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
ATTTTATTTTAATTTT
Done.