Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 12 of 31
Found at i:6148817 original size:26 final size:26
Alignment explanation
Indices: 6148774--6148880 Score: 144
Period size: 26 Copynumber: 4.1 Consensus size: 26
6148764 ATATTATTAC
* *
6148774 TACATGTCATGTTTAAAACAAGTTGT
1 TACATGTCATATTCAAAACAAGTTGT
* *
6148800 TACACGTCATATTCAAAATAAGTTGT
1 TACATGTCATATTCAAAACAAGTTGT
* *
6148826 TACATGTCATGTGCAAAACAAGTTGT
1 TACATGTCATATTCAAAACAAGTTGT
6148852 TACATGTCATATTCAAAA-ATAGTTGT
1 TACATGTCATATTCAAAACA-AGTTGT
6148878 TAC
1 TAC
6148881 TCATTAAGTT
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
25 1 0.01
26 69 0.99
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (26 bp):
TACATGTCATATTCAAAACAAGTTGT
Found at i:6148836 original size:52 final size:52
Alignment explanation
Indices: 6148774--6148880 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
6148764 ATATTATTAC
**
6148774 TACATGTCATGTTTAAAACAAGTTGTTACACGTCATATTC-AAAATAAGTTGT
1 TACATGTCATGTGCAAAACAAGTTGTTACACGTCATATTCAAAAAT-AGTTGT
*
6148826 TACATGTCATGTGCAAAACAAGTTGTTACATGTCATATTCAAAAATAGTTGT
1 TACATGTCATGTGCAAAACAAGTTGTTACACGTCATATTCAAAAATAGTTGT
6148878 TAC
1 TAC
6148881 TCATTAAGTT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 46 0.90
53 5 0.10
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (52 bp):
TACATGTCATGTGCAAAACAAGTTGTTACACGTCATATTCAAAAATAGTTGT
Found at i:6149576 original size:214 final size:215
Alignment explanation
Indices: 6149193--6149657 Score: 598
Period size: 214 Copynumber: 2.1 Consensus size: 215
6149183 AATATGCAAA
* * * *
6149193 TTATATATAAATTAAATATATGTGTATGTAGT-ATATTACTTTATTATATATATAAAATGAGTGA
1 TTATGTATAAATTAAATATATGTATATATA-TAATATTACTTTATTATATATATAAAATGAATGA
* * * * *
6149257 CACAACTTATATGTTATAATATTTTAATTTTTACATCAAAGTTTGGATAAATAATAATTAATTAT
65 CACAACTCATATGCTATAATATTTTAA---TTA-ATCAAAATTTAGATAAATAATAAGTAATTAT
6149322 AAACAATATGTTATAAAAACTAAAGTGATAACTAATAAAATTATTAAGT-GTAATAATATAAATA
126 AAACAATATGTTATAAAAACTAAAGTGATAACTAATAAAATTATTAA-TCGTAATAATATAAATA
* *
6149386 AAATCTATTATAAATTACAATAATGC
190 AAATCTATTATAAATCACAACAATGC
* * *
6149412 TTATGTATAAATTAAGTATATGTATATATATAATATTACTTTATTATGTATATATGAAATTAATG
1 TTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTA--TATATATAAAATGAATG
*
6149477 ACACAACTCATATGCTATAATATTTT-A-T-ATCAAAATTTATATAAATAATAAGTAATTATAAA
64 ACACAACTCATATGCTATAATATTTTAATTAATCAAAATTTAGATAAATAATAAGTAATTATAAA
* * * *
6149539 CAATATGTTATAAAAACTAAGGTGATAACTGATAAAATTATTAATCGTAATCATATAAATAAAGT
129 CAATATGTTATAAAAACTAAAGTGATAACTAATAAAATTATTAATCGTAATAATATAAATAAAAT
* * * * *
6149604 TTATTATAAGTCATAGCAATGT
194 CTATTATAAATCACAACAATGC
*
6149626 TTAAGTATAAATTAAATATATGTATATATATA
1 TTATGTATAAATTAAATATATGTATATATATA
6149658 TAATATTTAT
Statistics
Matches: 216, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
213 1 0.00
214 134 0.62
216 1 0.00
218 1 0.00
219 40 0.19
220 1 0.00
221 38 0.18
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (215 bp):
TTATGTATAAATTAAATATATGTATATATATAATATTACTTTATTATATATATAAAATGAATGAC
ACAACTCATATGCTATAATATTTTAATTAATCAAAATTTAGATAAATAATAAGTAATTATAAACA
ATATGTTATAAAAACTAAAGTGATAACTAATAAAATTATTAATCGTAATAATATAAATAAAATCT
ATTATAAATCACAACAATGC
Found at i:6165000 original size:25 final size:25
Alignment explanation
Indices: 6164969--6165018 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
6164959 AAGGAATGAG
6164969 CCAAGCTCAAGTATTCCTTGAGTTA
1 CCAAGCTCAAGTATTCCTTGAGTTA
6164994 CCAAGCTCAAGTATTCCTTGAGTTA
1 CCAAGCTCAAGTATTCCTTGAGTTA
6165019 AGTCTGAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (25 bp):
CCAAGCTCAAGTATTCCTTGAGTTA
Found at i:6168513 original size:29 final size:30
Alignment explanation
Indices: 6168462--6168541 Score: 78
Period size: 29 Copynumber: 2.7 Consensus size: 30
6168452 ACCTAGTATA
* *
6168462 TAAAA-AAGTTTTTAAATTATTTA-AAAATT
1 TAAAATAAATTTTTATATT-TTTATAAAATT
* *
6168491 TAAAATAAATTTTTATATTTTTATTATATT
1 TAAAATAAATTTTTATATTTTTATAAAATT
6168521 T--AATCAAATTTTTATATTTTT
1 TAAAAT-AAATTTTTATATTTTT
6168542 TATTTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 3 0.07
29 25 0.57
30 16 0.36
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
TAAAATAAATTTTTATATTTTTATAAAATT
Found at i:6168577 original size:30 final size:29
Alignment explanation
Indices: 6168493--6168594 Score: 111
Period size: 30 Copynumber: 3.4 Consensus size: 29
6168483 TAAAAATTTA
6168493 AAATAAATTTTTATATTTTTATTATATTTAATC
1 AAATAAATTTTT-TATTTTTA-T-T-TTTAATC
*
6168526 AAAT---TTTTATATTTTTTATTTTTAATC
1 AAATAAATTTTTTA-TTTTTATTTTTAATC
6168553 AAATAAATATTTTTATTTTTATTTTTAATC
1 AAATAAAT-TTTTTATTTTTATTTTTAATC
*
6168583 AAATAAAATTTT
1 AAATAAATTTTT
6168595 ATAATTAATC
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
27 11 0.18
28 1 0.02
29 7 0.11
30 33 0.54
31 5 0.08
33 4 0.07
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (29 bp):
AAATAAATTTTTTATTTTTATTTTTAATC
Found at i:6168847 original size:25 final size:25
Alignment explanation
Indices: 6168819--6168867 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6168809 AAGTTATATT
*
6168819 TTAATTAATAATAA-TTAATTAATTA
1 TTAATT-ATAAAAATTTAATTAATTA
*
6168844 TTAATTATAAAAATTTATTTAATT
1 TTAATTATAAAAATTTAATTAATT
6168868 TAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TTAATTATAAAAATTTAATTAATTA
Found at i:6170141 original size:14 final size:14
Alignment explanation
Indices: 6170115--6170150 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
6170105 AAATTATTTG
6170115 ATAAATT-TTTTTT
1 ATAAATTATTTTTT
*
6170128 ATAAGTTATTTTTT
1 ATAAATTATTTTTT
6170142 ATAAATTAT
1 ATAAATTAT
6170151 AACTTTAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
ATAAATTATTTTTT
Found at i:6170863 original size:28 final size:23
Alignment explanation
Indices: 6170810--6170856 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
6170800 AGTAATTATT
*
6170810 TTAATTTTTTTATTTATGAAATA
1 TTAATTTTTTTAATTATGAAATA
*
6170833 TTAATTTATTTTAATTATGTAATA
1 TTAATTT-TTTTAATTATGAAATA
6170857 CTCATTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTAATTTTTTTAATTATGAAATA
Found at i:6171303 original size:6 final size:6
Alignment explanation
Indices: 6171268--6171299 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
6171258 CGAATCTCAC
*
6171268 TCCCAA TCCCAA TCCCAA TCCCAA TCTCAA TC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCCCAA TC
6171300 TCAACTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.31, C:0.47, G:0.00, T:0.22
Consensus pattern (6 bp):
TCCCAA
Found at i:6191839 original size:24 final size:24
Alignment explanation
Indices: 6191808--6191886 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
6191798 ACTCACTTTC
6191808 TATATATCTCTACCATTCTTAACA
1 TATATATCTCTACCATTCTTAACA
6191832 TATATATCTCTACCATTCTTAACA
1 TATATATCTCTACCATTCTTAACA
*
6191856 TATATATCTCTACCATTCTCAACA
1 TATATATCTCTACCATTCTTAACA
6191880 TATATAT
1 TATATAT
6191887 ATTAAGCCTC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATATCTCTACCATTCTTAACA
Found at i:6192285 original size:30 final size:29
Alignment explanation
Indices: 6192219--6192300 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
6192209 TTGTAAAGGT
6192219 AAAATTATAATATATTTTTAAAAAATAAAAAC
1 AAAATTATAA-A-A-TTTTAAAAAATAAAAAC
* * *
6192251 AAAATTATAAAATTTAAAAAAATAGATAAG
1 AAAATTATAAAATTTTAAAAAATA-AAAAC
*
6192281 AAAATTTTAAAATTTTAAAA
1 AAAATTATAAAATTTTAAAA
6192301 CTTTGTAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
29 11 0.25
30 22 0.50
31 1 0.02
32 10 0.23
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATTATAAAATTTTAAAAAATAAAAAC
Found at i:6193819 original size:23 final size:23
Alignment explanation
Indices: 6193793--6193836 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
6193783 ATCAAAGGTG
*
6193793 TCTTTATTAGAAT-ACTCTAAAGA
1 TCTTGATTA-AATAACTCTAAAGA
*
6193816 TCTTGCTTAAATAACTCTAAA
1 TCTTGATTAAATAACTCTAAA
6193837 AGAATTAGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (23 bp):
TCTTGATTAAATAACTCTAAAGA
Found at i:6208195 original size:15 final size:16
Alignment explanation
Indices: 6208165--6208204 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
6208155 AGAAATTGGT
6208165 TTCTTTTCTGGAAAATA
1 TTCTTTT-TGGAAAATA
*
6208182 TTCTTTTT-GAAAATT
1 TTCTTTTTGGAAAATA
6208197 TTCTTTTT
1 TTCTTTTT
6208205 TTCAGAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (16 bp):
TTCTTTTTGGAAAATA
Found at i:6226970 original size:6 final size:6
Alignment explanation
Indices: 6226959--6226986 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6226949 AAAATTAGCA
6226959 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
6226987 TTAGTTACGA
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:6231221 original size:16 final size:17
Alignment explanation
Indices: 6231200--6231231 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6231190 TGAGTGCGCA
6231200 TTTG-TTTCATTTAGAT
1 TTTGTTTTCATTTAGAT
6231216 TTTGTTTTCATTTAGA
1 TTTGTTTTCATTTAGA
6231232 AGGGTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.19, C:0.06, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTGTTTTCATTTAGAT
Found at i:6232636 original size:42 final size:42
Alignment explanation
Indices: 6232573--6232691 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
6232563 CTTTCAGAAT
* * *
6232573 CTGATCATTGGGGTAGCGGCAGTAGGGTGCCACCTTCACAAC
1 CTGATCACTGGGGTAGTGGCAGTAGGGCGCCACCTTCACAAC
* *
6232615 CTGATCACTGGGGTAGTGGCAGTAGGGCCCCACCTTCACAAT
1 CTGATCACTGGGGTAGTGGCAGTAGGGCGCCACCTTCACAAC
*
6232657 CTGATCACTGGGGTAGTGGCAGCAGGGCGCCACCT
1 CTGATCACTGGGGTAGTGGCAGTAGGGCGCCACCT
6232692 CAGGATCCTG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.20, C:0.28, G:0.32, T:0.20
Consensus pattern (42 bp):
CTGATCACTGGGGTAGTGGCAGTAGGGCGCCACCTTCACAAC
Found at i:6238885 original size:2 final size:2
Alignment explanation
Indices: 6238878--6238903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6238868 ATCATAAAGC
6238878 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
6238904 GGCGGGGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6246323 original size:15 final size:15
Alignment explanation
Indices: 6246303--6246332 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6246293 TGAGATGAGA
6246303 ATCATCATCATCATG
1 ATCATCATCATCATG
6246318 ATCATCATCATCATG
1 ATCATCATCATCATG
6246333 TAACATGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.07, T:0.33
Consensus pattern (15 bp):
ATCATCATCATCATG
Found at i:6248637 original size:3 final size:3
Alignment explanation
Indices: 6248629--6248659 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6248619 CAATGCTTTT
*
6248629 GCA GCA GCA GCA GCA ACA GCA GCA GCA GCA G
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA G
6248660 TTCCTTCAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:6252387 original size:5 final size:5
Alignment explanation
Indices: 6252377--6252401 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6252367 GTTTTTTCTT
6252377 TGGGG TGGGG TGGGG TGGGG TGGGG
1 TGGGG TGGGG TGGGG TGGGG TGGGG
6252402 GGCGTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (5 bp):
TGGGG
Found at i:6264092 original size:61 final size:61
Alignment explanation
Indices: 6263994--6264113 Score: 204
Period size: 61 Copynumber: 2.0 Consensus size: 61
6263984 AGAGAGATAT
*
6263994 ACAAATAGATGAATTAAAGGGAGAAAATAACGAATAAAGCACCTGTCCTGCACAGAGTTAA
1 ACAAATAGATGAATTAAAGGAAGAAAATAACGAATAAAGCACCTGTCCTGCACAGAGTTAA
* * *
6264055 ACAAATAGATGAATTAAAGGAAGAAAATAATGCATAAAGTACCTGTCCTGCACAGAGTT
1 ACAAATAGATGAATTAAAGGAAGAAAATAACGAATAAAGCACCTGTCCTGCACAGAGTT
6264114 TGTCCTCTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.47, C:0.14, G:0.19, T:0.20
Consensus pattern (61 bp):
ACAAATAGATGAATTAAAGGAAGAAAATAACGAATAAAGCACCTGTCCTGCACAGAGTTAA
Found at i:6265912 original size:2 final size:2
Alignment explanation
Indices: 6265905--6265955 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
6265895 AACTTCTTAG
6265905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6265947 AT AT AT AT A
1 AT AT AT AT A
6265956 GAGAGAGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6265960 original size:2 final size:2
Alignment explanation
Indices: 6265955--6265992 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6265945 ATATATATAT
6265955 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6265993 GAAGGATTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6288061 original size:3 final size:3
Alignment explanation
Indices: 6288047--6288080 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
6288037 CATTTATGTC
*
6288047 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6288081 CATTCTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6291763 original size:3 final size:3
Alignment explanation
Indices: 6291755--6291807 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
6291745 GTCTTTATCC
* * *
6291755 TCT TCT TCT TCT TCT TC- TCT TCT TCT T-T TCT TCT CCG TCT CCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
6291800 TCT TCT TC
1 TCT TCT TC
6291808 ACCATCTTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (3 bp):
TCT
Found at i:6291777 original size:11 final size:11
Alignment explanation
Indices: 6291755--6291788 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
6291745 GTCTTTATCC
6291755 TCTTCTTCTTCT
1 TCTTC-TCTTCT
6291767 TCTTCTCTTCT
1 TCTTCTCTTCT
*
6291778 TCTTTTCTTCT
1 TCTTCTCTTCT
6291789 CCGTCTCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (11 bp):
TCTTCTCTTCT
Found at i:6291807 original size:8 final size:8
Alignment explanation
Indices: 6291754--6291789 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
6291744 AGTCTTTATC
6291754 CTCTTCTT
1 CTCTTCTT
6291762 CTTCTTCTT
1 C-TCTTCTT
6291771 CTCTTCTT
1 CTCTTCTT
*
6291779 CTTTTCTT
1 CTCTTCTT
6291787 CTC
1 CTC
6291790 CGTCTCCTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (8 bp):
CTCTTCTT
Found at i:6308012 original size:43 final size:42
Alignment explanation
Indices: 6307954--6308036 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 42
6307944 GAATAAACAG
* *
6307954 AAATGAAATAGAATAATTATTATGTA-AAATTAAAATGAGATGT
1 AAATAAAATAGAATAATTATTATG-ACAAA-TAAAATAAGATGT
*
6307997 AAATAAAATATAATAATTATTATGACAAATAAAATAAGAT
1 AAATAAAATAGAATAATTATTATGACAAATAAAATAAGAT
6308037 AAGAATAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 11 0.31
43 25 0.69
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.31
Consensus pattern (42 bp):
AAATAAAATAGAATAATTATTATGACAAATAAAATAAGATGT
Found at i:6308109 original size:5 final size:6
Alignment explanation
Indices: 6308088--6308117 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
6308078 CAATAATTTC
*
6308088 AAAATT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
6308118 TACCTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:6309035 original size:14 final size:14
Alignment explanation
Indices: 6309016--6309067 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
6309006 TGTTAAAGAT
6309016 TAATTTATTTTATG
1 TAATTTATTTTATG
6309030 TAATTTA-TTTAT-
1 TAATTTATTTTATG
**
6309042 TTTTTTATATTTGATG
1 TAATTTAT-TTT-ATG
6309058 TAATTTATTT
1 TAATTTATTT
6309068 ATTTGTAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 10 0.33
15 4 0.13
16 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (14 bp):
TAATTTATTTTATG
Found at i:6310081 original size:27 final size:27
Alignment explanation
Indices: 6310050--6310175 Score: 108
Period size: 27 Copynumber: 4.7 Consensus size: 27
6310040 TTAATATGGT
* * *
6310050 ATGTAATAACTAAATTTTTAACTTGAC
1 ATGTAATAATTAAATTTTTAACATAAC
* * * * *
6310077 GTGTAATAATTACATTTTCAACATGAT
1 ATGTAATAATTAAATTTTTAACATAAC
* * * *
6310104 ATATAACAATTAAATTTTTAACTTAAT
1 ATGTAATAATTAAATTTTTAACATAAC
* *
6310131 ATATAATAATTATATTTTTAACATAAC
1 ATGTAATAATTAAATTTTTAACATAAC
* *
6310158 GTGTAAGAATTAAATTTT
1 ATGTAATAATTAAATTTT
6310176 AAAATATGAA
Statistics
Matches: 78, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 78 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (27 bp):
ATGTAATAATTAAATTTTTAACATAAC
Found at i:6310088 original size:55 final size:54
Alignment explanation
Indices: 6309989--6310154 Score: 161
Period size: 54 Copynumber: 3.1 Consensus size: 54
6309979 ATAACTACAC
* * * * *
6309989 CATGATATGTAATAACTAAATCTTCACCATAACGTATAACAATTACATTTTTTAA
1 CATGATATGTAATAACTAAATTTTTAACTTAACGTATAACAATTACA-TTTTCAA
* * * * *
6310044 TATGGTATGTAATAACTAAATTTTTAACTTGACGTGTAATAATTACATTTTCAA
1 CATGATATGTAATAACTAAATTTTTAACTTAACGTATAACAATTACATTTTCAA
* * * ** * * *
6310098 CATGATATATAACAATTAAATTTTTAACTTAATATATAATAATTATATTTTTAA
1 CATGATATGTAATAACTAAATTTTTAACTTAACGTATAACAATTACATTTTCAA
6310152 CAT
1 CAT
6310155 AACGTGTAAG
Statistics
Matches: 90, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
54 52 0.58
55 38 0.42
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (54 bp):
CATGATATGTAATAACTAAATTTTTAACTTAACGTATAACAATTACATTTTCAA
Found at i:6310169 original size:54 final size:54
Alignment explanation
Indices: 6310050--6310175 Score: 135
Period size: 54 Copynumber: 2.3 Consensus size: 54
6310040 TTAATATGGT
* * * * * * *
6310050 ATGTAATAACTAAATTTTTAACTTGACGTGTAATAATTACATTTTCAACATGAT
1 ATGTAACAATTAAATTTTTAACTTAACATATAATAATTACATTTTCAACATAAC
* * * *
6310104 ATATAACAATTAAATTTTTAACTTAATATATAATAATTATATTTTTAACATAAC
1 ATGTAACAATTAAATTTTTAACTTAACATATAATAATTACATTTTCAACATAAC
* *
6310158 GTGTAAGAATTAAATTTT
1 ATGTAACAATTAAATTTT
6310176 AAAATATGAA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (54 bp):
ATGTAACAATTAAATTTTTAACTTAACATATAATAATTACATTTTCAACATAAC
Found at i:6310209 original size:15 final size:15
Alignment explanation
Indices: 6310189--6310219 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
6310179 ATATGAAGCG
6310189 TAATATAATATTTTT
1 TAATATAATATTTTT
6310204 TAATATAATATTTTT
1 TAATATAATATTTTT
6310219 T
1 T
6310220 CATAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAATATAATATTTTT
Found at i:6313714 original size:2 final size:2
Alignment explanation
Indices: 6313707--6313733 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6313697 GTTTAGAGTT
6313707 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6313734 TATTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6314848 original size:17 final size:17
Alignment explanation
Indices: 6314826--6314864 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
6314816 CCAACAGAAA
6314826 TTTTCTGTTGGAAATGG
1 TTTTCTGTTGGAAATGG
6314843 TTTTCTGTTGGAAATGG
1 TTTTCTGTTGGAAATGG
6314860 TTTTC
1 TTTTC
6314865 CAACAGATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.15, C:0.08, G:0.26, T:0.51
Consensus pattern (17 bp):
TTTTCTGTTGGAAATGG
Found at i:6322016 original size:2 final size:2
Alignment explanation
Indices: 6322009--6322033 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6321999 GATAAAATTC
6322009 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
6322034 AAACGAGGAA
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:6322552 original size:2 final size:2
Alignment explanation
Indices: 6322545--6322582 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6322535 ATTTTCAAAG
6322545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6322583 TATCAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6323352 original size:2 final size:2
Alignment explanation
Indices: 6323347--6323384 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6323337 AAAAAGAGGA
6323347 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6323385 TAAGACTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6324481 original size:2 final size:2
Alignment explanation
Indices: 6324474--6324498 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6324464 TAACAGCATT
6324474 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6324499 TAAAACCAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6333906 original size:33 final size:33
Alignment explanation
Indices: 6333857--6333919 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
6333847 TGATGTAATA
* *
6333857 TATTAACATATTATAATTGATGATAACATGTTG
1 TATTAACATATCATAATTGATAATAACATGTTG
*
6333890 TATTGACATATCATAATTGATAATAACATG
1 TATTAACATATCATAATTGATAATAACATG
6333920 ACATTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.40
Consensus pattern (33 bp):
TATTAACATATCATAATTGATAATAACATGTTG
Found at i:6342599 original size:23 final size:23
Alignment explanation
Indices: 6342569--6342617 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
6342559 TTAAAAGCTA
6342569 TTAAGAGTTTTTCAAAATTTTAT
1 TTAAGAGTTTTTCAAAATTTTAT
*
6342592 TTAAGAGTTTTTTAAAATTTTAT
1 TTAAGAGTTTTTCAAAATTTTAT
6342615 TTA
1 TTA
6342618 GCTTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (23 bp):
TTAAGAGTTTTTCAAAATTTTAT
Found at i:6344527 original size:20 final size:19
Alignment explanation
Indices: 6344494--6344534 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
6344484 CTGAAATATT
6344494 AAATAAAATAAAAATATAAA
1 AAATAAAATAAAAAT-TAAA
6344514 AAAT-AAATAAAAAATTAAA
1 AAATAAAAT-AAAAATTAAA
6344533 AA
1 AA
6344535 GGTGCAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATAAAATAAAAATTAAA
Found at i:6345911 original size:28 final size:28
Alignment explanation
Indices: 6345871--6345950 Score: 144
Period size: 28 Copynumber: 2.9 Consensus size: 28
6345861 CCTTCCCTCT
6345871 TAAAATTTTTAAATTTAATAATTTTTTA
1 TAAAATTTTTAAATTTAATAATTTTTTA
6345899 TAAAATTTTTAAATTTAATAATTTTTTA
1 TAAAATTTTTAAATTTAATAATTTTTTA
*
6345927 TAAAATTTTTAAATTTTA-AATTTT
1 TAAAATTTTTAAATTTAATAATTTT
6345951 AATTTTTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 6 0.12
28 45 0.88
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TAAAATTTTTAAATTTAATAATTTTTTA
Found at i:6345973 original size:25 final size:23
Alignment explanation
Indices: 6345937--6346006 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
6345927 TAAAATTTTT
6345937 AAATTTTAAATTTTAATTTTTAAA
1 AAATTTTAAATTTT-ATTTTTAAA
*
6345961 AAATTTTATAATTTTATTTTT-AT
1 AAATTTTA-AATTTTATTTTTAAA
* *
6345984 AAATATTAAATTTTTTATTTTAA
1 AAATTTTAAATTTTAT-TTTTAA
6346007 CCTTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.17
23 12 0.30
24 15 0.38
25 6 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AAATTTTAAATTTTATTTTTAAA
Found at i:6350737 original size:16 final size:17
Alignment explanation
Indices: 6350709--6350740 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
6350699 TGGTTTGATG
6350709 AATAAAAATAATTATTA
1 AATAAAAATAATTATTA
6350726 AATAAAAA-AATTATT
1 AATAAAAATAATTATT
6350741 TTGCAAGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AATAAAAATAATTATTA
Found at i:6353192 original size:15 final size:14
Alignment explanation
Indices: 6353164--6353200 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
6353154 TTGATAAAAA
6353164 TAATA-TAATATTT
1 TAATATTAATATTT
6353177 TAATATTAATTATTT
1 TAATATTAA-TATTT
6353192 TAATATTAA
1 TAATATTAA
6353201 AATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 3 0.14
15 14 0.64
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAATATTAATATTT
Found at i:6354166 original size:27 final size:28
Alignment explanation
Indices: 6354128--6354185 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
6354118 TTTATAAATT
*
6354128 ATAAAAAATTAATATTTT-TAAATATTA
1 ATAAAAAATTAATATTTTAAAAATATTA
*
6354155 ATAAAATATTAATATTTTAAAAATATTA
1 ATAAAAAATTAATATTTTAAAAATATTA
6354183 ATA
1 ATA
6354186 TTTAACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATAAAAAATTAATATTTTAAAAATATTA
Found at i:6354168 original size:17 final size:17
Alignment explanation
Indices: 6354148--6354187 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
6354138 AATATTTTTA
6354148 AATATTA-ATAAAATATT
1 AATATTATA-AAAATATT
*
6354165 AATATTTTAAAAATATT
1 AATATTATAAAAATATT
6354182 AATATT
1 AATATT
6354188 TAACTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTATAAAAATATT
Found at i:6354299 original size:25 final size:27
Alignment explanation
Indices: 6354260--6354310 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
6354250 GCAAATAGAG
6354260 AAAAAATAAAAATTA-TA-AATAAAAT
1 AAAAAATAAAAATTATTATAATAAAAT
**
6354285 AAAAAATAACTATTATTATAATAAAA
1 AAAAAATAAAAATTATTATAATAAAA
6354311 AGTTTTAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 2 0.09
27 7 0.32
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAAATAAAAATTATTATAATAAAAT
Found at i:6354467 original size:25 final size:26
Alignment explanation
Indices: 6354426--6354477 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
6354416 ATTAGTATTG
* *
6354426 AAAATATTAATGATTAAATTAT-AAT
1 AAAATAGTAATGATTAAAATATCAAT
6354451 AAAATAGTAAT-ATTTAAAATATCAAT
1 AAAATAGTAATGA-TTAAAATATCAAT
6354477 A
1 A
6354478 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 1 0.04
25 18 0.78
26 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAATAGTAATGATTAAAATATCAAT
Found at i:6354470 original size:15 final size:15
Alignment explanation
Indices: 6354450--6354483 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6354440 TAAATTATAA
6354450 TAAAATAGT-AATATT
1 TAAAATA-TCAATATT
6354465 TAAAATATCAATATT
1 TAAAATATCAATATT
6354480 TAAA
1 TAAA
6354484 TTATTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 1 0.06
15 17 0.94
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (15 bp):
TAAAATATCAATATT
Found at i:6354470 original size:40 final size:40
Alignment explanation
Indices: 6354393--6354487 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 40
6354383 TTAATCATAA
* *
6354393 TAATATTAAATTATAAATAAAATATTAGTATTGAAAATAT
1 TAATATTAAATTATAAATAAAATAGTAATATTGAAAATAT
*
6354433 TAATGATTAAATTAT-AATAAAATAGTAATATTTAAAATAT
1 TAAT-ATTAAATTATAAATAAAATAGTAATATTGAAAATAT
*
6354473 CAATATTTAAATTAT
1 TAATA-TTAAATTAT
6354488 TAATTATTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 1 0.02
40 38 0.78
41 10 0.20
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (40 bp):
TAATATTAAATTATAAATAAAATAGTAATATTGAAAATAT
Found at i:6354527 original size:55 final size:54
Alignment explanation
Indices: 6354397--6354527 Score: 126
Period size: 55 Copynumber: 2.4 Consensus size: 54
6354387 TCATAATAAT
* * *
6354397 ATTAAATTATAAATAA--AATATTAGTATTGAAAATATTAATGATTAAATTATA
1 ATTAAATTATAAATAATTAATATCAATATTGAAAATATTAATGATTAAAGTATA
* * * * *
6354449 A-TAAAATAGT-AATATTTAAAATATCAATATTTAAATTATTAATTATTAATAGTATA
1 ATTAAATTA-TAAATAATT--AATATCAATATTGAAAATATTAATGATTAA-AGTATA
6354505 ATTAAATTATAAATAATTAATAT
1 ATTAAATTATAAATAATTAATAT
6354528 TTAAAAAATA
Statistics
Matches: 61, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
51 10 0.16
52 2 0.03
55 30 0.49
56 7 0.11
57 12 0.20
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (54 bp):
ATTAAATTATAAATAATTAATATCAATATTGAAAATATTAATGATTAAAGTATA
Found at i:6354532 original size:15 final size:15
Alignment explanation
Indices: 6354458--6354532 Score: 55
Period size: 15 Copynumber: 4.7 Consensus size: 15
6354448 AATAAAATAG
6354458 TAATATTTAAA-ATAT
1 TAATATTTAAATA-AT
* *
6354473 CAATATTTAAATTAT
1 TAATATTTAAATAAT
*
6354488 TAATTATTAATAGTATAAT
1 TAA-TATT--TA-AATAAT
6354507 TAA-ATTATAAATAAT
1 TAATATT-TAAATAAT
6354522 TAATATTTAAA
1 TAATATTTAAA
6354533 AAATAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
15 26 0.54
16 10 0.21
17 3 0.06
18 2 0.04
19 7 0.15
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (15 bp):
TAATATTTAAATAAT
Found at i:6354568 original size:30 final size:27
Alignment explanation
Indices: 6354513--6354570 Score: 73
Period size: 27 Copynumber: 2.0 Consensus size: 27
6354503 TAATTAAATT
6354513 ATAAATAATTAATATTTAAAAAATAAA
1 ATAAATAATTAATATTTAAAAAATAAA
6354540 ATAAAT-ATTAATAATTATATATAAAATAAA
1 ATAAATAATTAAT-ATT-TA-A-AAAATAAA
6354570 A
1 A
6354571 GATATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 6 0.22
27 9 0.33
28 2 0.07
29 1 0.04
30 9 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAAATAATTAATATTTAAAAAATAAA
Found at i:6366811 original size:24 final size:25
Alignment explanation
Indices: 6366751--6366811 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 25
6366741 CTTTGAAAAA
*
6366751 TTTAAATAATTTTTTAATTTTTAAT
1 TTTAAATAATTTTATAATTTTTAAT
* *
6366776 TTTAATTTAATTTTAT-GTTTTT-AT
1 TTTAA-ATAATTTTATAATTTTTAAT
6366800 TTTAAATCAATT
1 TTTAAAT-AATT
6366812 AAGTTTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.03
24 11 0.37
25 10 0.33
26 8 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTAAATAATTTTATAATTTTTAAT
Found at i:6366957 original size:29 final size:29
Alignment explanation
Indices: 6366924--6367001 Score: 156
Period size: 29 Copynumber: 2.7 Consensus size: 29
6366914 ATGTTATGTT
6366924 ATAATTTATTAAGATATATTTAAAAAATA
1 ATAATTTATTAAGATATATTTAAAAAATA
6366953 ATAATTTATTAAGATATATTTAAAAAATA
1 ATAATTTATTAAGATATATTTAAAAAATA
6366982 ATAATTTATTAAGATATATT
1 ATAATTTATTAAGATATATT
6367002 AACACGTTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (29 bp):
ATAATTTATTAAGATATATTTAAAAAATA
Found at i:6366959 original size:15 final size:15
Alignment explanation
Indices: 6366941--6366989 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
6366931 ATTAAGATAT
6366941 ATTTAAAAAATAATA
1 ATTTAAAAAATAATA
* *
6366956 ATTTATTAAGAT-AT-
1 ATTTA-AAAAATAATA
6366970 ATTTAAAAAATAATA
1 ATTTAAAAAATAATA
6366985 ATTTA
1 ATTTA
6366990 TTAAGATATA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 12 0.44
16 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTTAAAAAATAATA
Found at i:6368212 original size:2 final size:2
Alignment explanation
Indices: 6368205--6368229 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6368195 TTTTACCTTT
6368205 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
6368230 AGAGAGCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:6387468 original size:15 final size:14
Alignment explanation
Indices: 6387438--6387493 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
6387428 NNNNNNNNNN
6387438 AAAATACTAA-ATAT
1 AAAATA-TAATATAT
6387452 AAAACTATAATATAT
1 AAAA-TATAATATAT
6387467 AAAATATAA-ATAAT
1 AAAATATAATAT-AT
*
6387481 TAAATATAATATA
1 AAAATATAATATA
6387494 CGAAATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
13 2 0.05
14 23 0.62
15 12 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATATAATATAT
Found at i:6387499 original size:28 final size:29
Alignment explanation
Indices: 6387438--6387499 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
6387428 NNNNNNNNNN
*
6387438 AAAATACTAAATATAAAACTATAATATAT
1 AAAATACTAAATATAAAACTATAATATAC
*
6387467 AAAATA-TAAATAATTAAA-TATAATATAC
1 AAAATACTAAAT-ATAAAACTATAATATAC
*
6387495 GAAAT
1 AAAAT
6387500 TTTATGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 18 0.62
29 11 0.38
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAATACTAAATATAAAACTATAATATAC
Found at i:6387531 original size:16 final size:17
Alignment explanation
Indices: 6387507--6387544 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
6387497 AATTTTATGT
*
6387507 AATAATTAAAT-ATATA
1 AATAGTTAAATAATATA
6387523 AATAGTTAAATAATATA
1 AATAGTTAAATAATATA
6387540 AATAG
1 AATAG
6387545 AAAGAGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (17 bp):
AATAGTTAAATAATATA
Found at i:6387810 original size:15 final size:17
Alignment explanation
Indices: 6387790--6387821 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
6387780 ATTTATGAGG
6387790 TTATTT-TATT-ATTTT
1 TTATTTATATTAATTTT
6387805 TTATTTATATTAATTTT
1 TTATTTATATTAATTTT
6387822 AAAATAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
TTATTTATATTAATTTT
Found at i:6419094 original size:342 final size:346
Alignment explanation
Indices: 6418298--6419209 Score: 916
Period size: 356 Copynumber: 2.6 Consensus size: 346
6418288 ATTAAATTAC
* * * * ** *
6418298 ATAATAATAATTGTATTCTTTATAAATGAACATAATATATA-ATATAAAGTATATGTATTAAAAG
1 ATAATAGTAATTATATCCCTTATAAATGAACCCAATATATATAAATAAA-TATAT-TA--AAAA-
* * *
6418362 ACATTACAAGTTAATTAATAATCATAGTTTATTAATTAATTTAATTAATTAT-TAGTTTTTCCTT
61 ACATTTCAAGTTAATTAATAATCATAGTTTATGAATTAATTTAATTAATTATATAGTTTGTCCTT
* * *
6418426 AATTACATAAAATT-AAAAAAA-AACTAAGTTTCAAAACTATTCTAATCTC--ACTTTTTTTTAG
126 AATTACATAAAATTAAAAAAAATAACTAAGTCTCAAAACTATTCTAATCTCAAACTTCTTTTAAG
* * * * * * *
6418487 ATAATTAAGTTTATATAAACAAG--GATATATATATATATATATATATTATAATTAATAATTTTA
191 GT--TT--G--TATAT-TATAAGTTGATATAAACAAAGATATATATATTATAATTAATAATTTTA
* *
6418550 TAAGTTATAAGTTTTGTAATGTTAACACAAAATAAAAAGTAAATATGTTTTCATTTAAAGTGTAT
249 CAAGTTATAAGTTTTGTAATGTTAACACAAAATAAAAAGTAAATATATTTTCATTTAAAG-GTAT
* * *
6418615 ATACATATACACTCACATTAAAGGTATTTTACTATATGT
313 ATA-ATATA-ACT--CA-TAAAGGTAGTATACTATATAT
* *
6418654 ATAATAGTAATTATATTCTTTATAAATGAACCCAATATATATAAAATAAATATATTAAAAAACAT
1 ATAATAGTAATTATATCCCTTATAAATGAACCCAATATATAT-AAATAAATATATTAAAAAACAT
* * *
6418719 TAT-AAGATAATTAATAATAATAATTTTATGAATTAATTTAATTAATTATATAAGTTTGTCCTTA
65 T-TCAAGTTAATTAATAATCAT-AGTTTATGAATTAATTTAATTAATTATAT-AGTTTGTCCTTA
* *
6418783 ATTACATGAAATTAAAAAAAATAACTATGTCTCAAAACTATTCTAATCTCATAACTTCTTTTAAG
127 ATTACATAAAATTAAAAAAAATAACTAAGTCTCAAAACTATTCTAATCTCA-AACTTCTTTTAAG
* *
6418848 GTTTGTATATTATAAGTTTATATAAACAAAGATGTATATATTATAATTAATAATTTTACAAGTTA
191 GTTTGTATATTATAAGTTGATATAAACAAAGATATATATATTATAATTAATAATTTTACAAGTTA
* * * *
6418913 TAATTTTTGTAATGTTAATATAAAATAGAAAGTAAATATATTTAT-ATTTAAA-GTATAT-ATAT
256 TAAGTTTTGTAATGTTAACACAAAATAAAAAGTAAATATATTT-TCATTTAAAGGTATATAATAT
6418975 -ACT-A-AAAGTGTTAGTATA-TATATAT
320 AACTCATAAAG-G-TAGTATACTATATAT
* **
6419000 A-ATATAGTAGTTATATCCCTTATAAATGAACCC-A-ATATAT-AATGCATATATTAAAAAACAT
1 ATA-ATAGTAATTATATCCCTTATAAATGAACCCAATATATATAAATAAATATATTAAAAAACAT
* *
6419061 TTCAAGTTAATTAATAATCATAGTTTAATGAATTAATCTAATTAATTATATGTGTTTG-CCTTTA
65 TTCAAGTTAATTAATAATCATAGTTT-ATGAATTAATTTAATTAATTATAT-AGTTTGTCC-TTA
* * *
6419125 ATTATATAAAATTAAAAAAAAATAATTAAAATC-CAAAACTATTCTAATCTCAAAAACTCTCTTT
127 ATTACATAAAATT-AAAAAAAATAACT-AAGTCTCAAAACTATTCTAATCTC--AAACT-TCTTT
* *
6419189 TAA-GTGTATATATTATAAGTT
187 TAAGGTTTGTATATTATAAGTT
6419210 ATAATTTTTA
Statistics
Matches: 479, Mismatches: 52, Indels: 62
0.81 0.09 0.10
Matches are distributed among these distances:
341 7 0.01
342 78 0.16
343 30 0.06
344 29 0.06
345 15 0.03
346 35 0.07
347 6 0.01
350 3 0.01
352 4 0.01
353 21 0.04
354 39 0.08
355 6 0.01
356 147 0.31
357 14 0.03
358 32 0.07
359 2 0.00
361 11 0.02
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (346 bp):
ATAATAGTAATTATATCCCTTATAAATGAACCCAATATATATAAATAAATATATTAAAAAACATT
TCAAGTTAATTAATAATCATAGTTTATGAATTAATTTAATTAATTATATAGTTTGTCCTTAATTA
CATAAAATTAAAAAAAATAACTAAGTCTCAAAACTATTCTAATCTCAAACTTCTTTTAAGGTTTG
TATATTATAAGTTGATATAAACAAAGATATATATATTATAATTAATAATTTTACAAGTTATAAGT
TTTGTAATGTTAACACAAAATAAAAAGTAAATATATTTTCATTTAAAGGTATATAATATAACTCA
TAAAGGTAGTATACTATATAT
Found at i:6422577 original size:17 final size:16
Alignment explanation
Indices: 6422551--6422584 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
6422541 AACCTCTTAA
6422551 CTCAATGTCCACCAAG
1 CTCAATGTCCACCAAG
*
6422567 CTCATATGTCCAGCAAG
1 CTCA-ATGTCCACCAAG
6422584 C
1 C
6422585 ATATAATGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (16 bp):
CTCAATGTCCACCAAG
Found at i:6428776 original size:59 final size:59
Alignment explanation
Indices: 6428701--6428876 Score: 327
Period size: 59 Copynumber: 3.0 Consensus size: 59
6428691 GGCCGTAAAA
6428701 GAATAAAAATTAAAGAATTATGGGATGGACTCTATGGAAATGGATAATATAAGATTACT
1 GAATAAAAATTAAAGAATTATGGGATGGACTCTATGGAAATGGATAATATAAGATTACT
6428760 GAATAAAAATTAAAGAATTATGGGATGGACTCTATGGAAATGGATAATATAAGATTACT
1 GAATAAAAATTAAAGAATTATGGGATGGACTCTATGGAAATGGATAATATAAGATTACT
*
6428819 GAATAAAAATTAATA-AATTATGGGATGGACTCCATGGAAATGGATAATATAAGATTAC
1 GAATAAAAATTAA-AGAATTATGGGATGGACTCTATGGAAATGGATAATATAAGATTAC
6428877 AGTTTTTTCA
Statistics
Matches: 115, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
59 114 0.99
60 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (59 bp):
GAATAAAAATTAAAGAATTATGGGATGGACTCTATGGAAATGGATAATATAAGATTACT
Found at i:6430537 original size:2 final size:2
Alignment explanation
Indices: 6430530--6430557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6430520 TGCTTTTGTT
6430530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6430558 ATCCTGCCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6430641 original size:14 final size:13
Alignment explanation
Indices: 6430624--6430653 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
6430614 AAAATTTATT
6430624 ATTAAAATTTTTAA
1 ATTAAAA-TTTTAA
6430638 ATTAAAATTTTAA
1 ATTAAAATTTTAA
6430651 ATT
1 ATT
6430654 CTAATCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTAAAATTTTAA
Found at i:6431158 original size:2 final size:2
Alignment explanation
Indices: 6431151--6431176 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6431141 CTACTATGTA
6431151 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6431177 CACGGGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6443654 original size:12 final size:12
Alignment explanation
Indices: 6443637--6443663 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6443627 ACAACTCAGT
6443637 GAAGACAGCAAA
1 GAAGACAGCAAA
6443649 GAAGACAGCAAA
1 GAAGACAGCAAA
6443661 GAA
1 GAA
6443664 TGAATCCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (12 bp):
GAAGACAGCAAA
Found at i:6452385 original size:19 final size:21
Alignment explanation
Indices: 6452346--6452388 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
6452336 CTTTTGTTTC
6452346 TTTTCTTCTTTTCTTTCCTCT
1 TTTTCTTCTTTTCTTTCCTCT
*
6452367 TTTTCTT-TTTTTTTTCTCTCT
1 TTTTCTTCTTTTCTTTC-CTCT
6452388 T
1 T
6452389 CTCACCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTCTTCTTTTCTTTCCTCT
Found at i:6452861 original size:107 final size:107
Alignment explanation
Indices: 6452675--6452890 Score: 301
Period size: 107 Copynumber: 2.0 Consensus size: 107
6452665 AGAAATTTGT
* * *
6452675 TATGCTTACATGAGGTTTTAAATTCGAAATATAGTAAGCATATAATATTTTTATAAAAAATAAGA
1 TATGCTTACATGAGGTCTTAAATTCGAAATATAGTAAGCATATAATATCTTTATAAAAAACAAGA
6452740 AAGAGACACAAACATGCCATGTAGCTTGACATGGATGGGTGC
66 AAGAGACACAAACATGCCATGTAGCTTGACATGGATGGGTGC
* * * *
6452782 TATGCTTACATGAGGTCTTGAGTTGGAAACTCA-A-TAAGCATATAATATCTTTATAGAAAACAA
1 TATGCTTACATGAGGTCTTAAATTCGAAA-T-ATAGTAAGCATATAATATCTTTATAAAAAACAA
* * * *
6452845 GAAAGAGACATAAACATGCTATGTGGCTTGACATGTATGGGTGC
64 GAAAGAGACACAAACATGCCATGTAGCTTGACATGGATGGGTGC
6452889 TA
1 TA
6452891 AAGGCAAGTG
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 93 0.97
108 2 0.02
109 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (107 bp):
TATGCTTACATGAGGTCTTAAATTCGAAATATAGTAAGCATATAATATCTTTATAAAAAACAAGA
AAGAGACACAAACATGCCATGTAGCTTGACATGGATGGGTGC
Found at i:6455200 original size:5 final size:5
Alignment explanation
Indices: 6455190--6455236 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
6455180 ATCATATCAT
* * * *
6455190 TAATA TGATA TAATA TAATA TTAT- TAATA TGATA TAGTA TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAA
6455237 ATGGTATTAG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (5 bp):
TAATA
Found at i:6455202 original size:27 final size:24
Alignment explanation
Indices: 6455172--6455234 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
6455162 TGTATTTATC
6455172 ATAACATAATCATATCATTAATATGAT
1 ATAACATAAT-AT-T-ATTAATATGAT
*
6455199 ATAATATAATATTATTAATATGAT
1 ATAACATAATATTATTAATATGAT
**
6455223 ATAGTATAATAT
1 ATAACATAATAT
6455235 AAATGGTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 22 0.65
25 1 0.03
26 2 0.06
27 9 0.26
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (24 bp):
ATAACATAATATTATTAATATGAT
Found at i:6455215 original size:24 final size:24
Alignment explanation
Indices: 6455183--6455234 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
6455173 TAACATAATC
6455183 ATATCATTAATATGATATAATATA
1 ATATCATTAATATGATATAATATA
* *
6455207 ATATTATTAATATGATATAGTATA
1 ATATCATTAATATGATATAATATA
6455231 ATAT
1 ATAT
6455235 AAATGGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (24 bp):
ATATCATTAATATGATATAATATA
Found at i:6456300 original size:14 final size:15
Alignment explanation
Indices: 6456274--6456302 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6456264 CGAAGAAACA
6456274 GAAGAAGAAGAAAGG
1 GAAGAAGAAGAAAGG
6456289 GAAGAA-AAGAAAGG
1 GAAGAAGAAGAAAGG
6456303 CAGGTCCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAGAAAGG
Found at i:6457896 original size:47 final size:48
Alignment explanation
Indices: 6457844--6457939 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
6457834 CGGTTGAAAG
*
6457844 AAAGACAGGAAAAAGGGGAAAA-AACAGTTACTCATGAAACCAATTTC
1 AAAGACAGGAAAAAGGGGAAAACAACACTTACTCATGAAACCAATTTC
6457891 AAAGACAGGAAAAAGGGGAAAACAACACTTACTCATGAAACCAATTTC
1 AAAGACAGGAAAAAGGGGAAAACAACACTTACTCATGAAACCAATTTC
6457939 A
1 A
6457940 TAACAGCTCA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 22 0.47
48 25 0.53
ACGTcount: A:0.51, C:0.17, G:0.18, T:0.15
Consensus pattern (48 bp):
AAAGACAGGAAAAAGGGGAAAACAACACTTACTCATGAAACCAATTTC
Found at i:6460560 original size:111 final size:115
Alignment explanation
Indices: 6460346--6460561 Score: 300
Period size: 115 Copynumber: 1.9 Consensus size: 115
6460336 TGCATGGAAA
* *
6460346 CTTGTTAGCATGTTATAACCCAACTAAACTGTACAATCAAAAAGAAGAAAACTATAATACATAAA
1 CTTGTTAGCATGTTATAACCCAACTAAACTGTACAATCAAAAAGAAGAAAACTATAAGACAGAAA
6460411 AAACTTGCTATATTTGAAAGCAATAAAGCAAAGAGTTTATATTATGAACT
66 AAACTTGCTATATTTGAAAGCAATAAAGCAAAGAGTTTATATTATGAACT
* * * **
6460461 CTTGTTAGCATGTTATAACCCAAGTAAGCT-TACAATCAAAATG-A-AAAGGTAATAAGA-AGAA
1 CTTGTTAGCATGTTATAACCCAACTAAACTGTACAATCAAAAAGAAGAAAACT-ATAAGACAGAA
*
6460522 GAAAACTTGCTA-ATTTGAAA-CAATAAAGCTAAGAGTTTAT
65 -AAAACTTGCTATATTTGAAAGCAATAAAGCAAAGAGTTTAT
6460562 GCTAGCAACT
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
111 19 0.21
112 15 0.16
113 17 0.19
114 12 0.13
115 28 0.31
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.27
Consensus pattern (115 bp):
CTTGTTAGCATGTTATAACCCAACTAAACTGTACAATCAAAAAGAAGAAAACTATAAGACAGAAA
AAACTTGCTATATTTGAAAGCAATAAAGCAAAGAGTTTATATTATGAACT
Found at i:6463105 original size:11 final size:10
Alignment explanation
Indices: 6463089--6463121 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
6463079 ATAATGCTTT
6463089 AAAAATTCTTA
1 AAAAATT-TTA
6463100 AAAAATTTTA
1 AAAAATTTTA
6463110 AAAAA-TTTA
1 AAAAATTTTA
6463119 AAA
1 AAA
6463122 TTAAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.32
10 8 0.36
11 7 0.32
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:6472544 original size:73 final size:73
Alignment explanation
Indices: 6472445--6472588 Score: 200
Period size: 73 Copynumber: 2.0 Consensus size: 73
6472435 CGTCCACAAA
* * *
6472445 AATTATAATTTAAGTTTTCAAATTAATATCTTAATTGTGAAAATCTGAAATTTTACGTTTAAATC
1 AATTATAATTTAAATTTTCAAATTAATATCTTAATTGTGAAAATCTGAAATTTTACATTGAAATC
6472510 TTGAGATC
66 TTGAGATC
* * * * *
6472518 AATTATATTTTAAATCTTT-AAATTAATATCTTAATTGTTAAATTTTGAAATTTTACATTGGAAT
1 AATTATAATTTAAAT-TTTCAAATTAATATCTTAATTGTGAAAATCTGAAATTTTACATTGAAAT
6472582 CTTGAGA
65 CTTGAGA
6472589 GTAGGGAGAC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 59 0.95
74 3 0.05
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (73 bp):
AATTATAATTTAAATTTTCAAATTAATATCTTAATTGTGAAAATCTGAAATTTTACATTGAAATC
TTGAGATC
Found at i:6478633 original size:23 final size:22
Alignment explanation
Indices: 6478602--6478644 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6478592 TAAATTTTAT
* *
6478602 AAAATTATAATTAAATAATTAAC
1 AAAAATATAA-TAAAAAATTAAC
6478625 AAAAATATAATAAAAAATTA
1 AAAAATATAATAAAAAATTA
6478645 CAATGGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
AAAAATATAATAAAAAATTAAC
Found at i:6481084 original size:30 final size:30
Alignment explanation
Indices: 6481048--6481107 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
6481038 AGTACATCAT
*
6481048 TAAGATGGTCCACTATATTCAATACTCTTA
1 TAAGATGGTCCACTAAATTCAATACTCTTA
*
6481078 TAAGATGGTCTACTAAATTCAATACTCTTA
1 TAAGATGGTCCACTAAATTCAATACTCTTA
6481108 AAAGGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (30 bp):
TAAGATGGTCCACTAAATTCAATACTCTTA
Found at i:6485890 original size:21 final size:21
Alignment explanation
Indices: 6485860--6485908 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
6485850 ACTCATTCAT
*
6485860 TTTATTTGAATAAACTCTTAC
1 TTTATATGAATAAACTCTTAC
6485881 TTTATATGAATAAACTCTTAC
1 TTTATATGAATAAACTCTTAC
*
6485902 TTCATAT
1 TTTATAT
6485909 AAACAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (21 bp):
TTTATATGAATAAACTCTTAC
Found at i:6489243 original size:19 final size:19
Alignment explanation
Indices: 6489219--6489313 Score: 135
Period size: 19 Copynumber: 5.2 Consensus size: 19
6489209 GAGCTGAACC
6489219 TAAATGTTGTCATGTTTAG
1 TAAATGTTGTCATGTTTAG
6489238 TAAATGTTGTCATGTTTAG
1 TAAATGTTGTCATGTTTAG
**
6489257 TAAA----AACATGTTTAG
1 TAAATGTTGTCATGTTTAG
6489272 TAAATGTTGTCATGTTTAG
1 TAAATGTTGTCATGTTTAG
*
6489291 TAAATGTTGTCTTGTTTAG
1 TAAATGTTGTCATGTTTAG
6489310 TAAA
1 TAAA
6489314 AACAAGTCAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.19
19 54 0.81
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (19 bp):
TAAATGTTGTCATGTTTAG
Found at i:6489259 original size:53 final size:51
Alignment explanation
Indices: 6489213--6489313 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 51
6489203 GTAAACGAGC
6489213 TGAACCTAAATGTTGTCATGTTTAGTAAATGTTGTCATGTTTAGTAAAAACATG
1 TGAA-CTAAATGTTGTCATGTTTAGTAAATGTTGTCATGTTTAGT--AAACATG
** * *
6489267 TTTAGTAAATGTTGTCATGTTTAGTAAATGTTGTCTTGTTTAGTAAA
1 TGAACTAAATGTTGTCATGTTTAGTAAATGTTGTCATGTTTAGTAAA
6489314 AACAAGTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 3 0.07
53 38 0.88
54 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.44
Consensus pattern (51 bp):
TGAACTAAATGTTGTCATGTTTAGTAAATGTTGTCATGTTTAGTAAACATG
Found at i:6489267 original size:34 final size:34
Alignment explanation
Indices: 6489229--6489294 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
6489219 TAAATGTTGT
6489229 CATGTTTAGTAAATGTTGTCATGTTTAGTAAAAA
1 CATGTTTAGTAAATGTTGTCATGTTTAGTAAAAA
6489263 CATGTTTAGTAAATGTTGTCATGTTTAGTAAA
1 CATGTTTAGTAAATGTTGTCATGTTTAGTAAA
6489295 TGTTGTCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.42
Consensus pattern (34 bp):
CATGTTTAGTAAATGTTGTCATGTTTAGTAAAAA
Found at i:6493974 original size:33 final size:33
Alignment explanation
Indices: 6493937--6494055 Score: 82
Period size: 33 Copynumber: 3.6 Consensus size: 33
6493927 ACTGACCTTG
*
6493937 AGCTGATTGAGAAGGGTCTGTAAAGTGATCTTC
1 AGCTGATTGAGAAGGCTCTGTAAAGTGATCTTC
** * *
6493970 AGCTGA-TGAAGAAGGCTCAATGAACTGATCTTC
1 AGCTGATTG-AGAAGGCTCTGTAAAGTGATCTTC
* ** *
6494003 A-CGTGATGGAGAAGATTCTG-CAAGCTGATCTTC
1 AGC-TGATTGAGAAGGCTCTGTAAAG-TGATCTTC
** *
6494036 AGCTGACAGAGAAGACTCTG
1 AGCTGATTGAGAAGGCTCTG
6494056 CAAACAGATC
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
32 5 0.08
33 59 0.89
34 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (33 bp):
AGCTGATTGAGAAGGCTCTGTAAAGTGATCTTC
Found at i:6494056 original size:33 final size:33
Alignment explanation
Indices: 6493992--6494067 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
6493982 AGGCTCAATG
** *
6493992 AACTGATCTTCACGTGATGGAGAAGATTCTGCA
1 AACTGATCTTCACGTGACAGAGAAGACTCTGCA
*
6494025 AGCTGATCTTCA-GCTGACAGAGAAGACTCTGCA
1 AACTGATCTTCACG-TGACAGAGAAGACTCTGCA
*
6494058 AACAGATCTT
1 AACTGATCTT
6494068 GAGATGATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
32 1 0.03
33 35 0.97
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (33 bp):
AACTGATCTTCACGTGACAGAGAAGACTCTGCA
Found at i:6496675 original size:5 final size:5
Alignment explanation
Indices: 6496665--6496695 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
6496655 GAAGATTCCC
6496665 TTCTT TTCTT TTCTT TTCTT TT-TT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
6496696 TATATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTCTT
Found at i:6506076 original size:14 final size:15
Alignment explanation
Indices: 6506044--6506081 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
6506034 AATTCATCAT
6506044 TTTAATTTTTTCTTA
1 TTTAATTTTTTCTTA
*
6506059 TTTAATTTTTT-TTG
1 TTTAATTTTTTCTTA
6506073 TTT-ATTTTT
1 TTTAATTTTT
6506082 GGATATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 11 0.50
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (15 bp):
TTTAATTTTTTCTTA
Found at i:6515950 original size:57 final size:57
Alignment explanation
Indices: 6515857--6515966 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
6515847 TAACACATGA
*
6515857 TAGTTGGTATCAAAGCTAGTTCGGATCTTCACTGATATAGGGCCTCTATGAGAGATC
1 TAGTTGGTATCAAAGCTAGTTCGGATCTTCACTGATATAGGGCCCCTATGAGAGATC
* * * *
6515914 TAGTTGGTATCAGAGCTGGTAT-GGATCTTCATTGATATGGGGCCCCTATGAGA
1 TAGTTGGTATCAAAGCTAGT-TCGGATCTTCACTGATATAGGGCCCCTATGAGA
6515967 AATATAAGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
57 46 0.98
58 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (57 bp):
TAGTTGGTATCAAAGCTAGTTCGGATCTTCACTGATATAGGGCCCCTATGAGAGATC
Found at i:6516463 original size:43 final size:43
Alignment explanation
Indices: 6516402--6516574 Score: 283
Period size: 43 Copynumber: 3.9 Consensus size: 43
6516392 TATTCGACTT
* *
6516402 TTGTGAAACCAATAATGAATAGCATTTTACTTGATAAGATATA
1 TTGTGAAACCAAGAATGAATAGCACTTTACTTGATAAGATATA
*
6516445 TTGTGAAACCAAGCATGAATAGCACTTTACTTGATAAGATATA
1 TTGTGAAACCAAGAATGAATAGCACTTTACTTGATAAGATATA
6516488 TTGTGAAACCAAGCATGAATGAATAGCACTTTACTTGATAAGATATA
1 TTGTGAAACC-A--A-GAATGAATAGCACTTTACTTGATAAGATATA
6516535 TTGTGAAACCAAGAATGAATAGCACTTTACTTGATAAGAT
1 TTGTGAAACCAAGAATGAATAGCACTTTACTTGATAAGAT
6516575 TTAATACTTC
Statistics
Matches: 122, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
43 78 0.64
44 2 0.02
46 2 0.02
47 40 0.33
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (43 bp):
TTGTGAAACCAAGAATGAATAGCACTTTACTTGATAAGATATA
Found at i:6516642 original size:69 final size:70
Alignment explanation
Indices: 6516556--6516702 Score: 251
Period size: 69 Copynumber: 2.1 Consensus size: 70
6516546 AGAATGAATA
*
6516556 GCACTTTACTTGATAAGATTTAATACTTCAACTTGAGGG-TTTAGATTTGAATTATGGGATGTGA
1 GCACTTTACTTGATAAGATTTAATACTTCAACTTGAGGGTTTTAGATTTGAATTATGAGATGTGA
6516620 AAGGT
66 AAGGT
* *
6516625 GCACTTTACTTGATAAGATTTAATATTTCAACTTGAGGGTTTTTGATTTGAATTATGAGATGTGA
1 GCACTTTACTTGATAAGATTTAATACTTCAACTTGAGGGTTTTAGATTTGAATTATGAGATGTGA
6516690 AAGGT
66 AAGGT
*
6516695 GCAATTTA
1 GCACTTTA
6516703 TGATTGAAAG
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
69 38 0.52
70 35 0.48
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (70 bp):
GCACTTTACTTGATAAGATTTAATACTTCAACTTGAGGGTTTTAGATTTGAATTATGAGATGTGA
AAGGT
Found at i:6516722 original size:70 final size:68
Alignment explanation
Indices: 6516560--6516702 Score: 187
Period size: 70 Copynumber: 2.1 Consensus size: 68
6516550 TGAATAGCAC
* * * *
6516560 TTTACTTGATAAGATTTAATACTTCAACTTGAGGGTTTAGATTTGAATTATGGGATGTGAAAGGT
1 TTTAATTGATAAGA-TGAATATTTCAACTTGAGGGTTTAGATTTGAATTATGAGATGTGAAAGGT
*
6516625 GCAC
65 GCAA
* * *
6516629 TTTACTTGATAAGATTTAATATTTCAACTTGAGGGTTTTTGATTTGAATTATGAGATGTGAAAGG
1 TTTAATTGATAAGA-TGAATATTTCAACTTGAGGG-TTTAGATTTGAATTATGAGATGTGAAAGG
6516694 TGCAA
64 TGCAA
6516699 TTTA
1 TTTA
6516703 TGATTGAAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
69 34 0.49
70 35 0.51
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.41
Consensus pattern (68 bp):
TTTAATTGATAAGATGAATATTTCAACTTGAGGGTTTAGATTTGAATTATGAGATGTGAAAGGTG
CAA
Found at i:6521258 original size:2 final size:2
Alignment explanation
Indices: 6521246--6521283 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
6521236 CCAACATAAA
6521246 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6521284 AAACGACAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6522334 original size:2 final size:2
Alignment explanation
Indices: 6522329--6522365 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6522319 ACACACTCTC
*
6522329 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6522366 CAAACATGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6527020 original size:2 final size:2
Alignment explanation
Indices: 6527013--6527046 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
6527003 TCCAGCTGGC
* *
6527013 CT CT CT CT CT CT CT CT CT CT CT TT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
6527047 TTGACTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (2 bp):
CT
Found at i:6535179 original size:34 final size:33
Alignment explanation
Indices: 6535141--6535212 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
6535131 TCTTCTTTCA
* *
6535141 TTAATTATTCAAATT-AACTTTTGTATAATTTTTT
1 TTAATTA--CAAATTGAACTTTTGCATAAATTTTT
*
6535175 TTAATTACTAATTGAACTTTTGCATAAATTTTT
1 TTAATTACAAATTGAACTTTTGCATAAATTTTT
6535208 TTAAT
1 TTAAT
6535213 ACATATGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 5 0.15
33 22 0.65
34 7 0.21
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (33 bp):
TTAATTACAAATTGAACTTTTGCATAAATTTTT
Found at i:6535552 original size:18 final size:19
Alignment explanation
Indices: 6535529--6535564 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6535519 CAATCTAATT
6535529 TACATA-TAAATTTAGATA
1 TACATAGTAAATTTAGATA
*
6535547 TACATAGTATATTTAGAT
1 TACATAGTAAATTTAGAT
6535565 TTTCATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (19 bp):
TACATAGTAAATTTAGATA
Found at i:6536949 original size:15 final size:15
Alignment explanation
Indices: 6536922--6536959 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
6536912 GTTATTCTAT
6536922 TTCCTTATTCTTCTTC
1 TTCCTT-TTCTTCTTC
6536938 TTCCTTTTCTTCTTC
1 TTCCTTTTCTTCTTC
6536953 TT-CTTTT
1 TTCCTTTT
6536960 ACCTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.23
15 11 0.50
16 6 0.27
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (15 bp):
TTCCTTTTCTTCTTC
Found at i:6537178 original size:30 final size:28
Alignment explanation
Indices: 6537121--6537178 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
6537111 TAATTATATG
* *
6537121 TTTATAAATTAATTAGTTAACTAATTTA
1 TTTATAAAATAATTAATTAACTAATTTA
*
6537149 TTTATAAAATAATTTAAATTAATTAATTTA
1 TTTATAAAATAA-TT-AATTAACTAATTTA
6537179 ATTTTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.44
29 2 0.08
30 12 0.48
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TTTATAAAATAATTAATTAACTAATTTA
Found at i:6538703 original size:19 final size:20
Alignment explanation
Indices: 6538679--6538736 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 20
6538669 GAGATTTTAA
*
6538679 TTATTACTA-AATAATAAAT
1 TTATTAATATAATAATAAAT
*
6538698 TTATTAATATAAT-ATATAT
1 TTATTAATATAATAATAAAT
*
6538717 TTATTAATATAATATTAAAT
1 TTATTAATATAATAATAAAT
6538737 AAATAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 26 0.79
20 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTATTAATATAATAATAAAT
Found at i:6541167 original size:22 final size:22
Alignment explanation
Indices: 6541140--6541191 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
6541130 AATATGTAAA
* *
6541140 AAAATTAAAATATAAATTAATT
1 AAAATTAAAATAAAAACTAATT
* *
6541162 ACAATTAAAATAAAAACTACTT
1 AAAATTAAAATAAAAACTAATT
6541184 AAAATTAA
1 AAAATTAA
6541192 TTAAATCTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTAAAATAAAAACTAATT
Found at i:6552108 original size:16 final size:16
Alignment explanation
Indices: 6552087--6552124 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
6552077 TAGCTCTAAT
6552087 GATTTT-TTGAATCCTA
1 GATTTTGTT-AATCCTA
6552103 GATTTTGTTAATCCTA
1 GATTTTGTTAATCCTA
6552119 GTATTT
1 G-ATTT
6552125 ACAGACTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.53
Consensus pattern (16 bp):
GATTTTGTTAATCCTA
Found at i:6558481 original size:26 final size:27
Alignment explanation
Indices: 6558425--6558483 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
6558415 AAAATTTGAA
* *
6558425 TAAGTTTTAATTTTTTTATTTATGTTTAAT
1 TAAGTTTTAATTTTTTTATTCA---TAAAT
6558455 TAAGTTTTAATTTTTTTATTCA-AAAT
1 TAAGTTTTAATTTTTTTATTCATAAAT
6558481 TAA
1 TAA
6558484 ATAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (27 bp):
TAAGTTTTAATTTTTTTATTCATAAAT
Found at i:6567906 original size:4 final size:4
Alignment explanation
Indices: 6567899--6567941 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
6567889 TATATATATA
* * *
6567899 TATG TATG TATG TATG TATG TTTG TATG TATG CATG CATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
6567942 ATGTATATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:6573051 original size:2 final size:2
Alignment explanation
Indices: 6573039--6573082 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
6573029 CAGTCATGAA
* * *
6573039 AT AT AT CT AT AT AT CT AT AT AT CT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6573081 AT
1 AT
6573083 TCAGAAGCCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6573052 original size:8 final size:8
Alignment explanation
Indices: 6573039--6573082 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
6573029 CAGTCATGAA
6573039 ATATATCT
1 ATATATCT
6573047 ATATATCT
1 ATATATCT
6573055 ATATATCT
1 ATATATCT
*
6573063 ATATATAT
1 ATATATCT
*
6573071 ATATATAT
1 ATATATCT
6573079 ATAT
1 ATAT
6573083 TCAGAAGCCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATATCT
Found at i:6580864 original size:85 final size:86
Alignment explanation
Indices: 6580721--6580898 Score: 288
Period size: 85 Copynumber: 2.1 Consensus size: 86
6580711 GCCAGAGTTC
* *
6580721 TAGATAAATTATCAGATGAGCATATGGTCAACATATAAAAGTTCCAGTGATAGTACGAATCTTCT
1 TAGATATACTATCAGATGAGCATATGGTCAACATATAAAAGTTCCAGTGATAGTACGAATCTTCT
* *
6580786 CTAGTATAAATTGTCAAC-TA
66 CAAGCATAAATTGTCAACATA
*
6580806 TAGATATACTATCAGATGAGTATATGGTCAACATATAAAAGTTCCAGTGATAGTACGAATCTTCT
1 TAGATATACTATCAGATGAGCATATGGTCAACATATAAAAGTTCCAGTGATAGTACGAATCTTCT
*
6580871 CAAGCATAAGTTGTCAACATA
66 CAAGCATAAATTGTCAACATA
6580892 TA-ATATA
1 TAGATATA
6580899 TATAGGCACA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 82 0.95
86 4 0.05
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (86 bp):
TAGATATACTATCAGATGAGCATATGGTCAACATATAAAAGTTCCAGTGATAGTACGAATCTTCT
CAAGCATAAATTGTCAACATA
Found at i:6582616 original size:15 final size:16
Alignment explanation
Indices: 6582596--6582628 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6582586 TATATGGACC
6582596 AATCAA-TATCAAAAA
1 AATCAACTATCAAAAA
*
6582611 AATCAACTTTCAAAAA
1 AATCAACTATCAAAAA
6582627 AA
1 AA
6582629 ATATCAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (16 bp):
AATCAACTATCAAAAA
Found at i:6594111 original size:20 final size:20
Alignment explanation
Indices: 6594075--6594112 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6594065 ATTTTATTTT
*
6594075 AATCATATTAATTGTGTATG
1 AATCATATTAATCGTGTATG
6594095 AATCATA-TATATCGTGTA
1 AATCATATTA-ATCGTGTA
6594113 AATAGGTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (20 bp):
AATCATATTAATCGTGTATG
Found at i:6596177 original size:17 final size:17
Alignment explanation
Indices: 6596155--6596208 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
6596145 TAATGAAAGG
6596155 TAATTGTATTATCAGAT
1 TAATTGTATTATCAGAT
* *
6596172 TAATTGTCTTAACA-AT
1 TAATTGTATTATCAGAT
*
6596188 ATTATTGTATTATCAGAT
1 -TAATTGTATTATCAGAT
6596206 TAA
1 TAA
6596209 CAGAAATATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.46
Consensus pattern (17 bp):
TAATTGTATTATCAGAT
Found at i:6602258 original size:49 final size:49
Alignment explanation
Indices: 6602195--6602328 Score: 187
Period size: 49 Copynumber: 2.7 Consensus size: 49
6602185 AAGTTAAAGT
* *
6602195 TCTACATTTAAACTCGTGATAAATATTGCATGATTAGATAGGTTAAGGC
1 TCTAAATTTCAACTCGTGATAAATATTGCATGATTAGATAGGTTAAGGC
* *
6602244 TCTAAATTTCAACTCGTGATAAATATTTCATGATTAGATAGGTTAAGGT
1 TCTAAATTTCAACTCGTGATAAATATTGCATGATTAGATAGGTTAAGGC
* * * * *
6602293 TTTAAATTTCAACTCGTAATAAGTTTTGTATGATTA
1 TCTAAATTTCAACTCGTGATAAATATTGCATGATTA
6602329 AGTATTACGA
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 75 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (49 bp):
TCTAAATTTCAACTCGTGATAAATATTGCATGATTAGATAGGTTAAGGC
Found at i:6602512 original size:24 final size:24
Alignment explanation
Indices: 6602482--6602540 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
6602472 ATACGTCATA
6602482 TACAAAAACATATTACACGTAATG
1 TACAAAAACATATTACACGTAATG
* * *
6602506 TATAAAAACATATTACATGTTATG
1 TACAAAAACATATTACACGTAATG
6602530 TACAAAAACAT
1 TACAAAAACAT
6602541 GTTATAGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.29
Consensus pattern (24 bp):
TACAAAAACATATTACACGTAATG
Found at i:6602669 original size:29 final size:30
Alignment explanation
Indices: 6602619--6602718 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 30
6602609 ATTACATGTC
*
6602619 ATGTTAAAAAAAATATTATTGTTACACGCT
1 ATGTTAAAAAAAATATTGTTGTTACACGCT
** * **
6602649 ATGTT-GGAAAAATGTTGTTGTTACA-TAT
1 ATGTTAAAAAAAATATTGTTGTTACACGCT
6602677 CATGTTAAAAAAAATATTGTTGTTACACGCT
1 -ATGTTAAAAAAAATATTGTTGTTACACGCT
* *
6602708 ATATTCAAAAA
1 ATGTTAAAAAA
6602719 CATTTTATTA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
28 1 0.02
29 21 0.39
30 31 0.57
31 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (30 bp):
ATGTTAAAAAAAATATTGTTGTTACACGCT
Found at i:6602745 original size:59 final size:59
Alignment explanation
Indices: 6602606--6602745 Score: 140
Period size: 59 Copynumber: 2.4 Consensus size: 59
6602596 GATAAAAAAA
* * * * * **
6602606 GTTATTACATGTCATGTTAAAAAAAATATTATTGTTACACGCTATGTTGGAAAAATGTT
1 GTTATTACATATAATGCTAAAAAAAATATTATTGTTACACGCTATATTGCAAAAACATT
* * * *
6602665 GTTGTTACATATCATGTTAAAAAAAATATTGTTGTTACACGCTATATT-CAAAAACATT
1 GTTATTACATATAATGCTAAAAAAAATATTATTGTTACACGCTATATTGCAAAAACATT
*
6602723 -TTATTACACTTTAATGCCTAAAA
1 GTTATTACA-TATAATG-CTAAAA
6602746 TATTGTTGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
57 7 0.10
58 12 0.18
59 49 0.72
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (59 bp):
GTTATTACATATAATGCTAAAAAAAATATTATTGTTACACGCTATATTGCAAAAACATT
Found at i:6603204 original size:20 final size:20
Alignment explanation
Indices: 6603174--6603219 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
6603164 ATAAATATCG
6603174 AAAAGAGAAATA-AAAAAAATT
1 AAAA-AGAAATAGAAAAAAA-T
*
6603195 AAAAAGAAATAGAGAAAAAT
1 AAAAAGAAATAGAAAAAAAT
6603215 AAAAA
1 AAAAA
6603220 ACACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAAAGAAATAGAAAAAAAT
Found at i:6603307 original size:10 final size:10
Alignment explanation
Indices: 6603292--6603322 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
6603282 TTTATCAAAT
6603292 TATAATTAAA
1 TATAATTAAA
6603302 TATAATTAAA
1 TATAATTAAA
*
6603312 AATAATTAAA
1 TATAATTAAA
6603322 T
1 T
6603323 TTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TATAATTAAA
Done.