Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 16 of 19
Found at i:6972315 original size:22 final size:22
Alignment explanation
Indices: 6972290--6972331 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6972280 ATAAACTCTA
6972290 AAAAAAGAAAGA-ACTATATAGG
1 AAAAAA-AAAGACACTATATAGG
6972312 AAAAAAAAAGACACTATATA
1 AAAAAAAAAGACACTATATA
6972332 TGAATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.07, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAAAAAAAGACACTATATAGG
Found at i:6973803 original size:91 final size:91
Alignment explanation
Indices: 6973705--6973889 Score: 307
Period size: 91 Copynumber: 2.0 Consensus size: 91
6973695 CATAATTTGG
*
6973705 ATAGTATATAATCATTGCAATCAAAAAATAATTGAGTGATTTGTTAAGTGTAGACACTTATTTTT
1 ATAGTATATAATCATTGCAATCAAAAAATAATTGAGTGATTTGTTAAGTGAAGACACTTATTTTT
*
6973770 TACCCCAATAATAAATAATAAATAAA
66 TACCCAAATAATAAATAATAAATAAA
** * *
6973796 ATAGTATATAATCATTGCAATTGAGAATTAATTGAGTGATTTGTTAAGTGAAGACACTTATTTTT
1 ATAGTATATAATCATTGCAATCAAAAAATAATTGAGTGATTTGTTAAGTGAAGACACTTATTTTT
*
6973861 TACCCAAATAATAAATAATAAATATA
66 TACCCAAATAATAAATAATAAATAAA
6973887 ATA
1 ATA
6973890 AATAAATCAC
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (91 bp):
ATAGTATATAATCATTGCAATCAAAAAATAATTGAGTGATTTGTTAAGTGAAGACACTTATTTTT
TACCCAAATAATAAATAATAAATAAA
Found at i:6974183 original size:16 final size:18
Alignment explanation
Indices: 6974154--6974192 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
6974144 TCTGCAAAAC
*
6974154 AAAAAATCCTAGTAACTG
1 AAAAAATCCTAGTAACCG
6974172 AAAAAA-CC-AGTAACCG
1 AAAAAATCCTAGTAACCG
6974188 AAAAA
1 AAAAA
6974193 CCCATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.59, C:0.18, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAAAATCCTAGTAACCG
Found at i:6974365 original size:19 final size:19
Alignment explanation
Indices: 6974321--6974367 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
6974311 ACAAACTAGA
*
6974321 AAAAAAAAACCAAAAAAGC
1 AAAAAACAACCAAAAAAGC
*
6974340 AAAAAACAACCGAAAAA-C
1 AAAAAACAACCAAAAAAGC
6974358 AAAGAAACAA
1 AAA-AAACAA
6974368 AAAAGAGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (19 bp):
AAAAAACAACCAAAAAAGC
Found at i:6974381 original size:26 final size:27
Alignment explanation
Indices: 6974324--6974381 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
6974314 AACTAGAAAA
6974324 AAAAAACCAAAAAAGCAAAAAACAACC
1 AAAAAACCAAAAAAGCAAAAAACAACC
* * *
6974351 GAAAAA-CAAAGAAA-CAAAAAAGAGCC
1 AAAAAACCAAA-AAAGCAAAAAACAACC
6974377 AAAAA
1 AAAAA
6974382 CCATTAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.74, C:0.17, G:0.09, T:0.00
Consensus pattern (27 bp):
AAAAAACCAAAAAAGCAAAAAACAACC
Found at i:6975266 original size:3 final size:3
Alignment explanation
Indices: 6975258--6975291 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6975248 AAGGTAGAGC
6975258 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6975292 TATTTAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6976549 original size:12 final size:13
Alignment explanation
Indices: 6976531--6976562 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
6976521 TTTTAATTTG
6976531 TAAATAAAATAAA
1 TAAATAAAATAAA
6976544 -AAATAAAATAAA
1 TAAATAAAATAAA
6976556 TAAATAA
1 TAAATAA
6976563 TGATTAGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:6980835 original size:18 final size:18
Alignment explanation
Indices: 6980789--6980836 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
6980779 ATATGGATGC
*
6980789 ATAAATTTAAAAAATTAA
1 ATAAAATTAAAAAATTAA
* * *
6980807 AAAAAATTTAAAAATTTGA
1 ATAAAA-TTAAAAAATTAA
6980826 ATAAAATTAAA
1 ATAAAATTAAA
6980837 CGAAATTTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
ATAAAATTAAAAAATTAA
Found at i:6980850 original size:29 final size:27
Alignment explanation
Indices: 6980789--6980853 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 27
6980779 ATATGGATGC
6980789 ATAAATTTAAAAAATTAAAAAAAATTT
1 ATAAATTTAAAAAATTAAAAAAAATTT
* **
6980816 AAAAATTTGAATAAAATTAAACGAAATTT
1 ATAAATTT-AA-AAAATTAAAAAAAATTT
6980845 ATAAATTTA
1 ATAAATTTA
6980854 TTTCATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 7 0.22
28 3 0.09
29 22 0.69
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
ATAAATTTAAAAAATTAAAAAAAATTT
Found at i:6986816 original size:2 final size:2
Alignment explanation
Indices: 6986799--6986839 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
6986789 TAGATCTAGT
6986799 TA TA GTA TA T- TA TA 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 TA TA TA TA TA TA TA T
6986840 GTGAACCACG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6987419 original size:79 final size:77
Alignment explanation
Indices: 6987328--6987522 Score: 214
Period size: 79 Copynumber: 2.5 Consensus size: 77
6987318 TTATTATACA
* *
6987328 TCATATACAAAAATATATTACACGTCATAGTTAAAAAAAGTTATTACA--TACTATGTTGAAAAA
1 TCATATACAAAAATATGTTACACGTCATAGTTAAAAAAAGTTATTACACGT-C-ATGTAGAAAAA
6987391 AAATATTAATTACATG
64 AAA-A-TAATTACATG
* ** * *
6987407 TTATATACAAAAATATGTTACACACCATGGTTAAAAAAAGTTGTTACACGTCATGTAGAAAAAAA
1 TCATATACAAAAATATGTTACACGTCATAGTTAAAAAAAGTTATTACACGTCATGTAGAAAAAAA
**
6987472 AATCGTTACATG
66 AATAATTACATG
** * * *
6987484 TCATATATGAAAACATGTTACATGTCATATTTAAAAAAA
1 TCATATACAAAAATATGTTACACGTCATAGTTAAAAAAA
6987523 ATATTATTGT
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
77 38 0.40
78 1 0.01
79 55 0.57
80 1 0.01
81 1 0.01
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.31
Consensus pattern (77 bp):
TCATATACAAAAATATGTTACACGTCATAGTTAAAAAAAGTTATTACACGTCATGTAGAAAAAAA
AATAATTACATG
Found at i:6987469 original size:27 final size:28
Alignment explanation
Indices: 6987439--6987496 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
6987429 CACCATGGTT
* * *
6987439 AAAAAAAGTTGTTACACGTCATGTA-GA
1 AAAAAAAATCGTTACACGTCATATATGA
*
6987466 AAAAAAAATCGTTACATGTCATATATGA
1 AAAAAAAATCGTTACACGTCATATATGA
6987494 AAA
1 AAA
6987497 CATGTTACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 21 0.81
28 5 0.19
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (28 bp):
AAAAAAAATCGTTACACGTCATATATGA
Found at i:6987520 original size:24 final size:25
Alignment explanation
Indices: 6987467--6987522 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
6987457 TCATGTAGAA
6987467 AAAAAAATCGTTACATGTCATATAT
1 AAAAAAATCGTTACATGTCATATAT
* * *
6987492 GAAAACAT-GTTACATGTCATATTT
1 AAAAAAATCGTTACATGTCATATAT
6987516 AAAAAAA
1 AAAAAAA
6987523 ATATTATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (25 bp):
AAAAAAATCGTTACATGTCATATAT
Found at i:6987578 original size:30 final size:30
Alignment explanation
Indices: 6987499--6987585 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
6987489 TATGAAAACA
* *
6987499 TGTTACATGTCATATTTAAAAAAAATATTAT
1 TGTTACACGTCATGTTTAAAAAAAA-ATTAT
* *
6987530 TGTTACACATTATG-TTAAAAAAAAATTAT
1 TGTTACACGTCATGTTTAAAAAAAAATTAT
* *
6987559 TGTTATAGGTCATGTTTAAAAAAAAAT
1 TGTTACACGTCATGTTTAAAAAAAAAT
6987586 CGTTACACTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 15 0.32
30 22 0.47
31 10 0.21
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (30 bp):
TGTTACACGTCATGTTTAAAAAAAAATTAT
Found at i:6989434 original size:17 final size:17
Alignment explanation
Indices: 6989414--6989446 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6989404 AAATTGATAG
6989414 AAAATA-AAATGAAAAAC
1 AAAATAGAAA-GAAAAAC
6989431 AAAATAGAAAGAAAAA
1 AAAATAGAAAGAAAAA
6989447 GAAGAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAAGAAAAAC
Found at i:7000153 original size:2 final size:2
Alignment explanation
Indices: 7000146--7000170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7000136 GTTCAATTAA
7000146 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
7000171 GAGAGAGAGA
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:7001035 original size:2 final size:2
Alignment explanation
Indices: 7001028--7001056 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7001018 TTGAGCCGCC
7001028 TA 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 TA T
7001057 TTTCTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7018720 original size:21 final size:21
Alignment explanation
Indices: 7018696--7018736 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7018686 CCTTCTGCCA
7018696 CATCTTCCATCA-TTTCTTCTC
1 CATCTT-CATCACTTTCTTCTC
*
7018717 CATCTTCTTCACTTTCTTCT
1 CATCTTCATCACTTTCTTCT
7018737 AGTGGCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.12, C:0.37, G:0.00, T:0.51
Consensus pattern (21 bp):
CATCTTCATCACTTTCTTCTC
Found at i:7020040 original size:48 final size:48
Alignment explanation
Indices: 7019967--7020083 Score: 148
Period size: 48 Copynumber: 2.4 Consensus size: 48
7019957 GTAAGACTCT
* *
7019967 ACTTGTATTTG-TTATGTTTATGTTGT-CGAAGTATTGACTCTTTGTTTACA
1 ACTTGTA-TTGATT-TG-TTATGTTGTAC-AAGTATTGACTCCTGGTTTACA
**
7020017 ACTTGTATTGATTTGTTATGTTGTACAAGTATTGACTCCTGGTTTATG
1 ACTTGTATTGATTTGTTATGTTGTACAAGTATTGACTCCTGGTTTACA
7020065 ACTTGTATTGATTTGTTAT
1 ACTTGTATTGATTTGTTAT
7020084 TCTGTGGAGT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
48 46 0.75
49 6 0.10
50 9 0.15
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (48 bp):
ACTTGTATTGATTTGTTATGTTGTACAAGTATTGACTCCTGGTTTACA
Found at i:7026572 original size:53 final size:53
Alignment explanation
Indices: 7026508--7026611 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
7026498 CTACAGAAGC
* *
7026508 TGCAGCACCAATTTCCCAGCGCTGTAGCGCTGCCAAACTCCC-TTCCCAGCAGT
1 TGCAGCACCAATTTCCCAGCGCTGCAGCGCTGCCAAACGCCCATT-CCAGCAGT
* *
7026561 TGCAGCGCCAATTTCCCAGTGCTGCAGCGCTGCCAAACGCCCATTCCAGCA
1 TGCAGCACCAATTTCCCAGCGCTGCAGCGCTGCCAAACGCCCATTCCAGCA
7026612 ATTCCAGTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 44 0.96
54 2 0.04
ACGTcount: A:0.21, C:0.39, G:0.20, T:0.19
Consensus pattern (53 bp):
TGCAGCACCAATTTCCCAGCGCTGCAGCGCTGCCAAACGCCCATTCCAGCAGT
Found at i:7064108 original size:30 final size:30
Alignment explanation
Indices: 7064072--7064133 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
7064062 ATCAGATAAT
7064072 ACAAACAGGAAAAAGTAAAATACTTCTACA
1 ACAAACAGGAAAAAGTAAAATACTTCTACA
7064102 ACAAACAGGAAAAAGTAAAATACTTCTACA
1 ACAAACAGGAAAAAGTAAAATACTTCTACA
7064132 AC
1 AC
7064134 TTGCACCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.56, C:0.18, G:0.10, T:0.16
Consensus pattern (30 bp):
ACAAACAGGAAAAAGTAAAATACTTCTACA
Found at i:7067971 original size:6 final size:6
Alignment explanation
Indices: 7067962--7067986 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7067952 TAAATAGAAA
7067962 CAAGCT CAAGCT CAAGCT CAAGCT C
1 CAAGCT CAAGCT CAAGCT CAAGCT C
7067987 GTCTCCAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.16, T:0.16
Consensus pattern (6 bp):
CAAGCT
Found at i:7090431 original size:7 final size:7
Alignment explanation
Indices: 7090419--7090447 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
7090409 TTGGTGGTGA
7090419 TGAAAAT
1 TGAAAAT
7090426 TGAAAAT
1 TGAAAAT
7090433 TGAAAAT
1 TGAAAAT
7090440 TGAAAAT
1 TGAAAAT
7090447 T
1 T
7090448 TGTTAGGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (7 bp):
TGAAAAT
Found at i:7097281 original size:24 final size:25
Alignment explanation
Indices: 7097247--7097294 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
7097237 AGTAGAATCT
7097247 ATTTAAATTAA-AATAAAATATAAAA
1 ATTTAAATTAAGAATAAAA-ATAAAA
*
7097272 ATTT-AATTAAGTATAAAAATAAA
1 ATTTAAATTAAGAATAAAAATAAA
7097295 CAAATATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
ATTTAAATTAAGAATAAAAATAAAA
Found at i:7103557 original size:72 final size:70
Alignment explanation
Indices: 7103424--7103559 Score: 191
Period size: 71 Copynumber: 1.9 Consensus size: 70
7103414 ACTAGTAGGC
* * * *
7103424 AGCTGATCCTACAAACCTTCTTCTTTACTTGTATGCTTGTTAAAAAACCATAGATAATGGATAAT
1 AGCTGATCCTACAAACCCTCTGCTTTACTTGTATGCTTCTCAAAAAACCATAGATAATGGATAAT
7103489 GTGAT
66 GTGAT
* **
7103494 AGCTGATCCTACAGTACCCTCTGCTTTACTTGTATGCTTCTCATAAAAACCATAGATGTTGGATA
1 AGCTGATCCTACA-AACCCTCTGCTTTACTTGTATGCTTCTCA-AAAAACCATAGATAATGGATA
7103559 A
64 A
7103560 CATGAAAAGC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 13 0.23
71 24 0.42
72 20 0.35
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (70 bp):
AGCTGATCCTACAAACCCTCTGCTTTACTTGTATGCTTCTCAAAAAACCATAGATAATGGATAAT
GTGAT
Found at i:7122660 original size:20 final size:22
Alignment explanation
Indices: 7122622--7122665 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
7122612 GTTGCCCATG
*
7122622 TTATTAGAGTTTTTATTTTTTA
1 TTATTAGAGTTTTTATTTTATA
*
7122644 TTATTA-AG-TTTTGTTTTATA
1 TTATTAGAGTTTTTATTTTATA
7122664 TT
1 TT
7122666 GTGAGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 2 0.10
22 6 0.30
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (22 bp):
TTATTAGAGTTTTTATTTTATA
Found at i:7125464 original size:18 final size:18
Alignment explanation
Indices: 7125443--7125502 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
7125433 CCTTTCAGGC
7125443 TGCCTCGATCGCCACGAT
1 TGCCTCGATCGCCACGAT
* *
7125461 TGCCTCCA-CTGCCACGGT
1 TGCCTCGATC-GCCACGAT
* *
7125479 TGCCTCCG-TTGCCACCAT
1 TGCCT-CGATCGCCACGAT
7125497 TGCCTC
1 TGCCTC
7125503 CAATGCCACC
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.06
18 30 0.91
19 1 0.03
ACGTcount: A:0.12, C:0.43, G:0.20, T:0.25
Consensus pattern (18 bp):
TGCCTCGATCGCCACGAT
Found at i:7125483 original size:36 final size:36
Alignment explanation
Indices: 7125443--7125511 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
7125433 CCTTTCAGGC
* *
7125443 TGCCT-CGATCGCCACGATTGCCTCCACTGCCACGGT
1 TGCCTCCG-TCGCCACCATTGCCTCCAATGCCACGGT
*
7125479 TGCCTCCGTTGCCACCATTGCCTCCAATGCCAC
1 TGCCTCCGTCGCCACCATTGCCTCCAATGCCAC
7125512 CATTGCCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 27 0.93
37 2 0.07
ACGTcount: A:0.14, C:0.43, G:0.19, T:0.23
Consensus pattern (36 bp):
TGCCTCCGTCGCCACCATTGCCTCCAATGCCACGGT
Found at i:7125503 original size:18 final size:18
Alignment explanation
Indices: 7125453--7125518 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
7125443 TGCCTCGATC
* *
7125453 GCCACGATTGCCTCCACT
1 GCCACCATTGCCTCCAAT
** **
7125471 GCCACGGTTGCCTCCGTT
1 GCCACCATTGCCTCCAAT
7125489 GCCACCATTGCCTCCAAT
1 GCCACCATTGCCTCCAAT
7125507 GCCACCATTGCC
1 GCCACCATTGCC
7125519 CTTCTCAGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.15, C:0.44, G:0.18, T:0.23
Consensus pattern (18 bp):
GCCACCATTGCCTCCAAT
Found at i:7125518 original size:9 final size:9
Alignment explanation
Indices: 7125453--7125518 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 9
7125443 TGCCTCGATC
*
7125453 GCCACGATT
1 GCCACCATT
* *
7125462 GCCTCCACT
1 GCCACCATT
**
7125471 GCCACGGTT
1 GCCACCATT
* *
7125480 GCCTCCGTT
1 GCCACCATT
7125489 GCCACCATT
1 GCCACCATT
* *
7125498 GCCTCCAAT
1 GCCACCATT
7125507 GCCACCATT
1 GCCACCATT
7125516 GCC
1 GCC
7125519 CTTCTCAGAA
Statistics
Matches: 42, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.15, C:0.44, G:0.18, T:0.23
Consensus pattern (9 bp):
GCCACCATT
Found at i:7128938 original size:24 final size:24
Alignment explanation
Indices: 7128886--7128938 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
7128876 CAAATTATAA
*
7128886 ATTAAAAAATAATTGATTTTAAAT
1 ATTAAAAAATAATTGATTTGAAAT
7128910 A-TAAAATAATAATT-A-TTGAAAT
1 ATTAAAA-AATAATTGATTTGAAAT
7128932 CATTAAA
1 -ATTAAA
7128939 TATATATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
22 6 0.24
23 7 0.28
24 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTAAAAAATAATTGATTTGAAAT
Found at i:7132485 original size:16 final size:16
Alignment explanation
Indices: 7132464--7132518 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
7132454 GAATTCAAGT
*
7132464 TTTCAAGCTTGAAAGC
1 TTTCAAGCTTAAAAGC
* **
7132480 TTTCAAGGTTTATTAG-
1 TTTCAA-GCTTAAAAGC
7132496 TTTCAAGCTTAAAAGC
1 TTTCAAGCTTAAAAGC
7132512 TTTCAAG
1 TTTCAAG
7132519 GGTTGTTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 6 0.20
16 19 0.63
17 5 0.17
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (16 bp):
TTTCAAGCTTAAAAGC
Found at i:7132500 original size:32 final size:32
Alignment explanation
Indices: 7132464--7132556 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 32
7132454 GAATTCAAGT
7132464 TTTCAAGCTTGAAAGCTTTCAAGGTTTATTAG
1 TTTCAAGCTTGAAAGCTTTCAAGGTTTATTAG
* * * *
7132496 TTTCAAGCTTAAAAGCTTTCAAGGGTTGTTGG
1 TTTCAAGCTTGAAAGCTTTCAAGGTTTATTAG
* * * *
7132528 TTTTAGGCATGAAAGTTTTCAAGGTTTAT
1 TTTCAAGCTTGAAAGCTTTCAAGGTTTAT
7132557 CGATTTCAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (32 bp):
TTTCAAGCTTGAAAGCTTTCAAGGTTTATTAG
Found at i:7132651 original size:30 final size:30
Alignment explanation
Indices: 7132617--7132685 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
7132607 TTTCTTGATT
**
7132617 TTTCACTCTTGGTTTAGTGTTTAGG-CTAGG
1 TTTCACTCTCAGTTTAGTGTTTAGGTC-AGG
*
7132647 TTTCAATCTCAGTTTAGTGTTTAGGTCAGG
1 TTTCACTCTCAGTTTAGTGTTTAGGTCAGG
7132677 TTTCACTCT
1 TTTCACTCT
7132686 AGGCATACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.16, C:0.16, G:0.22, T:0.46
Consensus pattern (30 bp):
TTTCACTCTCAGTTTAGTGTTTAGGTCAGG
Found at i:7133944 original size:27 final size:26
Alignment explanation
Indices: 7133903--7133957 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
7133893 TTAAAAATTA
7133903 TTTTTTTATACAAATTTCATATTAACTT
1 TTTTTTTATACAAA--TCATATTAACTT
*
7133931 TTTTTTTA-ATAAATCATATTAACTT
1 TTTTTTTATACAAATCATATTAACTT
7133956 TT
1 TT
7133958 AAGTTAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 14 0.54
27 4 0.15
28 8 0.31
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTTTTATACAAATCATATTAACTT
Found at i:7153471 original size:72 final size:71
Alignment explanation
Indices: 7153386--7153529 Score: 182
Period size: 72 Copynumber: 2.0 Consensus size: 71
7153376 TATACATATG
* * * * *
7153386 AAAAAAAATTATTAGAGATCATTAAATGCATATTACCATTAATTGATTGCAAACAGAGA-AAATA
1 AAAAAAAAGTATTAAAGATCATTAAATACATATTACCATTAATTAATTGAAAACAG-GATAAATA
7153450 GTTGAGA
65 GTTGAGA
* * * *
7153457 AAAAAAAAGGTATTAAAGATCATTAAATATATATTATCATTACTTAATTGAAAATAGGATAAATA
1 AAAAAAAA-GTATTAAAGATCATTAAATACATATTACCATTAATTAATTGAAAACAGGATAAATA
7153522 GTTGAGA
65 GTTGAGA
7153529 A
1 A
7153530 TTAATAATAT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
71 10 0.16
72 52 0.84
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (71 bp):
AAAAAAAAGTATTAAAGATCATTAAATACATATTACCATTAATTAATTGAAAACAGGATAAATAG
TTGAGA
Found at i:7156204 original size:10 final size:10
Alignment explanation
Indices: 7156191--7156223 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
7156181 TATATATTTT
7156191 TATAAATATA
1 TATAAATATA
7156201 TATAAATATA
1 TATAAATATA
7156211 TATAAATATA
1 TATAAATATA
7156221 TAT
1 TAT
7156224 TTAATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TATAAATATA
Found at i:7161357 original size:46 final size:46
Alignment explanation
Indices: 7161290--7161400 Score: 222
Period size: 46 Copynumber: 2.4 Consensus size: 46
7161280 CCAGGTAATT
7161290 AACCAGATGAGTTGATTATGCAGCAATCTTAAAGAAAGAAAAAAAC
1 AACCAGATGAGTTGATTATGCAGCAATCTTAAAGAAAGAAAAAAAC
7161336 AACCAGATGAGTTGATTATGCAGCAATCTTAAAGAAAGAAAAAAAC
1 AACCAGATGAGTTGATTATGCAGCAATCTTAAAGAAAGAAAAAAAC
7161382 AACCAGATGAGTTGATTAT
1 AACCAGATGAGTTGATTAT
7161401 AGATATACAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.22
Consensus pattern (46 bp):
AACCAGATGAGTTGATTATGCAGCAATCTTAAAGAAAGAAAAAAAC
Found at i:7166335 original size:22 final size:23
Alignment explanation
Indices: 7166296--7166338 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
7166286 AAGAATTTGA
7166296 TTGTTGTTCCCTTCATTTTTTTT
1 TTGTTGTTCCCTTCATTTTTTTT
*
7166319 TTGTT-TT-CCTTCAATTTTTT
1 TTGTTGTTCCCTTCATTTTTTT
7166339 CTTAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (23 bp):
TTGTTGTTCCCTTCATTTTTTTT
Found at i:7181425 original size:33 final size:32
Alignment explanation
Indices: 7181381--7181509 Score: 134
Period size: 33 Copynumber: 3.9 Consensus size: 32
7181371 ACACTGCTGC
* *
7181381 ATCCTCATTAGGTCCAACCTCACTTGGAACTAT
1 ATCCTCCTTAGGTCCAACCTCACTTGGAAC-AA
*
7181414 ATCCTCCTTAGGTTCAACCTCACTTGGAACCAA
1 ATCCTCCTTAGGTCCAACCTCACTTGGAA-CAA
* *
7181447 ATCCTCCTTCA-GTCCAATCTCACTTGGAAACAC
1 ATCCTCCTT-AGGTCCAACCTCACTTGG-AACAA
*** *
7181480 ATCCTCGAGAGGTTCAACCTCACTTGGAAC
1 ATCCTCCTTAGGTCCAACCTCACTTGGAAC
7181510 CCCAACAGCC
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
32 4 0.05
33 73 0.90
34 4 0.05
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (32 bp):
ATCCTCCTTAGGTCCAACCTCACTTGGAACAA
Found at i:7183142 original size:18 final size:18
Alignment explanation
Indices: 7183119--7183153 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7183109 ATTTATTTTT
7183119 ATTAAT-AAATTATTTATA
1 ATTAATGAAA-TATTTATA
7183137 ATTAATGAAATATTTAT
1 ATTAATGAAATATTTAT
7183154 TAAAATTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATTAATGAAATATTTATA
Found at i:7185371 original size:88 final size:86
Alignment explanation
Indices: 7185223--7185397 Score: 242
Period size: 88 Copynumber: 2.0 Consensus size: 86
7185213 ATGTATTTAC
* * *
7185223 ATTAAAATTTAAAAATTATTGCATTTTTAACATTTAAATTGGAAATTTTTATATAATAACTCTTG
1 ATTAAAATTTAAAAATTATTACATTTTAAACATTTAAATTGGAAATATTTATATAATAACTCTTG
*
7185288 TTAGCTACTTTTAAGTAGATAT
66 TTAGCTA-GTTTAAGTAGATAT
* * * * *
7185310 ATTAAAATTTAAAAATATTTTACGTTTTAAACATTTAAATTTGAAATATTTATGTAATAACTTTT
1 ATTAAAATTTAAAAAT-TATTACATTTTAAACATTTAAATTGGAAATATTTATATAATAACTCTT
*
7185375 GTTGGCTAGTTTAAGTAGATAT
65 GTTAGCTAGTTTAAGTAGATAT
7185397 A
1 A
7185398 GATTACTTTA
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
87 30 0.39
88 47 0.61
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (86 bp):
ATTAAAATTTAAAAATTATTACATTTTAAACATTTAAATTGGAAATATTTATATAATAACTCTTG
TTAGCTAGTTTAAGTAGATAT
Found at i:7185621 original size:30 final size:29
Alignment explanation
Indices: 7185540--7185636 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
7185530 AAAAAAATTT
7185540 AAATAAGCTTTTATATTTTTATATTTAGGTC
1 AAATAAGCTTTTATATTTTTAT-TTTA-GTC
** * *
7185571 -AATCAAATTTTTGTACTTTTATTTTGAGTC
1 AAAT-AAGCTTTTATATTTTTATTTT-AGTC
*
7185601 AAATAAGCTTTTATATTTTTATTTTAAATC
1 AAATAAGCTTTTATATTTTTATTTT-AGTC
7185631 AAATAA
1 AAATAA
7185637 ACCCTTATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
30 35 0.66
31 18 0.34
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (29 bp):
AAATAAGCTTTTATATTTTTATTTTAGTC
Found at i:7185645 original size:30 final size:30
Alignment explanation
Indices: 7185587--7185645 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
7185577 ATTTTTGTAC
* * * **
7185587 TTTTATTTTGAGTCAAATAAGCTTTTATAT
1 TTTTATTTTAAATCAAATAAACCCTTATAT
7185617 TTTTATTTTAAATCAAATAAACCCTTATA
1 TTTTATTTTAAATCAAATAAACCCTTATA
7185646 ACTAATTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (30 bp):
TTTTATTTTAAATCAAATAAACCCTTATAT
Found at i:7196581 original size:28 final size:28
Alignment explanation
Indices: 7196550--7196604 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
7196540 AAAATTGAGC
*
7196550 TAGAATTTCACATTCTATATCTTGCTAG
1 TAGAATTTCACATTCTATAACTTGCTAG
7196578 TAGAATTTCACATTCTATAACTTGCTA
1 TAGAATTTCACATTCTATAACTTGCTA
7196605 CTTGAACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (28 bp):
TAGAATTTCACATTCTATAACTTGCTAG
Found at i:7204884 original size:20 final size:20
Alignment explanation
Indices: 7204859--7204922 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
7204849 TAATAATTTC
7204859 ATTTTTATAAAAATTTTAAA
1 ATTTTTATAAAAATTTTAAA
* * *
7204879 ATTTTTGTAACATATTTT--G
1 ATTTTTATAA-AAATTTTAAA
* *
7204898 ATTTTTTTTAAAATTTTAAA
1 ATTTTTATAAAAATTTTAAA
7204918 ATTTT
1 ATTTT
7204923 ATCCTTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 14 0.41
21 6 0.18
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (20 bp):
ATTTTTATAAAAATTTTAAA
Found at i:7231419 original size:40 final size:40
Alignment explanation
Indices: 7231372--7231568 Score: 116
Period size: 40 Copynumber: 4.7 Consensus size: 40
7231362 AAAAATATTT
7231372 TATAATATTATAATTAAAATAAAAATATTAAAATAAAATA
1 TATAATATTATAATTAAAATAAAAATATTAAAATAAAATA
* * *
7231412 TATAATATAAAAATTAAAA-AATATAATATAATATAATATAAAAAA
1 TATAATATTATAATTAAAATAA-A-AATAT--TA-AA-ATAAAATA
* * *
7231457 T-TAAAATTGAGATAA-TATAGATAAAATAAATTAAAATAAAATA
1 TATAATATT---ATAATTA-AAATAAAA-ATATTAAAATAAAATA
* * * * *
7231500 TATAATATAAAATATTATATTAAAAA-ATAAAAATAAAA-A
1 TATAATATTATA-ATTAAAATAAAAATATTAAAATAAAATA
* *
7231539 TATAAAATTATAATAATAAATAAAATATAT
1 TATAATATTATAATTA-AAATAAAA-ATAT
7231569 GATTCTTAAA
Statistics
Matches: 117, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
38 3 0.03
39 18 0.15
40 30 0.26
41 10 0.09
42 6 0.05
43 12 0.10
44 14 0.12
45 10 0.09
46 3 0.03
47 9 0.08
48 2 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (40 bp):
TATAATATTATAATTAAAATAAAAATATTAAAATAAAATA
Found at i:7231427 original size:26 final size:26
Alignment explanation
Indices: 7231389--7231563 Score: 124
Period size: 27 Copynumber: 6.3 Consensus size: 26
7231379 TTATAATTAA
7231389 AATA-AAAATATTAAAATAAAATATAT
1 AATATAAAA-ATTAAAATAAAATATAT
7231415 AATATAAAAATTAAAAAATATAATATAATAT
1 AATATAAAAATT--AAAATA-AA-AT-ATAT
* *
7231446 AATATAAAAAATTAAAATTGAGATAATAT
1 AATAT-AAAAATTAAAA-TAAAAT-ATAT
*
7231475 AGATAAAATAAATTAAAATAAAATATAT
1 A-ATATAA-AAATTAAAATAAAATATAT
* * *
7231503 AATATAAAATATTATATTAAAAAATA-
1 AATATAAAA-ATTAAAATAAAATATAT
* *
7231529 AAAATAAAAATATAAAATTATAATA-AT
1 AATATAAAAAT-TAAAA-TAAAATATAT
7231556 AA-ATAAAA
1 AATATAAAA
7231564 TATATGATTC
Statistics
Matches: 121, Mismatches: 14, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
25 2 0.02
26 27 0.22
27 29 0.24
28 11 0.09
29 16 0.13
30 19 0.16
31 10 0.08
32 7 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (26 bp):
AATATAAAAATTAAAATAAAATATAT
Found at i:7231495 original size:24 final size:23
Alignment explanation
Indices: 7231429--7231510 Score: 58
Period size: 24 Copynumber: 3.3 Consensus size: 23
7231419 TAAAAATTAA
*
7231429 AAAATATAATATAATATAATATAA-
1 AAAATA-AAT-TAAAATAATATAAT
* *
7231453 AAAATTAAAATTGAGATAATATAGAT
1 AAAA-T-AAATTAAAATAATATA-AT
*
7231479 AAAATAAATTAAAATAAAATATAT
1 AAAATAAATTAAAATAATATA-AT
*
7231503 AATATAAA
1 AAAATAAA
7231511 ATATTATATT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 36 0.77
25 6 0.13
26 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATAAATTAAAATAATATAAT
Found at i:7231508 original size:7 final size:7
Alignment explanation
Indices: 7231492--7231567 Score: 57
Period size: 7 Copynumber: 10.4 Consensus size: 7
7231482 ATAAATTAAA
7231492 ATAAAAT
1 ATAAAAT
*
7231499 ATATAAT
1 ATAAAAT
7231506 ATAAAAT
1 ATAAAAT
* *
7231513 ATTATAT
1 ATAAAAT
*
7231520 -TAAAAA
1 ATAAAAT
7231526 ATAAAA-
1 ATAAAAT
7231532 ATAAAAAT
1 AT-AAAAT
7231540 ATAAAATT
1 ATAAAA-T
7231548 ATAATAAT
1 ATAA-AAT
7231556 AAATAAAAT
1 --ATAAAAT
7231565 ATA
1 ATA
7231568 TGATTCTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
6 5 0.09
7 33 0.60
8 8 0.15
9 5 0.09
10 4 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATAAAAT
Found at i:7231525 original size:14 final size:14
Alignment explanation
Indices: 7231389--7231568 Score: 90
Period size: 15 Copynumber: 13.0 Consensus size: 14
7231379 TTATAATTAA
7231389 AATA-AAAATAT-T
1 AATATAAAATATAT
*
7231401 AAAATAAAATATAT
1 AATATAAAATATAT
* *
7231415 AATATAAAAATTAAAA
1 AATAT-AAAA-TATAT
*
7231431 AATATAATATAATAT
1 AATATAAAAT-ATAT
*
7231446 AATATAAAAAAT-T
1 AATATAAAATATAT
* * *
7231459 AAAATTGAGATA-AT
1 AATA-TAAAATATAT
* *
7231473 ATAGATAAAATAAATT
1 A-ATATAAAATATA-T
*
7231489 AAAATAAAATATAT
1 AATATAAAATATAT
7231503 AATATAAAATATTAT
1 AATATAAAATA-TAT
* * *
7231518 ATTAAAAAATA-AA
1 AATATAAAATATAT
*
7231531 AATA-AAAATATAA
1 AATATAAAATATAT
*
7231544 AAT-TATAATA-AT
1 AATATAAAATATAT
7231556 AA-ATAAAATATAT
1 AATATAAAATATAT
7231569 GATTCTTAAA
Statistics
Matches: 127, Mismatches: 26, Indels: 29
0.70 0.14 0.16
Matches are distributed among these distances:
12 18 0.14
13 27 0.21
14 30 0.24
15 42 0.33
16 10 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (14 bp):
AATATAAAATATAT
Found at i:7231549 original size:32 final size:35
Alignment explanation
Indices: 7231375--7231568 Score: 121
Period size: 32 Copynumber: 5.7 Consensus size: 35
7231365 AATATTTTAT
* *
7231375 AATATTATAAT-TAAAATAAAAATATTAAA-ATAA
1 AATATTATAATAAAAAATAAAAATATAAAATATAA
*
7231408 AATA-TATAATATAAAAATTAAAAA-ATATAATAT--
1 AATATTATAATA-AAAAA-TAAAAATATAAAATATAA
* *
7231441 AATATAAT-ATAAAAAATTAAAAT-TGAGATAATATAGA
1 AATATTATAATAAAAAATAAAAATAT-A-A-AATATA-A
* * *
7231478 TAA-AATA-AAT-TAAAAT-AAAATATATAATATAA
1 -AATATTATAATAAAAAATAAAAATATAAAATATAA
*
7231510 AATATTATATTAAAAAATAAAAATA-AAAATAT-A
1 AATATTATAATAAAAAATAAAAATATAAAATATAA
*
7231543 AA-ATTATAATAATAAATAAAATATAT
1 AATATTATAATAAAAAATAAAA-ATAT
7231569 GATTCTTAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 41
0.69 0.09 0.23
Matches are distributed among these distances:
31 8 0.06
32 33 0.27
33 25 0.20
34 26 0.21
35 20 0.16
36 6 0.05
37 4 0.03
38 2 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (35 bp):
AATATTATAATAAAAAATAAAAATATAAAATATAA
Found at i:7231799 original size:15 final size:15
Alignment explanation
Indices: 7231779--7231824 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
7231769 TAATATTTTT
7231779 TTTATAATAATATTA
1 TTTATAATAATATTA
*
7231794 TTTATAATCATATTA
1 TTTATAATAATATTA
*
7231809 TTTATAATTATATTA
1 TTTATAATAATATTA
7231824 T
1 T
7231825 ATTAAACGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATAATAATATTA
Found at i:7231822 original size:12 final size:14
Alignment explanation
Indices: 7231767--7231824 Score: 71
Period size: 15 Copynumber: 3.9 Consensus size: 14
7231757 TACCAAACAC
* *
7231767 TATAATATTTTTTT
1 TATAATATATTATT
7231781 TATAATAATATTATT
1 TATAAT-ATATTATT
7231796 TATAATCATATTATT
1 TATAAT-ATATTATT
7231811 TATAATTATATTAT
1 TATAA-TATATTAT
7231825 ATTAAACGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
14 6 0.15
15 32 0.82
16 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TATAATATATTATT
Found at i:7240098 original size:23 final size:23
Alignment explanation
Indices: 7240053--7240107 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
7240043 ATTTTTTAAA
*
7240053 ATTAAATTTGATAAATTTATTAT
1 ATTATATTTGATAAATTTATTAT
* * *
7240076 TTTTTATTT-ATATATTTATTTAT
1 ATTATATTTGATAAATTTA-TTAT
7240099 ATTATATTT
1 ATTATATTT
7240108 TTTAATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTATATTTGATAAATTTATTAT
Found at i:7240104 original size:15 final size:15
Alignment explanation
Indices: 7240073--7240111 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
7240063 ATAAATTTAT
*
7240073 TATTTTTTATTTATA
1 TATTTTTTATATATA
7240088 TATTTATTTATAT-TA
1 TATTT-TTTATATATA
7240103 TATTTTTTA
1 TATTTTTTA
7240112 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 4 0.18
15 12 0.55
16 6 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTTTATATATA
Found at i:7240283 original size:28 final size:28
Alignment explanation
Indices: 7240251--7240305 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 28
7240241 ATATTCATAA
7240251 TAAATTTG-ATTAGATTTT-TAATTAAAAT
1 TAAA-TTGAATTA-ATTTTATAATTAAAAT
7240279 TAAATTGAATTAATTTTAATAATTAAA
1 TAAATTGAATTAATTTT-ATAATTAAA
7240306 CTATCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 8 0.33
28 8 0.33
29 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (28 bp):
TAAATTGAATTAATTTTATAATTAAAAT
Found at i:7256335 original size:6 final size:6
Alignment explanation
Indices: 7256324--7256351 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
7256314 ACAAGGAAAC
7256324 GTTTTG GTTTTG GTTTTG GTTTTG GTTT
1 GTTTTG GTTTTG GTTTTG GTTTTG GTTT
7256352 ATCTATGGCT
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:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
GTTTTG
Found at i:7258193 original size:19 final size:19
Alignment explanation
Indices: 7258169--7258205 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7258159 TTTTATAAAA
7258169 ATTTAA-AAAATTTTAAATT
1 ATTTAACAAAA-TTTAAATT
7258188 ATTTAACAAAATTTAAAT
1 ATTTAACAAAATTTAAAT
7258206 GAATTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTAACAAAATTTAAATT
Found at i:7258211 original size:20 final size:19
Alignment explanation
Indices: 7258164--7258211 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
7258154 TATTTTTTTA
7258164 TAAA-AATTTAAAAAATTT
1 TAAATAATTTAAAAAATTT
*
7258182 TAAATTATTTAACAAAA-TT
1 TAAATAATTTAA-AAAATTT
7258201 TAAATGAATTT
1 TAAAT-AATTT
7258212 TTGTGTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 8 0.32
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (19 bp):
TAAATAATTTAAAAAATTT
Found at i:7268506 original size:21 final size:21
Alignment explanation
Indices: 7268477--7268520 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7268467 ATAATAATTT
*
7268477 ATTTGATTAAAAA-ATATAAAA
1 ATTTAATTAAAAATA-ATAAAA
7268498 ATTTAATTAAAAATAATAAAA
1 ATTTAATTAAAAATAATAAAA
7268519 AT
1 AT
7268521 ATGATTACGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTTAATTAAAAATAATAAAA
Found at i:7268527 original size:21 final size:21
Alignment explanation
Indices: 7268480--7268527 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
7268470 ATAATTTATT
*
7268480 TGATTAAAAAATATAAAAATT
1 TGATTAAAAAATATAAAAATA
*
7268501 TAATT-AAAAATAATAAAAATA
1 TGATTAAAAAAT-ATAAAAATA
7268522 TGATTA
1 TGATTA
7268528 CGAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (21 bp):
TGATTAAAAAATATAAAAATA
Found at i:7275694 original size:17 final size:17
Alignment explanation
Indices: 7275672--7275704 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
7275662 GGAACTTCAT
7275672 ATATATATATATATAAG
1 ATATATATATATATAAG
*
7275689 ATATATATATTTATAA
1 ATATATATATATATAA
7275705 TAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATATATATATATAAG
Found at i:7280822 original size:19 final size:21
Alignment explanation
Indices: 7280754--7280814 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
7280744 AATTTCACTA
* *
7280754 TTAAATATATTAACATAATAT
1 TTAATTATATTAATATAATAT
*
7280775 TTAATCA-AGTTAATATAATAT
1 TTAATTATA-TTAATATAATAT
7280796 TTAATTATATTAATATAAT
1 TTAATTATATTAATATAAT
7280815 TTTTTTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (21 bp):
TTAATTATATTAATATAATAT
Found at i:7287359 original size:21 final size:21
Alignment explanation
Indices: 7287334--7287373 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
7287324 CTAGATCCTT
7287334 ATTAATTAATTTATATTTAAG
1 ATTAATTAATTTATATTTAAG
7287355 ATTAATTAATTTATATTTA
1 ATTAATTAATTTATATTTA
7287374 TCAGATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATTAATTAATTTATATTTAAG
Found at i:7306321 original size:2 final size:2
Alignment explanation
Indices: 7306280--7306307 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7306270 CCCTCCCTCC
7306280 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
7306308 TGCTTATCCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:7310456 original size:24 final size:23
Alignment explanation
Indices: 7310416--7310460 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
7310406 CACTCATGTG
7310416 TCTTTTTCTTGCTCTTTGCTTGA
1 TCTTTTTCTTGCTCTTTGCTTGA
7310439 TCTTTTGTCTTTGC-CTTTGCTT
1 TCTTTT-TC-TTGCTCTTTGCTT
7310461 TTCAGGCTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.02, C:0.22, G:0.13, T:0.62
Consensus pattern (23 bp):
TCTTTTTCTTGCTCTTTGCTTGA
Found at i:7317476 original size:16 final size:16
Alignment explanation
Indices: 7317455--7317490 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
7317445 TAAAGGCAAC
*
7317455 AACAAGATCTACCAAG
1 AACAAGATCTACCAAA
*
7317471 AACAAGGTCTACCAAA
1 AACAAGATCTACCAAA
7317487 AACA
1 AACA
7317491 GGCATTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.25, G:0.11, T:0.11
Consensus pattern (16 bp):
AACAAGATCTACCAAA
Found at i:7325454 original size:2 final size:2
Alignment explanation
Indices: 7325447--7325479 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7325437 ATCCAAAAGT
7325447 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
7325480 GCAATACATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7329619 original size:16 final size:16
Alignment explanation
Indices: 7329598--7329634 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
7329588 CAAAAAAATA
7329598 TTATTAA-TAATATTTT
1 TTATTAATTAA-ATTTT
7329614 TTATTAATTAAATTTT
1 TTATTAATTAAATTTT
7329630 TTATT
1 TTATT
7329635 TTTTATCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTAATTAAATTTT
Found at i:7342960 original size:25 final size:27
Alignment explanation
Indices: 7342932--7342996 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
7342922 TTAAGAATTT
*
7342932 ATTTAATTTAAA-AT-AAAATATAAAG
1 ATTTAATTTAAATATAAAAATATAAAA
*
7342957 ATTTAATTGAAAATATAAAAATATAAAA
1 ATTTAATT-TAAATATAAAAATATAAAA
7342985 ATTT-ATTTAAAT
1 ATTTAATTTAAAT
7342997 TTTTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 8 0.24
26 7 0.21
27 5 0.15
28 14 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (27 bp):
ATTTAATTTAAATATAAAAATATAAAA
Found at i:7342962 original size:20 final size:20
Alignment explanation
Indices: 7342937--7342975 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7342927 AATTTATTTA
7342937 ATTTAAAAT-AAAATATAAAG
1 ATTT-AAATGAAAATATAAAG
*
7342957 ATTTAATTGAAAATATAAA
1 ATTTAAATGAAAATATAAA
7342976 AATATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTTAAATGAAAATATAAAG
Found at i:7374305 original size:16 final size:15
Alignment explanation
Indices: 7374245--7374307 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
7374235 AATGTTTAAC
*
7374245 TTAAAATATTAAAAAT
1 TTAAAATATT-AATAT
* *
7374261 TTATTAATATTTA-AT
1 TTA-AAATATTAATAT
7374276 TTAAAATATTAATAT
1 TTAAAATATTAATAT
*
7374291 TTAAATTATTTAATAT
1 TTAAAATA-TTAATAT
7374307 T
1 T
7374308 ACTTAAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 7 0.18
15 14 0.36
16 12 0.31
17 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAAAATATTAATAT
Found at i:7374579 original size:64 final size:63
Alignment explanation
Indices: 7374461--7374625 Score: 233
Period size: 64 Copynumber: 2.6 Consensus size: 63
7374451 TTATAGGTTC
* * * *
7374461 TGAATGTTTTATATAATTGATAAATATTATATTTTTATAATGAATACACATAAATATAAATTT
1 TGAATGTCTTACATAATTAATAAATATTATATTTTTATAATGAACACACATAAATATAAATTT
* * * *
7374524 TTAATGTCTTACGTAATTAATAAATATTAATATTTTTATAGTGAACGCACATAAATATAAATTT
1 TGAATGTCTTACATAATTAATAAATATT-ATATTTTTATAATGAACACACATAAATATAAATTT
7374588 TGAATGTCTTACATAATTAAT-AATATTGATATTTTTAT
1 TGAATGTCTTACATAATTAATAAATATT-ATATTTTTAT
7374626 CATGGGGAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 39 0.43
64 51 0.57
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (63 bp):
TGAATGTCTTACATAATTAATAAATATTATATTTTTATAATGAACACACATAAATATAAATTT
Found at i:7375715 original size:37 final size:37
Alignment explanation
Indices: 7375664--7375734 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
7375654 ACAAATGTGG
**
7375664 GAGAATTCCGGCCCACACATTTAGAGCAAAATTCCTA
1 GAGAATTCAAGCCCACACATTTAGAGCAAAATTCCTA
7375701 GAGAATTCAAGCCCACACATTTAGAGCAAAATTC
1 GAGAATTCAAGCCCACACATTTAGAGCAAAATTC
7375735 TTTAAAGTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.21
Consensus pattern (37 bp):
GAGAATTCAAGCCCACACATTTAGAGCAAAATTCCTA
Found at i:7376176 original size:20 final size:20
Alignment explanation
Indices: 7376140--7376177 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7376130 AAAAGCATGC
**
7376140 AAATAATAAAATTTAAATTT
1 AAATAATAAAAAATAAATTT
7376160 AAATAATAAAAAATAAAT
1 AAATAATAAAAAATAAAT
7376178 ATCTCAAATA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAAAATAAATTT
Found at i:7376193 original size:34 final size:33
Alignment explanation
Indices: 7376155--7376218 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
7376145 ATAAAATTTA
*
7376155 AATTTAAATAA-TAAAAAATAAATATCTCAAATAT
1 AATTTAAATAACT-AAAAACAAATATC-CAAATAT
7376189 AATTTAAATAACTAAAAACAAATATCCAAA
1 AATTTAAATAACTAAAAACAAATATCCAAA
7376219 CAACAACTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 23 0.82
35 1 0.04
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (33 bp):
AATTTAAATAACTAAAAACAAATATCCAAATAT
Found at i:7376230 original size:34 final size:34
Alignment explanation
Indices: 7376158--7376230 Score: 78
Period size: 34 Copynumber: 2.1 Consensus size: 34
7376148 AAATTTAAAT
* * * *
7376158 TTAAATAATAAAAAATAAATATCTCAAATATAAT
1 TTAAATAATAAAAAACAAATATCTCAAAAACAAC
7376192 TTAAATAACT-AAAAACAAATATC-CAAACAACAAC
1 TTAAATAA-TAAAAAACAAATATCTCAAA-AACAAC
7376226 TTAAA
1 TTAAA
7376231 GAACATTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
33 4 0.12
34 28 0.85
35 1 0.03
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.26
Consensus pattern (34 bp):
TTAAATAATAAAAAACAAATATCTCAAAAACAAC
Found at i:7376462 original size:15 final size:16
Alignment explanation
Indices: 7376442--7376478 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
7376432 TAAATATGTT
*
7376442 TATATATTTAAAA-TA
1 TATATATCTAAAAGTA
7376457 TATATA-CTAAAAGTA
1 TATATATCTAAAAGTA
7376472 TATATAT
1 TATATAT
7376479 AATAGTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (16 bp):
TATATATCTAAAAGTA
Found at i:7390305 original size:2 final size:2
Alignment explanation
Indices: 7390298--7390326 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7390288 CCTGACAGTA
7390298 TG TG 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 TG TG T
7390327 TGGGGGGTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:7395519 original size:2 final size:2
Alignment explanation
Indices: 7395512--7395549 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
7395502 ATGAACTTTG
7395512 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
7395550 TCTTCAGGTT
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:7401725 original size:22 final size:23
Alignment explanation
Indices: 7401682--7401732 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
7401672 TTGATTGCCA
*
7401682 TTTCTAATGAAATTGTTTTGAAT
1 TTTCTAATGAAATTGTTATGAAT
7401705 TTTC-AATGAAATTCG-TATGAAT
1 TTTCTAATGAAATT-GTTATGAAT
7401727 TTTCTA
1 TTTCTA
7401733 TAAACTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (23 bp):
TTTCTAATGAAATTGTTATGAAT
Found at i:7412259 original size:23 final size:24
Alignment explanation
Indices: 7412225--7412270 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
7412215 TTTTCACCCT
*
7412225 CCGCTGGTTTTCG-GGGGAATATG
1 CCGCTGGATTTCGAGGGGAATATG
7412248 CCGCTGGATTTCGAGGGGAATAT
1 CCGCTGGATTTCGAGGGGAATAT
7412271 TCCGATGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.17, C:0.17, G:0.37, T:0.28
Consensus pattern (24 bp):
CCGCTGGATTTCGAGGGGAATATG
Found at i:7413793 original size:48 final size:48
Alignment explanation
Indices: 7413712--7413850 Score: 224
Period size: 48 Copynumber: 2.9 Consensus size: 48
7413702 GATCGAGCGT
*
7413712 CTAGCCCTTCTACCACTAGCTTCTCAATTTCCCTATTTCCAACAACGG
1 CTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAACGG
* * *
7413760 CTAGTCCTTGTACCACTAGCTTCTCTATTTCCCTATTTCCAACATCGG
1 CTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAACGG
* *
7413808 CTAGCCCTTGCACCACTAGCTTCTCAATTTCCCTATATCCAAC
1 CTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAAC
7413851 TTTTAATGTC
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 83 1.00
ACGTcount: A:0.22, C:0.37, G:0.09, T:0.33
Consensus pattern (48 bp):
CTAGCCCTTGTACCACTAGCTTCTCAATTTCCCTATTTCCAACAACGG
Found at i:7417811 original size:26 final size:26
Alignment explanation
Indices: 7417739--7417793 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
7417729 ATTTAAAATT
* * * *
7417739 AATAATTATAAAAACAATTATAATAA
1 AATAATAACAAAATCAAATATAATAA
*
7417765 AATAATAACAACATCAAATATAATAA
1 AATAATAACAAAATCAAATATAATAA
7417791 AAT
1 AAT
7417794 TTAACATAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.27
Consensus pattern (26 bp):
AATAATAACAAAATCAAATATAATAA
Found at i:7418077 original size:26 final size:26
Alignment explanation
Indices: 7418041--7418091 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
7418031 ACCCCTAATA
* *
7418041 CAAAAGTAAGTGTTTGAAAAAGATTG
1 CAAAAATAAGTATTTGAAAAAGATTG
7418067 CAAAAATAAGTATTTGAAAAAGATT
1 CAAAAATAAGTATTTGAAAAAGATT
7418092 CTTAAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (26 bp):
CAAAAATAAGTATTTGAAAAAGATTG
Found at i:7420306 original size:2 final size:2
Alignment explanation
Indices: 7420299--7420329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
7420289 AGCGAGCGAA
7420299 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7420330 AATTATCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7437696 original size:27 final size:27
Alignment explanation
Indices: 7437654--7437706 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
7437644 AGACCATGGA
*
7437654 AGTTCGGAATAGGGAAACATAAGAACT
1 AGTTCGGAATAAGGAAACATAAGAACT
* *
7437681 AGTTTGGAATAAGGAAATATAAGAAC
1 AGTTCGGAATAAGGAAACATAAGAAC
7437707 CAGTGGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.08, G:0.25, T:0.21
Consensus pattern (27 bp):
AGTTCGGAATAAGGAAACATAAGAACT
Found at i:7439765 original size:16 final size:16
Alignment explanation
Indices: 7439741--7439780 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
7439731 TAAATTAAAT
7439741 ATTTAAATG-TAAAAA
1 ATTTAAATGTTAAAAA
7439756 ATTTATAATGTTAAAAA
1 ATTTA-AATGTTAAAAA
*
7439773 ATATAAAT
1 ATTTAAAT
7439781 TTTTTACTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 7 0.32
17 10 0.45
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTTAAATGTTAAAAA
Found at i:7439780 original size:40 final size:41
Alignment explanation
Indices: 7439691--7439780 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 41
7439681 AAAAATATAT
* * * *
7439691 AAATATAAATATTTAAATAGATGATAAATATATTTATTAAT
1 AAATATAAATATTTAAATAGATAAAAAATATATATATTAAA
* *
7439732 AAAT-TAAATATTTAAAT-G-TAAAAAATTTATAATGTTAAA
1 AAATATAAATATTTAAATAGATAAAAAATATAT-ATATTAAA
7439771 AAATATAAAT
1 AAATATAAAT
7439781 TTTTTACTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
38 9 0.22
39 10 0.24
40 18 0.44
41 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (41 bp):
AAATATAAATATTTAAATAGATAAAAAATATATATATTAAA
Found at i:7458454 original size:27 final size:27
Alignment explanation
Indices: 7458294--7458525 Score: 121
Period size: 27 Copynumber: 8.6 Consensus size: 27
7458284 ACCGTATTCT
* *
7458294 AAAATTTAATTGTTACATGTCATGTTA
1 AAAATTTAATTATTACATGTTATGTTA
* * *
7458321 GAAA--TAATTATT-CATATTATGTTG
1 AAAATTTAATTATTACATGTTATGTTA
* * * * *
7458345 AAAATGTAGTTATTATATGTTATATTT
1 AAAATTTAATTATTACATGTTATGTTA
* ** *
7458372 AAATTTTAATTATTATGTGTCTTAT-TGA
1 AAAATTTAATTATTACATG--TTATGTTA
* * * ** * *
7458400 AAAATGTAGTTATTATACATAATATTA
1 AAAATTTAATTATTACATGTTATGTTA
* *
7458427 AAAATTTAGTTATTACATGTCATGTTAA
1 AAAATTTAATTATTACATGTTATGTT-A
* * * *
7458455 AAAATATAATTGTTATAAGTTATGTTA
1 AAAATTTAATTATTACATGTTATGTTA
* * *
7458482 AAAATTTAATTGTTACAAGTTATTTTA
1 AAAATTTAATTATTACATGTTATGTTA
* *
7458509 AAATTTTAGTTATTACA
1 AAAATTTAATTATTACA
7458526 CACTACATGT
Statistics
Matches: 155, Mismatches: 43, Indels: 14
0.73 0.20 0.07
Matches are distributed among these distances:
24 12 0.08
25 7 0.05
26 10 0.06
27 87 0.56
28 35 0.23
29 4 0.03
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.47
Consensus pattern (27 bp):
AAAATTTAATTATTACATGTTATGTTA
Found at i:7458458 original size:55 final size:55
Alignment explanation
Indices: 7458345--7458498 Score: 139
Period size: 55 Copynumber: 2.8 Consensus size: 55
7458335 TATTATGTTG
** * * * ** * *
7458345 AAAATGTAGTTATTATATGTTATATTTAAATTTTAATTATTATGTGTCTTATTGA
1 AAAATGTAGTTATTATACATAATATTAAAAATTTAATTATTACATGTCATATTAA
* *
7458400 AAAATGTAGTTATTATACATAATATTAAAAATTTAGTTATTACATGTCATGTTAA
1 AAAATGTAGTTATTATACATAATATTAAAAATTTAATTATTACATGTCATATTAA
* * * * * *
7458455 AAAATATAATTGTTATA-AGTTATGTTAAAAATTTAATTGTTACA
1 AAAATGTAGTTATTATACA-TAATATTAAAAATTTAATTATTACA
7458499 AGTTATTTTA
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
54 1 0.01
55 79 0.99
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (55 bp):
AAAATGTAGTTATTATACATAATATTAAAAATTTAATTATTACATGTCATATTAA
Found at i:7496461 original size:67 final size:66
Alignment explanation
Indices: 7496338--7496469 Score: 176
Period size: 67 Copynumber: 2.0 Consensus size: 66
7496328 TACACCTATC
* * * *
7496338 CATATAATATTTCTATATTTAGCTCTCTTTTGTCATTAATATGGGTAACCGTAATCACTTTTTGG
1 CATATAATATATCTATAATTAGC-CTCTTTTATCATTAATATGGGTAACCGTAATCACATTTTGG
7496403 TT
65 TT
* *
7496405 CATATAATATATCTATAATTAG-CTCTTTTATCATTAATATGGGTACCCCTTAAATCACATTTTG
1 CATATAATATATCTATAATTAGCCTCTTTTATCATTAATATGGGTA-ACCGT-AATCACATTTTG
7496469 G
64 G
7496470 GGTGAGATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
65 22 0.39
66 3 0.05
67 32 0.56
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.45
Consensus pattern (66 bp):
CATATAATATATCTATAATTAGCCTCTTTTATCATTAATATGGGTAACCGTAATCACATTTTGGT
T
Found at i:7497521 original size:24 final size:24
Alignment explanation
Indices: 7497494--7497540 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
7497484 GTTAAAAACT
*
7497494 AAGTCAAATTAGAATCTAAATTTC
1 AAGTCAAATTAGAATATAAATTTC
*
7497518 AAGTCAAATTATAATATAAATTT
1 AAGTCAAATTAGAATATAAATTT
7497541 TAAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.36
Consensus pattern (24 bp):
AAGTCAAATTAGAATATAAATTTC
Found at i:7502679 original size:29 final size:27
Alignment explanation
Indices: 7502633--7502692 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
7502623 AATTTTCTTG
* *
7502633 AGAGAGGGAAAGAGTCGAAAGAGAGTGAA
1 AGAGAGGGAAAGAATCG--AGAGAGGGAA
*
7502662 AGAGAGTGAAAGAATCGAGAGAGGGAA
1 AGAGAGGGAAAGAATCGAGAGAGGGAA
7502689 AGAG
1 AGAG
7502693 TGGAAAGGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 13 0.46
29 15 0.54
ACGTcount: A:0.48, C:0.03, G:0.42, T:0.07
Consensus pattern (27 bp):
AGAGAGGGAAAGAATCGAGAGAGGGAA
Found at i:7502692 original size:10 final size:10
Alignment explanation
Indices: 7502643--7502674 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
7502633 AGAGAGGGAA
7502643 AGAGTCGAAAG
1 AGAGT-GAAAG
7502654 AGAGTGAAAG
1 AGAGTGAAAG
7502664 AGAGTGAAAG
1 AGAGTGAAAG
7502674 A
1 A
7502675 ATCGAGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.76
11 5 0.24
ACGTcount: A:0.50, C:0.03, G:0.38, T:0.09
Consensus pattern (10 bp):
AGAGTGAAAG
Found at i:7512812 original size:21 final size:22
Alignment explanation
Indices: 7512776--7512817 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
7512766 ATCATTAATT
*
7512776 ATAAAAATTTATTTAATTTAAA
1 ATAAAAATATATTTAATTTAAA
7512798 ATAAAAATATA-TTAATTTAA
1 ATAAAAATATATTTAATTTAA
7512818 TTAAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAAAATATATTTAATTTAAA
Found at i:7518864 original size:19 final size:21
Alignment explanation
Indices: 7518831--7518885 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
7518821 AAATAATATA
* *
7518831 AAAATAATAAATATT-TTTTT
1 AAAATAATGATTATTCTTTTT
* *
7518851 -GAATATTGATTATTCTTTTT
1 AAAATAATGATTATTCTTTTT
7518871 AAAATAATGATTATT
1 AAAATAATGATTATT
7518886 ATTATGATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 10 0.37
20 5 0.19
21 12 0.44
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
AAAATAATGATTATTCTTTTT
Found at i:7519825 original size:42 final size:40
Alignment explanation
Indices: 7519779--7519871 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 40
7519769 TGTATAATAT
* * *
7519779 TATAATTTGTTTTGGTACTTTATTAAAACTATTTTATGATG
1 TATAATTTGTTTT-GTACTTTATTAAAAATATTTCATAATG
* * *
7519820 ATATAATTTATTTTTTATTTTATTAAAAATATTTCATAATG
1 -TATAATTTGTTTTGTACTTTATTAAAAATATTTCATAATG
7519861 TAATAATTTGT
1 T-ATAATTTGT
7519872 CTTTTTATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 1 0.02
41 30 0.70
42 12 0.28
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (40 bp):
TATAATTTGTTTTGTACTTTATTAAAAATATTTCATAATG
Found at i:7519845 original size:41 final size:40
Alignment explanation
Indices: 7519751--7519879 Score: 116
Period size: 42 Copynumber: 3.1 Consensus size: 40
7519741 TGTAATATTA
* * *
7519751 TTATTTTATTGAACATATTGT-ATAATATTATAATTTGTTTT
1 TTATTTTATTAAAAATATT-TCATAAT-GTATAATTTGTTTT
* * * * * *
7519792 GGTACTTTATTAAAACTATTTTATGATGATATAATTTATTTT
1 -TTATTTTATTAAAAATATTTCATAATG-TATAATTTGTTTT
7519834 TTATTTTATTAAAAATATTTCATAATGTAATAATTTGTCTTT
1 TTATTTTATTAAAAATATTTCATAATGT-ATAATTTGT-TTT
7519876 TTAT
1 TTAT
7519880 GTATAAATTT
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
41 31 0.45
42 37 0.54
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (40 bp):
TTATTTTATTAAAAATATTTCATAATGTATAATTTGTTTT
Found at i:7520017 original size:26 final size:26
Alignment explanation
Indices: 7519952--7520024 Score: 87
Period size: 25 Copynumber: 2.8 Consensus size: 26
7519942 TATATTATTT
*
7519952 TTAAAAATTAAAATAAAATATATACTA
1 TTAAAAATTAATA-AAAATATATACTA
* *
7519979 TTTAAAATT-ATAAAAATA-ATATTA
1 TTAAAAATTAATAAAAATATATACTA
7520003 TATAAAAATTAATAAAAATATA
1 T-TAAAAATTAATAAAAATATA
7520025 AATATATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 6 0.15
25 13 0.33
26 11 0.28
27 9 0.23
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (26 bp):
TTAAAAATTAATAAAAATATATACTA
Found at i:7520025 original size:28 final size:27
Alignment explanation
Indices: 7519952--7520035 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
7519942 TATATTATTT
*
7519952 TTAAAAATTAAAATAAAATAT-ATACTA
1 TTAAAAATTAATA-AAAATATAATACTA
* *
7519979 TTTAAAATT-AT-AAAA-ATAATATTA
1 TTAAAAATTAATAAAAATATAATACTA
7520003 TATAAAAATTAATAAAAATATAAATA-TA
1 T-TAAAAATTAATAAAAATAT-AATACTA
7520031 TTAAA
1 TTAAA
7520036 TTTATATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.04
24 10 0.21
25 7 0.15
26 3 0.06
27 16 0.34
28 5 0.11
29 4 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (27 bp):
TTAAAAATTAATAAAAATATAATACTA
Found at i:7520030 original size:26 final size:27
Alignment explanation
Indices: 7519953--7520031 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
7519943 ATATTATTTT
* *
7519953 TAAAAATTAAAATAAAATATATACTAT-
1 TAAAAATTAATA-AAAATATATAATATA
* *
7519980 TTAAAATT-ATAAAAATA-ATATTATA
1 TAAAAATTAATAAAAATATATAATATA
7520005 TAAAAATTAATAAAAATATA-AATATA
1 TAAAAATTAATAAAAATATATAATATA
7520031 T
1 T
7520032 TAAATTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
24 6 0.14
25 13 0.30
26 17 0.39
27 8 0.18
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (27 bp):
TAAAAATTAATAAAAATATATAATATA
Found at i:7520036 original size:25 final size:26
Alignment explanation
Indices: 7519956--7520037 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 26
7519946 TTATTTTTAA
* *
7519956 AAATTAAAATAAAATATATACTAT-TT
1 AAATTAATA-AAAATATATAATATATT
* *
7519982 AAAATT-ATAAAAATA-ATATTATATAA
1 -AAATTAATAAAAATATATAATATAT-T
7520008 AAATTAATAAAAATATA-AATATATT
1 AAATTAATAAAAATATATAATATATT
7520033 AAATT
1 AAATT
7520038 TATATTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
24 6 0.13
25 17 0.37
26 17 0.37
27 6 0.13
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATTAATAAAAATATATAATATATT
Found at i:7520070 original size:18 final size:19
Alignment explanation
Indices: 7520041--7520076 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
7520031 TTAAATTTAT
7520041 ATTTTAATAAATAAATATA
1 ATTTTAATAAATAAATATA
*
7520060 ATTTTAA-AAATTAATAT
1 ATTTTAATAAATAAATAT
7520077 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTAATAAATAAATATA
Found at i:7520134 original size:18 final size:19
Alignment explanation
Indices: 7520107--7520155 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
7520097 TATAAATTAA
7520107 ATATTATAA-TATTATTTT
1 ATATTATAATTATTATTTT
* *
7520125 ATATTTTAATTATTATTTC
1 ATATTATAATTATTATTTT
7520144 AT-TTATATATTA
1 ATATTATA-ATTA
7520156 AACACTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATATTATAATTATTATTTT
Found at i:7520140 original size:19 final size:18
Alignment explanation
Indices: 7520107--7520155 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
7520097 TATAAATTAA
7520107 ATATTATAATATTATTTT
1 ATATTATAATATTATTTT
* *
7520125 ATATTTTAATTATTATTTC
1 ATATTATAA-TATTATTTT
7520144 AT-TTAT-ATATTA
1 ATATTATAATATTA
7520156 AACACTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 1 0.04
18 11 0.41
19 10 0.37
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTATAATATTATTTT
Found at i:7520960 original size:3 final size:3
Alignment explanation
Indices: 7520952--7520978 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
7520942 GAAAGGTAAG
7520952 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
7520979 TTAATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:7541122 original size:43 final size:43
Alignment explanation
Indices: 7541060--7541142 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
7541050 TACGTAGTTT
* *
7541060 GAACATGTTTTCTTGTATATTTCCTTGCTTAATTGGAGAATTC
1 GAACATGTTTTCTTATATATTTCCTTGCTTAATAGGAGAATTC
*
7541103 GAACATGTTTTCTTATATATTTCCTTGCTTTATAGGAGAA
1 GAACATGTTTTCTTATATATTTCCTTGCTTAATAGGAGAA
7541143 ATCTTATGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.46
Consensus pattern (43 bp):
GAACATGTTTTCTTATATATTTCCTTGCTTAATAGGAGAATTC
Found at i:7544695 original size:2 final size:2
Alignment explanation
Indices: 7544688--7544714 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7544678 ACCCAGTTCC
7544688 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
7544715 TAAGAACTAA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7546690 original size:84 final size:84
Alignment explanation
Indices: 7546549--7546719 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 84
7546539 GTAGTAGATC
*
7546549 AGAGTAAATTGACACTTGCTGTTGTGGAGTGAGGATGGGTACTCTCGCTGTCCTGGTGCAGTGAT
1 AGAGTAAATTGACACTTGCCGTTGTGGAGTGAGGATGGGTACTCTCGCTGTCCTGGTGCAGTGAT
7546614 ATATAGTTTTATTGGCAAG
66 ATATAGTTTTATTGGCAAG
7546633 AGAGTAAATTGACACTTGCCGTTGTGGAGTGAGGATGGGTACTCTCGCTGTCCTGGTGCAGTGAT
1 AGAGTAAATTGACACTTGCCGTTGTGGAGTGAGGATGGGTACTCTCGCTGTCCTGGTGCAGTGAT
7546698 ATATAGTTTTATTGGCAAG
66 ATATAGTTTTATTGGCAAG
7546717 AGA
1 AGA
7546720 TCTTGATTTT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.32
Consensus pattern (84 bp):
AGAGTAAATTGACACTTGCCGTTGTGGAGTGAGGATGGGTACTCTCGCTGTCCTGGTGCAGTGAT
ATATAGTTTTATTGGCAAG
Found at i:7546761 original size:19 final size:20
Alignment explanation
Indices: 7546725--7546762 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7546715 AGAGATCTTG
*
7546725 ATTTTGCTGTAGTATTTGCT
1 ATTTTGCTATAGTATTTGCT
7546745 ATTTTGCTATA-TATTTGC
1 ATTTTGCTATAGTATTTGC
7546763 CTGTTGGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (20 bp):
ATTTTGCTATAGTATTTGCT
Found at i:7554759 original size:20 final size:20
Alignment explanation
Indices: 7554736--7554774 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7554726 AAAATAGAAA
*
7554736 AACAAAAATAAATAACAAAT
1 AACAAAAATAAAAAACAAAT
*
7554756 AACAAAAGTAAAAAACAAA
1 AACAAAAATAAAAAACAAA
7554775 ATCAAATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (20 bp):
AACAAAAATAAAAAACAAAT
Found at i:7554904 original size:135 final size:135
Alignment explanation
Indices: 7554774--7555032 Score: 455
Period size: 135 Copynumber: 1.9 Consensus size: 135
7554764 TAAAAAACAA
* * **
7554774 AATCAAATACAGTATAAAATTTTATTTTTCTAAACAAATTATTTAATATATGCCTACGTGAATCA
1 AATCAAATACAGTATAAAATTTTATTTTTCTAAACAAATTATTGAATATATACCTACGAAAATCA
*
7554839 CGTTGTAGATTTGAAAACACAATAATGCAATAATGCGATGTTGAAGTCAATCATGTTAAAAAAAA
66 CGTTGTAGATTTGAAAACACAATAATGCAATAATGCAATGTTGAAGTCAATCATGTTAAAAAAAA
7554904 ATATC
131 ATATC
*
7554909 AATCAAATACAGTATAAAATTTTATTTTTTTAAACAAATTATTGAATATATACCTACGAAAATCA
1 AATCAAATACAGTATAAAATTTTATTTTTCTAAACAAATTATTGAATATATACCTACGAAAATCA
*
7554974 CGTTGTAGATTTGAAAACACAATAATGCAATCATGCAATGTTGAAGTCAATCATGTTAA
66 CGTTGTAGATTTGAAAACACAATAATGCAATAATGCAATGTTGAAGTCAATCATGTTAA
7555033 GTATACATAA
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 117 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.34
Consensus pattern (135 bp):
AATCAAATACAGTATAAAATTTTATTTTTCTAAACAAATTATTGAATATATACCTACGAAAATCA
CGTTGTAGATTTGAAAACACAATAATGCAATAATGCAATGTTGAAGTCAATCATGTTAAAAAAAA
ATATC
Found at i:7556918 original size:24 final size:25
Alignment explanation
Indices: 7556883--7556929 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
7556873 ACATTCTATT
7556883 TATTTATTTTAA-AATATTTGATATA
1 TATTTATTTTAACAA-ATTTGATATA
7556908 TATTT-TTTTAACAAATTTGATA
1 TATTTATTTTAACAAATTTGATA
7556930 CATTGTCATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (25 bp):
TATTTATTTTAACAAATTTGATATA
Found at i:7600974 original size:12 final size:12
Alignment explanation
Indices: 7600959--7601003 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
7600949 TTCATAGCCA
*
7600959 TCATCGTCATCG
1 TCATCATCATCG
*
7600971 TCATCATCATTG
1 TCATCATCATCG
* *
7600983 TCATCATCTTCC
1 TCATCATCATCG
7600995 TCATCATCA
1 TCATCATCA
7601004 ATTTCATCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.22, C:0.33, G:0.07, T:0.38
Consensus pattern (12 bp):
TCATCATCATCG
Found at i:7633793 original size:2 final size:2
Alignment explanation
Indices: 7633786--7633815 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7633776 AAGAATAACC
7633786 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
7633816 AATAATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:7637824 original size:134 final size:134
Alignment explanation
Indices: 7637570--7637841 Score: 445
Period size: 134 Copynumber: 2.0 Consensus size: 134
7637560 AAAATGCCAC
* *
7637570 AAGTATCAGGAGATGAACAATAAGGCAGACGGACAAAAGGTGAACATGAAAATAGATGTCATCAG
1 AAGTATCAGGAGATGAACAATAAGGCAGACAGACAAAAGGTGAACATGAAAATAGATGTCATCAC
* * * *
7637635 ACACAAGCACACCTAAAACTGAAATCAACAAAAGATAGCAGGTGAGGAAGAATGGCTCTGCGGTA
66 ACACAAGCACACCTAAAACTAAAATCAACAAAAGATAGCAGGTGAGAAAGAATGGCTATGAGGTA
*
7637700 ACAA
131 AAAA
7637704 AAGTATCAGGAGATGAACAATAAGGCAGACAGACAAAAGGTGAACATGAAAATAGATGTCATCAC
1 AAGTATCAGGAGATGAACAATAAGGCAGACAGACAAAAGGTGAACATGAAAATAGATGTCATCAC
* * * *
7637769 ACACAGGCACGCCTAAAACTAAAATCAACAAAAGATAGCAGTTGAGAAAGCATGGCTATGAGGTA
66 ACACAAGCACACCTAAAACTAAAATCAACAAAAGATAGCAGGTGAGAAAGAATGGCTATGAGGTA
7637834 AAAA
131 AAAA
7637838 AAGT
1 AAGT
7637842 TGGACTTTTA
Statistics
Matches: 127, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 127 1.00
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.15
Consensus pattern (134 bp):
AAGTATCAGGAGATGAACAATAAGGCAGACAGACAAAAGGTGAACATGAAAATAGATGTCATCAC
ACACAAGCACACCTAAAACTAAAATCAACAAAAGATAGCAGGTGAGAAAGAATGGCTATGAGGTA
AAAA
Found at i:7641921 original size:18 final size:17
Alignment explanation
Indices: 7641892--7641926 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
7641882 TTAATATTAA
7641892 AATTTTATTTTATATAT
1 AATTTTATTTTATATAT
7641909 AATTTTATATTTATATAT
1 AATTTTAT-TTTATATAT
7641927 TTCTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTTATTTTATATAT
Found at i:7641937 original size:18 final size:16
Alignment explanation
Indices: 7641892--7641945 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
7641882 TTAATATTAA
*
7641892 AATTTTATTTTATATAT
1 AATTTTATATT-TATAT
7641909 AATTTTATATTTATAT
1 AATTTTATATTTATAT
* *
7641925 ATTTCTTATTATTAATAT
1 AATT-TTA-TATTTATAT
7641943 AAT
1 AAT
7641946 ACTTACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
16 8 0.26
17 13 0.42
18 10 0.32
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTTATATTTATAT
Done.