Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 169 of 185
Found at i:51620420 original size:5 final size:5
Alignment explanation
Indices: 51620406--51620434 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
51620396 ACATAAGTGC
51620406 TTTA- TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
51620435 ATTGTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:51622242 original size:37 final size:37
Alignment explanation
Indices: 51622190--51622263 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
51622180 CTTTCATAGC
*
51622190 CATGTTGACAGCACAAGAAGTAGAATAAGCAGTGCGA
1 CATGTTGACACCACAAGAAGTAGAATAAGCAGTGCGA
*
51622227 CATGTTGACTCCACAAGAAGTAGAATAAGCAGTGCGA
1 CATGTTGACACCACAAGAAGTAGAATAAGCAGTGCGA
51622264 ATGGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.18
Consensus pattern (37 bp):
CATGTTGACACCACAAGAAGTAGAATAAGCAGTGCGA
Found at i:51624621 original size:5 final size:5
Alignment explanation
Indices: 51624611--51624636 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
51624601 GATTGAATAG
51624611 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
51624637 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:51634417 original size:19 final size:19
Alignment explanation
Indices: 51634393--51634458 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
51634383 TTTAATACTT
51634393 AAATTTACCATTTCAATTA
1 AAATTTACCATTTCAATTA
** *
51634412 AAATTTATGTAATTTTTACA-T-
1 AAATTTA--CCA-TTTCA-ATTA
51634433 AAATTTACCATTTCAATTA
1 AAATTTACCATTTCAATTA
51634452 AAATTTA
1 AAATTTA
51634459 TGTAATTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
17 1 0.03
18 5 0.14
19 15 0.43
21 8 0.23
22 5 0.14
23 1 0.03
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.45
Consensus pattern (19 bp):
AAATTTACCATTTCAATTA
Found at i:51634438 original size:40 final size:40
Alignment explanation
Indices: 51634392--51634474 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
51634382 TTTTAATACT
*
51634392 TAAATTTACCATTTCAATTAAAATTTATGTAATTTTTACA
1 TAAATTTACCATTTCAATTAAAATTTATGTAATTATTACA
51634432 TAAATTTACCATTTCAATTAAAATTTATGTAATTATTACA
1 TAAATTTACCATTTCAATTAAAATTTATGTAATTATTACA
51634472 TAA
1 TAA
51634475 TTTTTAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (40 bp):
TAAATTTACCATTTCAATTAAAATTTATGTAATTATTACA
Found at i:51634669 original size:16 final size:16
Alignment explanation
Indices: 51634645--51634677 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51634635 ATTAATATTT
51634645 TTATAATATTTTTATA
1 TTATAATATTTTTATA
*
51634661 TTATCATATTTTTATA
1 TTATAATATTTTTATA
51634677 T
1 T
51634678 AATCTTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATAATATTTTTATA
Found at i:51635469 original size:44 final size:44
Alignment explanation
Indices: 51635421--51635507 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
51635411 TAGAAATGCC
*
51635421 ATCTTAATTTTGCATTCAATCAAATTTTGGCAGGACAGTTTGGT
1 ATCTTAATTTTGCATTCAATCAAATTTTAGCAGGACAGTTTGGT
* *
51635465 ATCTTAATTTTGCATTTAATCAAATTTTAGCAGGGCAGTTTGG
1 ATCTTAATTTTGCATTCAATCAAATTTTAGCAGGACAGTTTGG
51635508 CATGACAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (44 bp):
ATCTTAATTTTGCATTCAATCAAATTTTAGCAGGACAGTTTGGT
Found at i:51638638 original size:37 final size:37
Alignment explanation
Indices: 51638597--51638772 Score: 289
Period size: 37 Copynumber: 4.8 Consensus size: 37
51638587 TTTGAGTACT
51638597 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
* *
51638634 TCTGATCAAGAAACGAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
51638671 TCTGATCAAGAAACAAAGTGATAAGTGGTTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
*
51638708 TCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTA
1 TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
** *
51638745 TCTGATCAAGTGATAAAGTGATAAGTGG
1 TCTGATCAAGAAACAAAGTGATAAGTGG
51638773 TAGCTTCAGC
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 132 1.00
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.26
Consensus pattern (37 bp):
TCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTA
Found at i:51638844 original size:45 final size:46
Alignment explanation
Indices: 51638735--51638858 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
51638725 GTGATAAGTG
* *
51638735 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
*
51638781 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGCCT-A
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
51638826 GCTACACTTATCTGATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
51638859 AGGTCATATG
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.28
46 41 0.55
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTCA
Found at i:51642949 original size:56 final size:54
Alignment explanation
Indices: 51642868--51643077 Score: 179
Period size: 56 Copynumber: 4.0 Consensus size: 54
51642858 AATTTGATTG
*
51642868 TTTATAGAAATGTCATTTTAATTTTGCATTCAATCAAATTTTGACAGGACAGTTTA
1 TTTATAGAAATGT--TTTTAATTTTACATTCAATCAAATTTTGACAGGACAGTTTA
* * *
51642924 TTTATAGAAATGTTTTCTTAATTTTGCATTCAATCAAATTTTG---GCA-AG-ATA
1 TTTATAGAAATG-TTT-TTAATTTTACATTCAATCAAATTTTGACAGGACAGTTTA
* * * * * ** *
51642975 GTT-TAG-CA---TCTTAATTTTACATTCAATTAAATTTTGGCAGGGTAGTTTG
1 TTTATAGAAATGTTTTTAATTTTACATTCAATCAAATTTTGACAGGACAGTTTA
* *
51643024 CTTATAGAAATGTCTTTTAATTTTACATTCAATCAAATTTTGACAAGACAGTTT
1 TTTATAGAAATGT-TTTTAATTTTACATTCAATCAAATTTTGACAGGACAGTTT
51643078 GGCATCTTAA
Statistics
Matches: 122, Mismatches: 19, Indels: 27
0.73 0.11 0.16
Matches are distributed among these distances:
44 24 0.20
45 1 0.01
47 1 0.01
48 2 0.02
49 4 0.03
50 6 0.05
51 5 0.04
52 2 0.02
53 2 0.02
55 36 0.30
56 38 0.31
57 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (54 bp):
TTTATAGAAATGTTTTTAATTTTACATTCAATCAAATTTTGACAGGACAGTTTA
Found at i:51643007 original size:44 final size:44
Alignment explanation
Indices: 51642939--51643112 Score: 168
Period size: 44 Copynumber: 3.7 Consensus size: 44
51642929 AGAAATGTTT
*
51642939 TCTTAATTTTGCATTCAATCAAATTTTGGCAAGATAGTTTAGCA
1 TCTTAATTTTACATTCAATCAAATTTTGGCAAGATAGTTTAGCA
* * * *
51642983 TCTTAATTTTACATTCAATTAAATTTTGGCAGGGTAGTTTGCTTATAGAAA
1 TCTTAATTTTACATTCAATCAAATTTTGGCA----AGATAG-TT-TAG-CA
* * *
51643034 TGTCTTTTAATTTTACATTCAATCAAATTTTGACAAGACAGTTTGGCA
1 --TC--TTAATTTTACATTCAATCAAATTTTGGCAAGATAGTTTAGCA
*
51643082 TCTTAATTTTACATTCAATCAAAATTTGGCA
1 TCTTAATTTTACATTCAATCAAATTTTGGCA
51643113 GGGCAATTTG
Statistics
Matches: 105, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
44 56 0.53
46 2 0.02
48 5 0.05
49 4 0.04
50 5 0.05
51 4 0.04
53 2 0.02
55 27 0.26
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (44 bp):
TCTTAATTTTACATTCAATCAAATTTTGGCAAGATAGTTTAGCA
Found at i:51643084 original size:99 final size:100
Alignment explanation
Indices: 51642885--51643117 Score: 342
Period size: 99 Copynumber: 2.3 Consensus size: 100
51642875 AAATGTCATT
* * * * * *
51642885 TTAATTTTGCATTCAATCAAATTTTGACAGGACAGTTTATTTATAGAAATGTTTTCTTAATTTTG
1 TTAATTTTACATTCAATCAAATTTTGGCAGGGCAGTTTACTTATAGAAATGTCTTCTTAATTTTA
* *
51642950 CATTCAATCAAATTTTGGCAAGATAGTTTAGCATC
66 CATTCAATCAAATTTTGACAAGACAGTTTAGCATC
* * *
51642985 TTAATTTTACATTCAATTAAATTTTGGCAGGGTAGTTTGCTTATAGAAATGTCTT-TTAATTTTA
1 TTAATTTTACATTCAATCAAATTTTGGCAGGGCAGTTTACTTATAGAAATGTCTTCTTAATTTTA
*
51643049 CATTCAATCAAATTTTGACAAGACAGTTTGGCATC
66 CATTCAATCAAATTTTGACAAGACAGTTTAGCATC
*
51643084 TTAATTTTACATTCAATCAAAATTTGGCAGGGCA
1 TTAATTTTACATTCAATCAAATTTTGGCAGGGCA
51643118 ATTTGGCATG
Statistics
Matches: 118, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
99 71 0.60
100 47 0.40
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (100 bp):
TTAATTTTACATTCAATCAAATTTTGGCAGGGCAGTTTACTTATAGAAATGTCTTCTTAATTTTA
CATTCAATCAAATTTTGACAAGACAGTTTAGCATC
Found at i:51643123 original size:44 final size:44
Alignment explanation
Indices: 51643040--51643126 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
51643030 GAAATGTCTT
* *
51643040 TTAATTTTACATTCAATCAAATTTTGACAAGACAGTTTGGCATC
1 TTAATTTTACATTCAATCAAAATTTGACAAGACAATTTGGCATC
* * *
51643084 TTAATTTTACATTCAATCAAAATTTGGCAGGGCAATTTGGCAT
1 TTAATTTTACATTCAATCAAAATTTGACAAGACAATTTGGCAT
51643127 GACAATCTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (44 bp):
TTAATTTTACATTCAATCAAAATTTGACAAGACAATTTGGCATC
Found at i:51649239 original size:7 final size:7
Alignment explanation
Indices: 51649229--51649256 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
51649219 ATAAATTAAT
51649229 AATTTTA
1 AATTTTA
51649236 AATTTTA
1 AATTTTA
51649243 AATTTTA
1 AATTTTA
51649250 AATTTTA
1 AATTTTA
51649257 TTTTACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:51651162 original size:186 final size:186
Alignment explanation
Indices: 51650848--51651223 Score: 707
Period size: 186 Copynumber: 2.0 Consensus size: 186
51650838 TGTTCTTATT
51650848 TTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTTTCACT
1 TTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTTTCACT
51650913 TAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTATTTCCT
66 TAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTATTTCCT
*
51650978 GCTTTCGGATCCAAAGCTGCCAGCCTGAACTTCCCTTTGTTTGCATCTAGATCATC
131 GCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGATCATC
* *
51651034 TTGGATTTCTCTTCCTCTTACCGTATCAACCCCTCAAATGAATAAGTACATGCTACATTTTCACT
1 TTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTTTCACT
*
51651099 TAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTAGCTATTATTTCCT
66 TAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTATTTCCT
*
51651164 GCTTTCGGATTCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGATCATC
131 GCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGATCATC
51651220 TTGG
1 TTGG
51651224 CCTTGCTTCA
Statistics
Matches: 185, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
186 185 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.40
Consensus pattern (186 bp):
TTGGATTTCTCTTCCTCTTACAGTATCAACCCCTCAAATGAATAAGTACATACTACATTTTCACT
TAGGTGAACCCACATTGATTGTTTCTCTGTATCTGATGGTTGTGTGTTTTTACCTATTATTTCCT
GCTTTCGGATCCAAAGCTACCAGCCTGAACTTCCCTTTGTTTGCATCTAGATCATC
Found at i:51678509 original size:13 final size:13
Alignment explanation
Indices: 51678491--51678517 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
51678481 AAGTTAGACT
51678491 AGGAAAAGATAAC
1 AGGAAAAGATAAC
51678504 AGGAAAAGATAAC
1 AGGAAAAGATAAC
51678517 A
1 A
51678518 AAGTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.07
Consensus pattern (13 bp):
AGGAAAAGATAAC
Found at i:51683479 original size:2 final size:2
Alignment explanation
Indices: 51683472--51683498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
51683462 TCTAACTGAA
51683472 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
51683499 GCTGTTGCAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:51685379 original size:25 final size:24
Alignment explanation
Indices: 51685343--51685409 Score: 89
Period size: 25 Copynumber: 2.8 Consensus size: 24
51685333 GGGCCTGGAT
*
51685343 TATATATTAAATATATATTTTTTA
1 TATATATCAAATATATATTTTTTA
* *
51685367 TTTTTAATCAAATATATATTTTTTA
1 TATAT-ATCAAATATATATTTTTTA
*
51685392 TATATATTAAATATATAT
1 TATATATCAAATATATAT
51685410 AAAATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
24 15 0.42
25 21 0.58
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATATCAAATATATATTTTTTA
Found at i:51685427 original size:11 final size:11
Alignment explanation
Indices: 51685391--51685421 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
51685381 TATATTTTTT
*
51685391 ATATATATTAA
1 ATATATATAAA
51685402 ATATATATAAA
1 ATATATATAAA
51685413 ATATATATA
1 ATATATATA
51685422 TGATATGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATATAAA
Found at i:51691090 original size:13 final size:12
Alignment explanation
Indices: 51691056--51691095 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
51691046 ATTTTATTTT
51691056 TATT-TTTAAAA
1 TATTATTTAAAA
51691067 -A-TATTTAAAA
1 TATTATTTAAAA
51691077 TATTATTATAAAA
1 TATTATT-TAAAA
51691090 TATTAT
1 TATTAT
51691096 ATTTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 1 0.04
10 8 0.32
11 1 0.04
12 4 0.16
13 11 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTATTTAAAA
Found at i:51697411 original size:16 final size:16
Alignment explanation
Indices: 51697390--51697425 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
51697380 TATCACATTC
51697390 AACCTATATTTATTTA
1 AACCTATATTTATTTA
51697406 AACCTATATTTATTTA
1 AACCTATATTTATTTA
51697422 AACC
1 AACC
51697426 CCTTCTCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (16 bp):
AACCTATATTTATTTA
Found at i:51697642 original size:11 final size:11
Alignment explanation
Indices: 51697626--51697652 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
51697616 AAATCTAAAG
51697626 TTTTAAAATTA
1 TTTTAAAATTA
51697637 TTTTAAAATTA
1 TTTTAAAATTA
51697648 TTTTA
1 TTTTA
51697653 TGTGTTTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:51698192 original size:21 final size:22
Alignment explanation
Indices: 51698161--51698201 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
51698151 GCTTGGTTTT
51698161 TTAAGTGTTTAATGATAGATTA
1 TTAAGTGTTTAATGATAGATTA
*
51698183 TTAAG-GTTTAATGTTAGAT
1 TTAAGTGTTTAATGATAGAT
51698202 ATACAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (22 bp):
TTAAGTGTTTAATGATAGATTA
Found at i:51698894 original size:25 final size:25
Alignment explanation
Indices: 51698855--51698934 Score: 128
Period size: 25 Copynumber: 3.2 Consensus size: 25
51698845 TTTTATGAGT
51698855 TTACCG-T-TTCAGCTCGATAGAGC
1 TTACCGTTCTTCAGCTCGATAGAGC
51698878 TTACCGTTCTTCAGCTCGATAGAGC
1 TTACCGTTCTTCAGCTCGATAGAGC
*
51698903 TTACCGTTCTTCAGCTCGAAATGAGC
1 TTACCGTTCTTCAGCTCGATA-GAGC
51698929 TTACCG
1 TTACCG
51698935 ATCATGGCTC
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
23 6 0.11
24 1 0.02
25 36 0.68
26 10 0.19
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (25 bp):
TTACCGTTCTTCAGCTCGATAGAGC
Found at i:51704069 original size:25 final size:25
Alignment explanation
Indices: 51704041--51704117 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
51704031 CCTTAGAGCA
* *
51704041 CTCTCTGATTATTAACACGTTAGTG
1 CTCTCCGATTATTAACACATTAGTG
*
51704066 CTCTCCGATTATTAGCACATTAGTG
1 CTCTCCGATTATTAACACATTAGTG
* * *
51704091 CCCTCCG--T-TTAGCACATTTGTG
1 CTCTCCGATTATTAACACATTAGTG
51704113 CTCTC
1 CTCTC
51704118 TGTATATTAC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 17 0.37
23 1 0.02
25 28 0.61
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.38
Consensus pattern (25 bp):
CTCTCCGATTATTAACACATTAGTG
Found at i:51705738 original size:18 final size:18
Alignment explanation
Indices: 51705715--51705749 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
51705705 CCGAAACTTC
51705715 ATTTTAAT-TTTTATACAA
1 ATTTTAATATTTT-TACAA
51705733 ATTTTAATATTTTTACA
1 ATTTTAATATTTTTACA
51705750 CAAAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATATTTTTACAA
Found at i:51706155 original size:20 final size:19
Alignment explanation
Indices: 51706100--51706157 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
51706090 AATTAAAAAA
*
51706100 AAAAAACTAAAATAATTAAT
1 AAAAAA-TAAAATAAATAAT
*
51706120 AAAAAATAGAAA-AAATCAT
1 AAAAAATA-AAATAAATAAT
51706139 AAAAGAATAAAATAAATAA
1 AAAA-AATAAAATAAATAA
51706158 ATTATAACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
AAAAAATAAAATAAATAAT
Found at i:51710881 original size:21 final size:21
Alignment explanation
Indices: 51710847--51710887 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
51710837 ACATTCATTC
*
51710847 AATTTAATCTCTATTTTTTTT
1 AATTTAATCGCTATTTTTTTT
*
51710868 AATTTGATCGCTATTTTTTT
1 AATTTAATCGCTATTTTTTT
51710888 ATTTGAAGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.10, G:0.05, T:0.63
Consensus pattern (21 bp):
AATTTAATCGCTATTTTTTTT
Found at i:51711016 original size:21 final size:20
Alignment explanation
Indices: 51710992--51711039 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
51710982 TTTTTAATAT
*
51710992 TAAAAAAAATCATAAAAATTA
1 TAAAAAAAATCATAAAAA-AA
* *
51711013 TAAACAAAATTTATAAAAAAA
1 TAAA-AAAAATCATAAAAAAA
51711034 TAAAAA
1 TAAAAA
51711040 TACTGACCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 9 0.39
22 12 0.52
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAAAAAATCATAAAAAAA
Found at i:51711806 original size:14 final size:15
Alignment explanation
Indices: 51711778--51711808 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
51711768 CACATATCAA
51711778 ATTTCTATGTATTTC
1 ATTTCTATGTATTTC
51711793 ATTTCTAT-TATTTC
1 ATTTCTATGTATTTC
51711807 AT
1 AT
51711809 CAACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTCTATGTATTTC
Found at i:51714469 original size:15 final size:15
Alignment explanation
Indices: 51714451--51714481 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51714441 ATATTATTAT
*
51714451 TTTTTGTTAAATAAA
1 TTTTTATTAAATAAA
51714466 TTTTTATTAAATAAA
1 TTTTTATTAAATAAA
51714481 T
1 T
51714482 AAGATAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTTATTAAATAAA
Found at i:51714748 original size:29 final size:28
Alignment explanation
Indices: 51714666--51714749 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
51714656 GTAAGTAATA
51714666 AAAAGAAAAA-AGAAATAAAAGAAGAACAG
1 AAAAGAAAAAGAGAAA-AAAAGAA-AACAG
* *
51714695 AAAAGAAACAGAGAACAAAAGGAAAACAG
1 AAAAGAAAAAGAGAA-AAAAAGAAAACAG
** *
51714724 GGAAGAAAAAGTGAAAGAAAAGAAAA
1 AAAAGAAAAAGAGAAA-AAAAGAAAA
51714750 GGGGAAAATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.02
29 33 0.73
30 10 0.22
31 1 0.02
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.02
Consensus pattern (28 bp):
AAAAGAAAAAGAGAAAAAAAGAAAACAG
Found at i:51715110 original size:23 final size:24
Alignment explanation
Indices: 51715075--51715119 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
51715065 AATATGGCAA
51715075 GAAATTAAGTAGAAAAG-AAGTAT
1 GAAATTAAGTAGAAAAGTAAGTAT
51715098 GAAA-TAAGCTAGAAAAGTAAGT
1 GAAATTAAG-TAGAAAAGTAAGT
51715120 GAGCTTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (24 bp):
GAAATTAAGTAGAAAAGTAAGTAT
Found at i:51715400 original size:24 final size:23
Alignment explanation
Indices: 51715373--51715417 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
51715363 ATCATGGGAC
51715373 ATTT-AAAGTAAGGTAAGTAATAAT
1 ATTTGAAAGTAA-GTAAG-AATAAT
*
51715397 ATTTGAAATTAAGTAAGAATA
1 ATTTGAAAGTAAGTAAGAATA
51715418 TGTGTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 9 0.47
25 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (23 bp):
ATTTGAAAGTAAGTAAGAATAAT
Found at i:51719323 original size:21 final size:23
Alignment explanation
Indices: 51719282--51719324 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
51719272 GAGATAAAAA
51719282 GGAAAATAGAAACAGAAATGAAG
1 GGAAAATAGAAACAGAAATGAAG
51719305 GGAAAATA-AAACA-AAATGAA
1 GGAAAATAGAAACAGAAATGAA
51719325 ATAATGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 7 0.35
22 5 0.25
23 8 0.40
ACGTcount: A:0.65, C:0.05, G:0.21, T:0.09
Consensus pattern (23 bp):
GGAAAATAGAAACAGAAATGAAG
Found at i:51719681 original size:30 final size:29
Alignment explanation
Indices: 51719647--51719710 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
51719637 AATTTAAAAG
51719647 AATTAGATC-AAATTAAAATTTCATGTATAA
1 AATTAGA-CAAAATTAAAATTT-ATGTATAA
*
51719677 AATTATACAAAATTAAAATTTATGTATAA
1 AATTAGACAAAATTAAAATTTATGTATAA
51719706 AATTA
1 AATTA
51719711 TACATTAAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (29 bp):
AATTAGACAAAATTAAAATTTATGTATAA
Found at i:51719702 original size:29 final size:30
Alignment explanation
Indices: 51719656--51719714 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
51719646 GAATTAGATC
51719656 AAATTAAAATTTCATGTATAAAATTATACA
1 AAATTAAAATTTCATGTATAAAATTATACA
51719686 AAATTAAAATTT-ATGTATAAAATTATACA
1 AAATTAAAATTTCATGTATAAAATTATACA
51719715 TTAAACTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTAAAATTTCATGTATAAAATTATACA
Found at i:51725822 original size:19 final size:19
Alignment explanation
Indices: 51725798--51725841 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
51725788 TCTTTCACAG
*
51725798 TAAAAA-ATATTAATTATTA
1 TAAAAAGATATTAA-TATGA
*
51725817 TAAAAAGTTATTAATATGA
1 TAAAAAGATATTAATATGA
51725836 TAAAAA
1 TAAAAA
51725842 TAAACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TAAAAAGATATTAATATGA
Found at i:51726661 original size:18 final size:20
Alignment explanation
Indices: 51726625--51726662 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
51726615 AAACTATGTA
51726625 TATTTTTATGAATAAGTATAT
1 TATTTTTATGAAT-AGTATAT
51726646 TATTTTTAT-AAT-GTATA
1 TATTTTTATGAATAGTATA
51726663 GCATGGACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
20 3 0.18
21 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (20 bp):
TATTTTTATGAATAGTATAT
Found at i:51728706 original size:31 final size:31
Alignment explanation
Indices: 51728669--51728738 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
51728659 TATTTTTTAT
51728669 GAAGAAAATGAATCTTTTTATC-AGAGGATCA
1 GAAGAAAATGAATCTTTTTATCGA-AGGATCA
51728700 GAAGAAAATGAATCTTTTTATCGAAGGATCA
1 GAAGAAAATGAATCTTTTTATCGAAGGATCA
*
51728731 GAAAAAAA
1 GAAGAAAA
51728739 AGGGTCCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (31 bp):
GAAGAAAATGAATCTTTTTATCGAAGGATCA
Found at i:51734589 original size:16 final size:16
Alignment explanation
Indices: 51734570--51734603 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
51734560 GACTAAATTG
51734570 AAAAGTTATGGAAGTT
1 AAAAGTTATGGAAGTT
51734586 AAAAGTTATGGAAGTT
1 AAAAGTTATGGAAGTT
51734602 AA
1 AA
51734604 TAAGAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (16 bp):
AAAAGTTATGGAAGTT
Found at i:51737876 original size:20 final size:20
Alignment explanation
Indices: 51737851--51737890 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
51737841 AATTATGCTG
51737851 ATAACTCTAGTTTTACTGGA
1 ATAACTCTAGTTTTACTGGA
51737871 ATAACTCTAGTTTTACTGGA
1 ATAACTCTAGTTTTACTGGA
51737891 GCGTTTCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
ATAACTCTAGTTTTACTGGA
Found at i:51743546 original size:31 final size:32
Alignment explanation
Indices: 51743511--51743585 Score: 125
Period size: 31 Copynumber: 2.4 Consensus size: 32
51743501 GGAGGAAAAC
**
51743511 TTATTGACTTAAATGCTAAATGTTGCTGTTG-
1 TTATTGACTTAAATGCTAAATGTTGCTACTGT
51743542 TTATTGACTTAAATGCTAAATGTTGCTACTGT
1 TTATTGACTTAAATGCTAAATGTTGCTACTGT
51743574 TTATTGACTTAA
1 TTATTGACTTAA
51743586 CTGTGAAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 29 0.71
32 12 0.29
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (32 bp):
TTATTGACTTAAATGCTAAATGTTGCTACTGT
Found at i:51753232 original size:5 final size:5
Alignment explanation
Indices: 51753202--51753244 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
51753192 AGAAGAGAAT
51753202 AAAGA GAAAG- AAAGAA AAATGA AAAGA AAAGA AAAGA AAAGA A
1 AAAGA -AAAGA AAAG-A AAA-GA AAAGA AAAGA AAAGA AAAGA A
51753245 TTAATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
4 4 0.12
5 18 0.53
6 11 0.32
7 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:51753240 original size:15 final size:16
Alignment explanation
Indices: 51753192--51753244 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
51753182 AGGGTGTCGG
*
51753192 AGAAGAGAATAAAGAGAA
1 AGAAAAGAA-AAAGA-AA
51753210 AG-AAAGAAAAATGAAA
1 AGAAAAGAAAAA-GAAA
51753226 AGAAAAG-AAAAGAAA
1 AGAAAAGAAAAAGAAA
51753241 AGAA
1 AGAA
51753245 TTAATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.25
16 11 0.34
17 11 0.34
18 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.04
Consensus pattern (16 bp):
AGAAAAGAAAAAGAAA
Found at i:51756085 original size:19 final size:19
Alignment explanation
Indices: 51756040--51756085 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
51756030 GCCTTTTATT
*
51756040 TATTATT-TATTTTATATT
1 TATTATTATATTTTATATA
51756058 TACTT-TTATATTTTATATA
1 TA-TTATTATATTTTATATA
51756077 TATTATTAT
1 TATTATTAT
51756086 CGACCAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTATTATATTTTATATA
Found at i:51757480 original size:6 final size:6
Alignment explanation
Indices: 51757469--51757502 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
51757459 ACCTGTTTTT
51757469 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAG
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAG
51757503 CTTTGCATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:51761616 original size:3 final size:3
Alignment explanation
Indices: 51761608--51761651 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
51761598 ATACTAAACT
51761608 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
51761652 TCAAATTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:51777231 original size:17 final size:17
Alignment explanation
Indices: 51777211--51777244 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
51777201 AATTTTTTAA
51777211 ATGTCTATGTTTTGTCC
1 ATGTCTATGTTTTGTCC
51777228 ATGTCTATGTTTTGTCC
1 ATGTCTATGTTTTGTCC
51777245 CCCAACCTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.18, T:0.53
Consensus pattern (17 bp):
ATGTCTATGTTTTGTCC
Found at i:51779499 original size:4 final size:4
Alignment explanation
Indices: 51779490--51779526 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
51779480 TTACTTGATG
51779490 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
51779527 ATGTCCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:51782247 original size:15 final size:17
Alignment explanation
Indices: 51782229--51782262 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
51782219 TTTTTCTCTT
51782229 AAATTATT-TTTT-ATA
1 AAATTATTATTTTAATA
51782244 AAATTATTATTTTAATA
1 AAATTATTATTTTAATA
51782261 AA
1 AA
51782263 TAAACCTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 4 0.24
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTATTATTTTAATA
Found at i:51783156 original size:16 final size:18
Alignment explanation
Indices: 51783106--51783157 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
51783096 TATCAAATTT
51783106 AAAAT-TTAAAATTAATAA
1 AAAATCTTAAAATT-ATAA
*
51783124 AAAATCTTAAAAATATAA
1 AAAATCTTAAAATTATAA
*
51783142 AAATTC-T-AAATTATAA
1 AAAATCTTAAAATTATAA
51783158 TTAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.27
17 1 0.03
18 14 0.47
19 7 0.23
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATCTTAAAATTATAA
Found at i:51787616 original size:19 final size:18
Alignment explanation
Indices: 51787575--51787616 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
51787565 TGTTAAGATG
* *
51787575 ATTATATAAAAAATTTCA
1 ATTAAATAAAAAATTTAA
51787593 A-TAAATAAAAAATATTAA
1 ATTAAATAAAAAAT-TTAA
51787611 ATTAAA
1 ATTAAA
51787617 ATATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 11 0.55
18 5 0.25
19 4 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTAAATAAAAAATTTAA
Found at i:51791061 original size:32 final size:32
Alignment explanation
Indices: 51791025--51791105 Score: 135
Period size: 32 Copynumber: 2.5 Consensus size: 32
51791015 TGGGCCAGAC
* *
51791025 CGTGTGGGCCACACGGGTAAGGCCAATCTGAG
1 CGTGTGAGCCACACGGGAAAGGCCAATCTGAG
*
51791057 CGTGTGAGCCACACGGAAAAGGCCAATCTGAG
1 CGTGTGAGCCACACGGGAAAGGCCAATCTGAG
51791089 CGTGTGAGCCACACGGG
1 CGTGTGAGCCACACGGG
51791106 CATGTGAGCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.25, C:0.26, G:0.36, T:0.14
Consensus pattern (32 bp):
CGTGTGAGCCACACGGGAAAGGCCAATCTGAG
Found at i:51791118 original size:18 final size:18
Alignment explanation
Indices: 51791091--51791135 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
51791081 AATCTGAGCG
51791091 TGTGAG-CCACACGGGCA
1 TGTGAGCCCACACGGGCA
51791108 TGTGAGCCCACACGGGCA
1 TGTGAGCCCACACGGGCA
*
51791126 TGTGGGCCCA
1 TGTGAGCCCA
51791136 TAATTCTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.20, C:0.31, G:0.36, T:0.13
Consensus pattern (18 bp):
TGTGAGCCCACACGGGCA
Found at i:51791848 original size:17 final size:18
Alignment explanation
Indices: 51791823--51791856 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51791813 TTACTTAATA
51791823 AATTATGG-TTTATTTAT
1 AATTATGGTTTTATTTAT
*
51791840 AATTTTGGTTTTATTTA
1 AATTATGGTTTTATTTA
51791857 GGAGTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.62
Consensus pattern (18 bp):
AATTATGGTTTTATTTAT
Found at i:51794743 original size:21 final size:21
Alignment explanation
Indices: 51794717--51794783 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
51794707 ATATAAATGC
*
51794717 TAAATGGAAACTCGTAAGGGT
1 TAAATGGAAACTCATAAGGGT
* * *
51794738 TAAATGGAAGCTCATAAGAGC
1 TAAATGGAAACTCATAAGGGT
* * *
51794759 TGAACGGAAACCCATAAGGGT
1 TAAATGGAAACTCATAAGGGT
51794780 TAAA
1 TAAA
51794784 CTGAAGCTCA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.19
Consensus pattern (21 bp):
TAAATGGAAACTCATAAGGGT
Found at i:51794781 original size:42 final size:42
Alignment explanation
Indices: 51794716--51794827 Score: 136
Period size: 42 Copynumber: 2.7 Consensus size: 42
51794706 TATATAAATG
* * * * *
51794716 CTAAATGGAAACTCGTAAGGGTTAAA-TGGAAGCTCATAAGAG
1 CTAAACGGAAACCCATAAGGGTTAAACT-GAAGCTCAAAAGAA
*
51794758 CTGAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAA
1 CTAAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAA
* *
51794800 CTAAACTGAAACCCAGAAGGGTTAAACT
1 CTAAACGGAAACCCATAAGGGTTAAACT
51794828 AAAACTCATA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
42 59 0.98
43 1 0.02
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.18
Consensus pattern (42 bp):
CTAAACGGAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAA
Found at i:51794825 original size:21 final size:21
Alignment explanation
Indices: 51794765--51794832 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
51794755 GAGCTGAACG
*
51794765 GAAACCCATAAGGGTTAAACT
1 GAAACCCAAAAGGGTTAAACT
* * ***
51794786 GAAGCTCAAAAGAACTAAACT
1 GAAACCCAAAAGGGTTAAACT
*
51794807 GAAACCCAGAAGGGTTAAACT
1 GAAACCCAAAAGGGTTAAACT
*
51794828 AAAAC
1 GAAAC
51794833 TCATATGAGT
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.15
Consensus pattern (21 bp):
GAAACCCAAAAGGGTTAAACT
Found at i:51801707 original size:39 final size:40
Alignment explanation
Indices: 51801662--51801829 Score: 106
Period size: 40 Copynumber: 4.2 Consensus size: 40
51801652 CGGGGTTTAG
* * *
51801662 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
51801701 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * * **
51801741 CCGGATATAGTCGCTAGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGA-CTTAAC
* ** * * * *
51801781 CCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAACCAC-TAGCATAAAGGCCTTCGGGACTTAAC
51801822 CCGGATAT
1 CCGGATAT
51801830 CATTCGAGTA
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 18 0.17
40 61 0.56
41 27 0.25
42 3 0.03
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:51801812 original size:41 final size:40
Alignment explanation
Indices: 51801685--51801829 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
51801675 CTCGCACAAG
* * * * *
51801685 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
51801725 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
51801765 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
51801806 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
51801830 CATTCGAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.03
40 59 0.64
41 27 0.29
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:51807008 original size:22 final size:21
Alignment explanation
Indices: 51806985--51807062 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
51806975 TCCAAACAAT
*
51806985 AACAACAAAATAGTAGCAATAT
1 AACAACAAAATAGTAGCAA-AC
* * *
51807007 AATATCAAAATGGTAGCAAAAC
1 AACAACAAAATAGTAGC-AAAC
* * * *
51807029 AACATCAAAATGGCAACAAAC
1 AACAACAAAATAGTAGCAAAC
51807050 AACAACAAAATAG
1 AACAACAAAATAG
51807063 CAGTGAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.33
22 29 0.63
23 2 0.04
ACGTcount: A:0.59, C:0.17, G:0.10, T:0.14
Consensus pattern (21 bp):
AACAACAAAATAGTAGCAAAC
Found at i:51807051 original size:21 final size:22
Alignment explanation
Indices: 51807010--51807060 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
51807000 GCAATATAAT
* *
51807010 ATCAAAATGGTAGCAAAACAAC
1 ATCAAAATGGCAACAAAACAAC
51807032 ATCAAAATGGCAAC-AAACAAC
1 ATCAAAATGGCAACAAAACAAC
*
51807053 AACAAAAT
1 ATCAAAAT
51807061 AGCAGTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.59, C:0.20, G:0.10, T:0.12
Consensus pattern (22 bp):
ATCAAAATGGCAACAAAACAAC
Found at i:51810186 original size:21 final size:21
Alignment explanation
Indices: 51810147--51810186 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51810137 TAAACCTGAT
*
51810147 CAAAACATAACAATTTCAATC
1 CAAAACATAACAATATCAATC
51810168 CAAAACAT-ACATATATCAA
1 CAAAACATAACA-ATATCAA
51810187 CCTACTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (21 bp):
CAAAACATAACAATATCAATC
Found at i:51811331 original size:18 final size:17
Alignment explanation
Indices: 51811304--51811337 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
51811294 ATGTATTTTA
51811304 AAATTATAAAATATAAC
1 AAATTATAAAATATAAC
*
51811321 AAATATATAAATTATAA
1 AAAT-TATAAAATATAA
51811338 GATATAGGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATTATAAAATATAAC
Found at i:51812599 original size:40 final size:42
Alignment explanation
Indices: 51812525--51812607 Score: 125
Period size: 40 Copynumber: 2.0 Consensus size: 42
51812515 TGAGATTGAT
*
51812525 TCTTAAGAAATAAAAAAGGAATGAATAAGTAAATAAATGGAGA
1 TCTTAAGAAATAAAAAA-GAATAAATAAGTAAATAAATGGAGA
*
51812568 TCTTGAGAAAT-AAAAA-AATAAATAAGTAAATAAATGGAGA
1 TCTTAAGAAATAAAAAAGAATAAATAAGTAAATAAATGGAGA
51812608 GCAAGCAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 23 0.61
42 5 0.13
43 10 0.26
ACGTcount: A:0.59, C:0.02, G:0.17, T:0.22
Consensus pattern (42 bp):
TCTTAAGAAATAAAAAAGAATAAATAAGTAAATAAATGGAGA
Found at i:51812869 original size:13 final size:13
Alignment explanation
Indices: 51812839--51812874 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
51812829 AGTGGTGGCA
*
51812839 GAGGCGTGCGAGTG
1 GAGGCGTG-GACTG
51812853 GAGGCGTGGACTG
1 GAGGCGTGGACTG
51812866 GAGGCGTGG
1 GAGGCGTGG
51812875 CAGACGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.14, C:0.14, G:0.58, T:0.14
Consensus pattern (13 bp):
GAGGCGTGGACTG
Found at i:51813608 original size:22 final size:22
Alignment explanation
Indices: 51813583--51813663 Score: 99
Period size: 22 Copynumber: 3.7 Consensus size: 22
51813573 ACCACACCAG
* *
51813583 TAGGCACCAAAGTGCTGAGCAG
1 TAGGCACCAAAGTGCTGAACAA
**
51813605 TAGGCACTGAAGTGCTGAACAA
1 TAGGCACCAAAGTGCTGAACAA
**
51813627 TAGGCACTGAAGTGCTGAACAA
1 TAGGCACCAAAGTGCTGAACAA
*
51813649 TAGGCACCATAGTGC
1 TAGGCACCAAAGTGC
51813664 AAATCAGTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.17
Consensus pattern (22 bp):
TAGGCACCAAAGTGCTGAACAA
Found at i:51813704 original size:20 final size:22
Alignment explanation
Indices: 51813659--51813707 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
51813649 TAGGCACCAT
*
51813659 AGTGCAAATCAGTAGCCATTGA
1 AGTGCAAATCAGTAGCCATCGA
*
51813681 AGTGCAAA-CAGT-GGCATCGA
1 AGTGCAAATCAGTAGCCATCGA
51813701 AGTGCAA
1 AGTGCAA
51813708 TCCTGTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.52
21 4 0.16
22 8 0.32
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (22 bp):
AGTGCAAATCAGTAGCCATCGA
Found at i:51814621 original size:15 final size:17
Alignment explanation
Indices: 51814603--51814639 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
51814593 ATTTTTTATG
51814603 TTTTAATTT-ACAT-AT
1 TTTTAATTTAACATAAT
51814618 TTTT-ATTTAACATAAT
1 TTTTAATTTAACATAAT
51814634 TTTTAA
1 TTTTAA
51814640 CTAAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.21
15 8 0.42
16 6 0.32
17 1 0.05
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTAATTTAACATAAT
Found at i:51817702 original size:28 final size:28
Alignment explanation
Indices: 51817662--51817715 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
51817652 AGCCCCCTAA
*
51817662 AATCGCTTCTGGATAAAATGATAATTAG
1 AATCGCCTCTGGATAAAATGATAATTAG
51817690 AATCGCCTCTGGATAAAATGATAATT
1 AATCGCCTCTGGATAAAATGATAATT
51817716 TTATATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (28 bp):
AATCGCCTCTGGATAAAATGATAATTAG
Found at i:51818248 original size:19 final size:19
Alignment explanation
Indices: 51818224--51818261 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
51818214 TAAAAGTATG
51818224 ATGCTATGGGAATTTATTA
1 ATGCTATGGGAATTTATTA
51818243 ATGCTATGGGAATTTATTA
1 ATGCTATGGGAATTTATTA
51818262 TCAATACTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (19 bp):
ATGCTATGGGAATTTATTA
Found at i:51818494 original size:29 final size:30
Alignment explanation
Indices: 51818461--51818537 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 30
51818451 TTTCTCTCGG
*
51818461 GTTACATTTTAGTCACTTATGTT-TGAAAT
1 GTTACATTTTAGTCACTTACGTTATGAAAT
* * * *
51818490 GTTACGTTTTAGTCTCTTACGTTAATGTAGT
1 GTTACATTTTAGTCACTTACGTT-ATGAAAT
*
51818521 GTAACATTTTAGTCACT
1 GTTACATTTTAGTCACT
51818538 GAGCTGTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.53
31 18 0.47
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.47
Consensus pattern (30 bp):
GTTACATTTTAGTCACTTACGTTATGAAAT
Found at i:51836587 original size:17 final size:15
Alignment explanation
Indices: 51836575--51836605 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
51836565 AAAAAGAATT
51836575 TATTTAAAAAAAGTA
1 TATTTAAAAAAAGTA
51836590 TATTTAAAAAAAGTA
1 TATTTAAAAAAAGTA
51836605 T
1 T
51836606 TGTAAAATGG
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
TATTTAAAAAAAGTA
Found at i:51836606 original size:13 final size:14
Alignment explanation
Indices: 51836575--51836612 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
51836565 AAAAAGAATT
51836575 TATTTAAAAAAAGTA
1 TATTTAAAAAAAG-A
51836590 TATTTAAAAAAAG-
1 TATTTAAAAAAAGA
51836603 TATTGTAAAA
1 TATT-TAAAA
51836613 TGGTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 5 0.23
15 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (14 bp):
TATTTAAAAAAAGA
Found at i:51838051 original size:9 final size:9
Alignment explanation
Indices: 51838039--51838080 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
51838029 AAATTGTAAA
51838039 AAAATATAT
1 AAAATATAT
51838048 AAAATATAT
1 AAAATATAT
51838057 AAAATAT-T
1 AAAATATAT
*
51838065 AGAAA-ATGT
1 A-AAATATAT
51838074 AAAATAT
1 AAAATAT
51838081 TGTAAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.23
9 23 0.77
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (9 bp):
AAAATATAT
Found at i:51838351 original size:11 final size:11
Alignment explanation
Indices: 51838335--51838366 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
51838325 CTCTAAAATT
51838335 CTCTCAATTTC
1 CTCTCAATTTC
*
51838346 CTCTCAATTTT
1 CTCTCAATTTC
51838357 CTCTCAATTT
1 CTCTCAATTT
51838367 GCCCTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:51838361 original size:22 final size:22
Alignment explanation
Indices: 51838333--51838385 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
51838323 TTCTCTAAAA
*
51838333 TTCTCTCAATTT-CCTCTCAATT
1 TTCTCTCAATTTGCC-CTCAAAT
*
51838355 TTCTCTCAATTTGCCCTGAAAT
1 TTCTCTCAATTTGCCCTCAAAT
51838377 TTCTCTCAA
1 TTCTCTCAA
51838386 ATCCCTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.21, C:0.30, G:0.04, T:0.45
Consensus pattern (22 bp):
TTCTCTCAATTTGCCCTCAAAT
Found at i:51840131 original size:30 final size:30
Alignment explanation
Indices: 51840088--51840148 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
51840078 ACGCAAACCT
* * *
51840088 ATCACCAAGGCCCAGACATTCACCTGGCCC
1 ATCACCAACGCCCAGACAATCACCAGGCCC
* *
51840118 ATCATCAACGCCCATACAATCACCAGGCCC
1 ATCACCAACGCCCAGACAATCACCAGGCCC
51840148 A
1 A
51840149 GCAACAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.43, G:0.13, T:0.13
Consensus pattern (30 bp):
ATCACCAACGCCCAGACAATCACCAGGCCC
Found at i:51844158 original size:126 final size:126
Alignment explanation
Indices: 51843902--51844180 Score: 470
Period size: 126 Copynumber: 2.2 Consensus size: 126
51843892 ACATGGGAGC
*
51843902 TTTTTTCAGGAGCTACTGTAGCAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
* *
51843967 CAAAGCATCCTGCTTAAAACGTTTTTGACACTGTTTGCTCAGAAACATCTACTCGAAATTA
66 CAAAGCATCCTGCTTAAAACGTTTTTGACACTGTTTACTCAGAAACATCTACTCGAAATGA
* * * *
51844028 TTTTTTCAGGAGCTACTGTAGCAAAAGCACGTCCACGTGGGAGCTTTTTTCAGTACTTTTGCTGA
1 TTTTTTCAGGAGCTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
* *
51844093 CAAAGCATCCTGCTTAAAGCGTTTTT-ACACTGTTTACTCAGAAACGTCTACTCGAAATGA
66 CAAAGCATCCTGCTTAAAACGTTTTTGACACTGTTTACTCAGAAACATCTACTCGAAATGA
51844153 TTTTTTCAGGAGCTACTGTAGCAAAAGC
1 TTTTTTCAGGAGCTACTGTAGCAAAAGC
51844181 GAGTTCAACC
Statistics
Matches: 144, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
125 59 0.41
126 85 0.59
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (126 bp):
TTTTTTCAGGAGCTACTGTAGCAAAAGCACATCCACGTGGGAGCTTCTTTCAGTACTTCTACTGA
CAAAGCATCCTGCTTAAAACGTTTTTGACACTGTTTACTCAGAAACATCTACTCGAAATGA
Found at i:51845095 original size:16 final size:16
Alignment explanation
Indices: 51845074--51845110 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
51845064 TTGGTTCGCT
51845074 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
51845090 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
51845106 GTAAT
1 GTAAT
51845111 AACAATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:51845185 original size:44 final size:45
Alignment explanation
Indices: 51845092--51845186 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 45
51845082 ATAGAGGCGT
* *
51845092 AATGGAATAGAGGCGTAATAACAATTCAATTGTTTGATTGAATGT
1 AATGGAATAGAGGCGTAATAACAATTCAATTGTTTGATTGAACGG
** * *
51845137 AATGGAATAGAGGCGTAAT-AGGATTC-TTGTGTTTGGTTGAACGG
1 AATGGAATAGAGGCGTAATAACAATTCAAT-TGTTTGATTGAACGG
51845181 AATGGA
1 AATGGA
51845187 GGTGTAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (45 bp):
AATGGAATAGAGGCGTAATAACAATTCAATTGTTTGATTGAACGG
Found at i:51849553 original size:17 final size:16
Alignment explanation
Indices: 51849523--51849564 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
51849513 TTAAAAAAAT
51849523 ATTTTTTT-TATTTTC
1 ATTTTTTTCTATTTTC
51849538 ATTTTTTTCTACTTTTC
1 ATTTTTTTCTA-TTTTC
51849555 -TTTCTTTTCT
1 ATTT-TTTTCT
51849565 TTTATAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.33
16 5 0.21
17 11 0.46
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTTCTATTTTC
Found at i:51850553 original size:24 final size:22
Alignment explanation
Indices: 51850500--51850554 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
51850490 TTTTCCTGAC
*
51850500 TCTTTTATTTGTTTGTCATTTT
1 TCTTTTTTTTGTTTGTCATTTT
*
51850522 TCGTTTTTTTTTGTTTTTCATTATT
1 TC--TTTTTTTTGTTTGTCATT-TT
51850547 TACTTTTT
1 T-CTTTTT
51850555 CAGTTATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
24 21 0.78
25 3 0.11
26 1 0.04
ACGTcount: A:0.09, C:0.09, G:0.07, T:0.75
Consensus pattern (22 bp):
TCTTTTTTTTGTTTGTCATTTT
Found at i:51850555 original size:15 final size:16
Alignment explanation
Indices: 51850535--51850564 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51850525 TTTTTTTTTG
51850535 TTTTTCA-TTATTTAC
1 TTTTTCAGTTATTTAC
51850550 TTTTTCAGTTATTTA
1 TTTTTCAGTTATTTA
51850565 TTTATTTGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.10, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTTTCAGTTATTTAC
Found at i:51850665 original size:22 final size:22
Alignment explanation
Indices: 51850594--51850678 Score: 73
Period size: 23 Copynumber: 3.7 Consensus size: 22
51850584 TTTTTATTGG
* * *
51850594 TTTTATAATATTTTTAATGTATA
1 TTTTA-AATATTTTAAATATAAA
* **
51850617 TTTTAAATGTTTTATAATATTATT
1 TTTTAAATATTTTA-AATA-TAAA
51850641 TTTTAAA-ATTTTAAATATAAA
1 TTTTAAATATTTTAAATATAAA
51850662 TTTTAAATTATTTTAAA
1 TTTTAAA-TATTTTAAA
51850679 AAAAATTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
21 9 0.18
22 11 0.22
23 21 0.41
24 10 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAATATTTTAAATATAAA
Found at i:51850684 original size:22 final size:21
Alignment explanation
Indices: 51850641--51850685 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
51850631 TAATATTATT
*
51850641 TTTTAAAATTTTAAATATAAA
1 TTTTAAAATTTTAAATAAAAA
51850662 TTTTAAATTATTTTAAA-AAAAA
1 TTTTAAA--ATTTTAAATAAAAA
51850684 TT
1 TT
51850686 AAATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 6 0.29
23 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTTAAAATTTTAAATAAAAA
Found at i:51850856 original size:23 final size:22
Alignment explanation
Indices: 51850830--51850879 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
51850820 ACTTTTAAAG
* *
51850830 ATATTCAAACTTTTTAAAAAATT
1 ATATTCAAA-ATTTTAAAAAATA
*
51850853 ATATTTAAAATTTTAAAAAATA
1 ATATTCAAAATTTTAAAAAATA
51850875 ATATT
1 ATATT
51850880 TTATTTGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATTCAAAATTTTAAAAAATA
Found at i:51850948 original size:7 final size:7
Alignment explanation
Indices: 51850936--51850970 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
51850926 TTTTAATATA
51850936 AAAATTT
1 AAAATTT
51850943 AAAATTT
1 AAAATTT
51850950 AAAATTT
1 AAAATTT
51850957 AAAATTT
1 AAAATTT
51850964 AAAATTT
1 AAAATTT
51850971 TGTTTTAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:51857748 original size:39 final size:40
Alignment explanation
Indices: 51857703--51857874 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
51857693 GCTCCTCGTT
* * *
51857703 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
51857743 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
51857782 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
51857822 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
51857862 CAAATGCCTTCGG
1 CAAATGCCTTCGG
51857875 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:51857803 original size:40 final size:39
Alignment explanation
Indices: 51857705--51857927 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
51857695 TCCTCGTTCA
* * * *
51857705 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
51857744 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
51857783 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
51857823 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
51857863 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
51857904 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
51857928 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:51857887 original size:80 final size:79
Alignment explanation
Indices: 51857703--51857927 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
51857693 GCTCCTCGTT
* * * * *
51857703 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
51857767 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
51857782 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
51857847 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
51857862 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
51857926 GA
63 GA
51857928 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:51857936 original size:41 final size:41
Alignment explanation
Indices: 51857859--51857936 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
51857849 TTTGTATCTC
* * *
51857859 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
51857900 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
51857937 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:51864437 original size:30 final size:32
Alignment explanation
Indices: 51864379--51864440 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
51864369 AAATAAATAA
*
51864379 TAAATAAAGGACAAATAAAAAAACTGAAAAAG
1 TAAATAAAGGACAAACAAAAAAACTGAAAAAG
*
51864411 TAAATAAAGTA-AAACAAAAAAA-TGAAAAAG
1 TAAATAAAGGACAAACAAAAAAACTGAAAAAG
51864441 GACAAACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 8 0.29
31 10 0.36
32 10 0.36
ACGTcount: A:0.71, C:0.05, G:0.11, T:0.13
Consensus pattern (32 bp):
TAAATAAAGGACAAACAAAAAAACTGAAAAAG
Found at i:51864455 original size:31 final size:31
Alignment explanation
Indices: 51864395--51864455 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
51864385 AAGGACAAAT
* *
51864395 AAAAAAACTGAAAAAGTAAATAAAGTAAAAC
1 AAAAAAACTGAAAAAGGAAATAAAATAAAAC
51864426 AAAAAAA-TGAAAAAGGACAA-ACAAATAAAA
1 AAAAAAACTGAAAAAGGA-AATA-AAATAAAA
51864456 GAACAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.74, C:0.07, G:0.10, T:0.10
Consensus pattern (31 bp):
AAAAAAACTGAAAAAGGAAATAAAATAAAAC
Found at i:51864473 original size:11 final size:11
Alignment explanation
Indices: 51864444--51864480 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
51864434 GAAAAAGGAC
51864444 AAACAAATAAA
1 AAACAAATAAA
51864455 AGAACAAATAAA
1 A-AACAAATAAA
51864467 AAACAAATAAA
1 AAACAAATAAA
51864478 AAA
1 AAA
51864481 AGCAGGGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.81, C:0.08, G:0.03, T:0.08
Consensus pattern (11 bp):
AAACAAATAAA
Found at i:51864481 original size:12 final size:12
Alignment explanation
Indices: 51864444--51864481 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
51864434 GAAAAAGGAC
51864444 AAACAAATAAAA
1 AAACAAATAAAA
*
51864456 GAACAAAT-AAA
1 AAACAAATAAAA
51864467 AAACAAATAAAA
1 AAACAAATAAAA
51864479 AAA
1 AAA
51864482 GCAGGGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (12 bp):
AAACAAATAAAA
Found at i:51865294 original size:17 final size:17
Alignment explanation
Indices: 51865272--51865329 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
51865262 TTCAACATAC
51865272 TTAAAATTTTAATATAT
1 TTAAAATTTTAATATAT
51865289 TTAAAATTCTTTAAGT-T-T
1 TTAAAA-T-TTTAA-TATAT
51865307 TTAAAATTTTAA-ATAT
1 TTAAAATTTTAATATAT
51865323 ATTAAAA
1 -TTAAAA
51865330 AGTATTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.03
16 6 0.17
17 13 0.37
18 8 0.23
19 6 0.17
20 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TTAAAATTTTAATATAT
Found at i:51865401 original size:40 final size:41
Alignment explanation
Indices: 51865350--51865429 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 41
51865340 ATTTTACGTA
*
51865350 TTAAAAAATATATTAAATATATT-AAAATTTTAATATATTT
1 TTAAAAAATATATTAAATATATTAAAAAATTTAATATATTT
*
51865390 TTAAAAAATATATTGAATATATTAAAAAATTTAATATATT
1 TTAAAAAATATATTAAATATATTAAAAAATTTAATATATT
51865430 ACAATTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
40 22 0.59
41 15 0.41
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (41 bp):
TTAAAAAATATATTAAATATATTAAAAAATTTAATATATTT
Found at i:51865488 original size:18 final size:18
Alignment explanation
Indices: 51865465--51865548 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 18
51865455 TATGCTTAAC
51865465 ATTTTTTTAATATATTTA
1 ATTTTTTTAATATATTTA
*
51865483 ATTTTTTAAATATA-TT-
1 ATTTTTTTAATATATTTA
** * *
51865499 ATTAAAATTTATTATACTTA
1 ATT--TTTTTAATATATTTA
*
51865519 ACATTTTTTAATATATTTAA
1 A-TTTTTTTAATATATTT-A
51865539 ATTTTTTTAA
1 ATTTTTTTAA
51865549 GTTTTTTTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
16 3 0.06
17 2 0.04
18 20 0.41
19 20 0.41
20 3 0.06
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTTTTTAATATATTTA
Found at i:51865546 original size:19 final size:19
Alignment explanation
Indices: 51865460--51865563 Score: 74
Period size: 19 Copynumber: 5.5 Consensus size: 19
51865450 TTGTTTATGC
51865460 TTAACATTTTTTTAATATAT
1 TTAA-ATTTTTTTAATATAT
*
51865480 TT-AATTTTTTAAATATATT
1 TTAAATTTTTTTAATATA-T
* * *
51865499 ATTAAA---ATTTATTATAC
1 -TTAAATTTTTTTAATATAT
51865516 TTAACA-TTTTTTAATATAT
1 TTAA-ATTTTTTTAATATAT
* *
51865535 TTAAATTTTTTTAAGTTTTT
1 TTAAATTTTTTTAA-TATAT
51865555 TTAAATTTT
1 TTAAATTTT
51865564 AAATATATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
16 4 0.06
17 1 0.02
18 21 0.32
19 22 0.33
20 16 0.24
21 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.61
Consensus pattern (19 bp):
TTAAATTTTTTTAATATAT
Found at i:51872627 original size:29 final size:30
Alignment explanation
Indices: 51872566--51872631 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
51872556 AAGTACAGCA
*
51872566 ACTAAAAGTGATCAATTCAAAAAGCATAAAG
1 ACTAAAAGTGATCAAAT-AAAAAGCATAAAG
* * *
51872597 ACTAAAATTGATCAAAT-AAAAGTATAGAG
1 ACTAAAAGTGATCAAATAAAAAGCATAAAG
51872626 ACTAAA
1 ACTAAA
51872632 TTTACAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
31 15 0.48
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21
Consensus pattern (30 bp):
ACTAAAAGTGATCAAATAAAAAGCATAAAG
Found at i:51873320 original size:13 final size:13
Alignment explanation
Indices: 51873302--51873329 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
51873292 ATAATATATT
51873302 TATTAATTAAAAA
1 TATTAATTAAAAA
51873315 TATTAATTAAAAA
1 TATTAATTAAAAA
51873328 TA
1 TA
51873330 ATAAAAAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:51884134 original size:14 final size:14
Alignment explanation
Indices: 51884115--51884143 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
51884105 AATGATGAGA
51884115 TTCAGCCCATTATT
1 TTCAGCCCATTATT
51884129 TTCAGCCCATTATT
1 TTCAGCCCATTATT
51884143 T
1 T
51884144 AAGGGTGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.45
Consensus pattern (14 bp):
TTCAGCCCATTATT
Found at i:51902986 original size:108 final size:108
Alignment explanation
Indices: 51902797--51903341 Score: 901
Period size: 108 Copynumber: 5.0 Consensus size: 108
51902787 ATATAACTAT
**
51902797 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGGTGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
*
51902862 ACTCAACACAACCCTATTCCCTATCCCATCGAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
*
51902905 ATAAATCTCAACCTTTTGTTATTAACTATCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
*
51902970 ACTCAACACAACCCTATTCCCTATCCCATCGAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* * * *
51903013 ATAAATCCCAACCTTTTGTTATTAACTAGCATAACAAAAATAACATAAACCCTAAATTGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
51903078 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* ** *
51903121 ATAAATCCCAATATTTTGTTATTAGCTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
*
51903186 ACTCAACACAACCTTATTCCCTATCCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
* * * *
51903229 ATAAATCTCAACCTTTTGTTATTAATTAGCATAACGAAAATGACGTAAACCCTAAATTGATTTAA
1 ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
* *
51903294 ACTAAACACAACCCTATTCCCTAACCCATCCAACCTCTTTGTA
66 ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
51903337 TATAA
1 -ATAA
51903342 CTAAATATTG
Statistics
Matches: 409, Mismatches: 27, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
108 405 0.99
109 4 0.01
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.30
Consensus pattern (108 bp):
ATAAATCTCAACCTTTTGTTATTAACTAGCATAACAAAAATGACGTAAACCCTAAATCGATCTAA
ACTCAACACAACCCTATTCCCTATCCCATCCAACCTCTTTGTA
Found at i:51904819 original size:210 final size:211
Alignment explanation
Indices: 51904296--51904838 Score: 537
Period size: 205 Copynumber: 2.6 Consensus size: 211
51904286 AAAATCAGTT
* **
51904296 TTTTGGACTAAAAATGATAGCTTTCATGGGTCAAAGATCTATGGTGAATTTGAGGTGACTGATGA
1 TTTTGGAC-CAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGA-G-G--TGATGA
* * * * * *
51904361 TCTAATTGGATTTATGGGG-TTGCTCTTTCCTTAATTATTAATTTATACAGTTCTTCTCTACTTC
61 TCTAATTGGATTGATGGGGTTTTC-CTTCCCTTAATGATTAATATATACAGTTCTTCTCTACTTA
* * * *
51904425 AGTGTAAAGGGTGTTTTGCTATCTTTCTAGATTGATATCATGTTTGGTTTCATCAACTGCTATAT
125 AATGTAAAGGGTGTTTTGCCATCTTTCTACATTGATATCATGTTTGGTTTCATCAACTACTATAT
51904490 GTAATTCAACATTGAAAATTCCTC
190 GTAATTCAACATTG--AATTCCTC
*
51904514 TTTTGGACTAAAATGATAGCTTTCATATGTCAAAGATCTAT-G-G----T--GGTGATGATCTAA
1 TTTTGGACCAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCTAA
* * ** *
51904571 TTGGATTGATGGTGTTTTTCTTGACTGT-ATGATTAATATGTACAGTTCTTCTCTACTTAAATGT
66 TTGGATTGATGGGGTTTTCCTTCCCT-TAATGATTAATATATACAGTTCTTCTCTACTTAAATGT
* * ** * *
51904635 AGAGGGTGTTTTGCCATCTCTTC-ACATTGA-ATAATTAGTTTTTTTTTATCAAATTAC-AT-TG
130 AAAGGGTGTTTTGCCATCT-TTCTACATTGATATCA-T-GTTTGGTTTCATC-AACTACTATATG
* * *
51904696 -AATAT-TA-GTTG-ATTCAGTC
191 TAAT-TCAACATTGAATTC-CTC
* *
51904715 TTGTTGGACCAAAATGATAGATTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCCA
1 TT-TTGGACCAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCTA
*
51904780 ATTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATATAGTTCTTCTCTACTT
65 ATTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATACAGTTCTTCTCTACTT
51904839 CAGAGTTACG
Statistics
Matches: 272, Mismatches: 35, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
200 4 0.01
201 4 0.01
202 37 0.14
203 4 0.01
204 8 0.03
205 86 0.32
206 18 0.07
207 5 0.02
208 2 0.01
209 1 0.00
210 62 0.23
211 1 0.00
215 1 0.00
216 1 0.00
217 30 0.11
218 8 0.03
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (211 bp):
TTTTGGACCAAAATGATAGCTTTCATATGTCAAAGATCTATGGTGAATTTGAGGTGATGATCTAA
TTGGATTGATGGGGTTTTCCTTCCCTTAATGATTAATATATACAGTTCTTCTCTACTTAAATGTA
AAGGGTGTTTTGCCATCTTTCTACATTGATATCATGTTTGGTTTCATCAACTACTATATGTAATT
CAACATTGAATTCCTC
Found at i:51913340 original size:28 final size:30
Alignment explanation
Indices: 51913309--51913387 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 30
51913299 TCAAAATATT
*
51913309 TTTTTTATCAC-AAG-TGGTACCTAAACTA
1 TTTTTTACCACTAAGTTGGTACCTAAACTA
* *
51913337 --TTTTCCCCCTAAGTTGGTACCTAAACTA
1 TTTTTTACCACTAAGTTGGTACCTAAACTA
* * *
51913365 TTTTTT-CCCCCAAGTTGGAACCT
1 TTTTTTACCACTAAGTTGGTACCT
51913388 TTGTCGTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
26 6 0.14
27 3 0.07
28 14 0.33
29 15 0.36
30 4 0.10
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38
Consensus pattern (30 bp):
TTTTTTACCACTAAGTTGGTACCTAAACTA
Found at i:51913379 original size:29 final size:27
Alignment explanation
Indices: 51913319--51913387 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 27
51913309 TTTTTTATCA
51913319 CAAG-TGGTACCTAAACTATTTTCCCC
1 CAAGTTGGTACCTAAACTATTTTCCCC
51913345 CTAAGTTGGTACCTAAACTATTTTTTCCCC
1 C-AAGTTGGTACCTAAACTA--TTTTCCCC
*
51913375 CAAGTTGGAACCT
1 CAAGTTGGTACCT
51913388 TTGTCGTTAG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
26 1 0.03
27 3 0.08
28 14 0.37
29 11 0.29
30 9 0.24
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (27 bp):
CAAGTTGGTACCTAAACTATTTTCCCC
Found at i:51918267 original size:46 final size:46
Alignment explanation
Indices: 51918198--51918336 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 46
51918188 ACATTACTAT
* *
51918198 AACTCAGTATGGTTTTCTACACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
51918244 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
* * * *
51918290 AACTCAATATGGTTTTCTTTA-TCGAAATAACATACCTGCTTTTCAC
1 AACTCAGTATGGTTTTCTTCACT-GAAATACCATACCTACTTTTCAC
51918336 A
1 A
51918337 CTTTGCCATG
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
45 1 0.01
46 85 0.99
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
Found at i:51921563 original size:21 final size:21
Alignment explanation
Indices: 51921537--51921579 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
51921527 ACGAGTTTAA
51921537 GCTTTTTGGATACTTGCAAAT
1 GCTTTTTGGATACTTGCAAAT
51921558 GCTTTTTGGATACTTGCAAAT
1 GCTTTTTGGATACTTGCAAAT
51921579 G
1 G
51921580 ATGTCTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (21 bp):
GCTTTTTGGATACTTGCAAAT
Found at i:51923887 original size:21 final size:20
Alignment explanation
Indices: 51923861--51923918 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
51923851 AATAAACACC
51923861 AAAAAA-AATTTTAGAAAATTA
1 AAAAAAGAATTTTA-AAAA-TA
*
51923882 AAAAAAGTATTTTAAAAATA
1 AAAAAAGAATTTTAAAAATA
*
51923902 AAAAAAGTATTTTAAAA
1 AAAAAAGAATTTTAAAA
51923919 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.54
21 10 0.29
22 6 0.17
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAAAGAATTTTAAAAATA
Found at i:51923920 original size:19 final size:20
Alignment explanation
Indices: 51923868--51923918 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
51923858 ACCAAAAAAA
51923868 ATTTTAGAAAATTAAAAAAAGT
1 ATTTTA-AAAA-TAAAAAAAGT
51923890 ATTTTAAAAATAAAAAAAGT
1 ATTTTAAAAATAAAAAAAGT
51923910 ATTTTAAAA
1 ATTTTAAAA
51923919 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 19 0.66
21 4 0.14
22 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTTTAAAAATAAAAAAAGT
Found at i:51924064 original size:32 final size:33
Alignment explanation
Indices: 51924008--51924079 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 33
51923998 GTTTTCTAAA
* *
51924008 CGGGCCTTATTTTTTTTCCCAAG-CCCATATTT
1 CGGGCCTTATATTTTTACCCAAGCCCCATATTT
51924040 CGGGCC-TATATTTTTACCCAAAGCCTCCCATATTT
1 CGGGCCTTATATTTTTACCC-AAG-C-CCCATATTT
51924075 CGGGC
1 CGGGC
51924080 GGGCAACACC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 11 0.32
32 9 0.26
35 14 0.41
ACGTcount: A:0.18, C:0.31, G:0.15, T:0.36
Consensus pattern (33 bp):
CGGGCCTTATATTTTTACCCAAGCCCCATATTT
Found at i:51925250 original size:3 final size:3
Alignment explanation
Indices: 51925244--51925276 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
51925234 GCCATCGCCG
51925244 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
51925277 ACCCATTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:51926742 original size:31 final size:31
Alignment explanation
Indices: 51926707--51926787 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
51926697 ATTCAATTTC
51926707 AAAAGTTATAATATT-A-TTATTAAATTATTCA
1 AAAAGTT-TAAT-TTAAGTTATTAAATTATTCA
* **
51926738 AAAAGTTTCATTTAAGTTATTAAATTATTTG
1 AAAAGTTTAATTTAAGTTATTAAATTATTCA
* *
51926769 AAAATTTTCATTTAAGTTA
1 AAAAGTTTAATTTAAGTTA
51926788 CTAGATAGTT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.05
30 4 0.09
31 38 0.86
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (31 bp):
AAAAGTTTAATTTAAGTTATTAAATTATTCA
Found at i:51929807 original size:31 final size:31
Alignment explanation
Indices: 51929772--51929831 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
51929762 CCAGTGACTA
**
51929772 AAATAAAAGTTTTTGAATAGTTCAATGATTT
1 AAATAAAAACTTTTGAATAGTTCAATGATTT
*
51929803 AAATAAAAACTTTTGAATAGTTCAGTGAT
1 AAATAAAAACTTTTGAATAGTTCAATGAT
51929832 CAAATTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.38
Consensus pattern (31 bp):
AAATAAAAACTTTTGAATAGTTCAATGATTT
Found at i:51930891 original size:25 final size:25
Alignment explanation
Indices: 51930858--51930911 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
51930848 AATATTTTTT
* **
51930858 TAAATTTAAATATTTTAATTAATAA
1 TAAAGTTAAATATAATAATTAATAA
51930883 TAAAGTTAAATATAATAATTAATAA
1 TAAAGTTAAATATAATAATTAATAA
51930908 TAAA
1 TAAA
51930912 TATAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TAAAGTTAAATATAATAATTAATAA
Found at i:51931270 original size:10 final size:10
Alignment explanation
Indices: 51931250--51931341 Score: 75
Period size: 10 Copynumber: 9.1 Consensus size: 10
51931240 GCCCATTTTT
51931250 ATTTT-AAAA
1 ATTTTAAAAA
51931259 ATTTTAAAAA
1 ATTTTAAAAA
**
51931269 ATTAAAAAAA
1 ATTTTAAAAA
51931279 GTATTTTAAAAA
1 --ATTTTAAAAA
*
51931291 TATTTTAAAAT
1 -ATTTTAAAAA
51931302 ATTTT--AAA
1 ATTTTAAAAA
*
51931310 A-TTAAAAAA
1 ATTTTAAAAA
51931319 ATTTTAAAAA
1 ATTTTAAAAA
51931329 AGTATTTAAAAA
1 A-T-TTTAAAAA
51931341 A
1 A
51931342 AATTTAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 9 0.13
10 25 0.37
11 11 0.16
12 17 0.25
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:51931291 original size:21 final size:20
Alignment explanation
Indices: 51931255--51931397 Score: 72
Period size: 21 Copynumber: 7.2 Consensus size: 20
51931245 TTTTTATTTT
*
51931255 AAAAAT-TTTAAAAAATTAA
1 AAAAATATTTTAAAAATTAA
**
51931274 AAAAAGTATTTTAAAAATATTT
1 AAAAA-TATTTTAAAAAT-TAA
*
51931296 TAAAATATTTT-AAAATTAA
1 AAAAATATTTTAAAAATTAA
*
51931315 AAAAAT-TTTAAAAAAGTATTTAA
1 AAAAATATTT-TAAAA--A-TTAA
51931338 AAAAA-A-TTT-AAAATT-A
1 AAAAATATTTTAAAAATTAA
* **
51931354 AAAAA-A-TTAAAAAAGTATGT
1 AAAAATATTTTAAAAA-T-TAA
51931374 AAAAATATTTT-AAAATTAA
1 AAAAATATTTTAAAAATTAA
51931393 AAAAA
1 AAAAA
51931398 ATAAATATAT
Statistics
Matches: 95, Mismatches: 14, Indels: 30
0.68 0.10 0.22
Matches are distributed among these distances:
16 9 0.09
17 6 0.06
18 5 0.05
19 18 0.19
20 18 0.19
21 20 0.21
22 10 0.11
23 9 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAAATATTTTAAAAATTAA
Found at i:51931327 original size:11 final size:11
Alignment explanation
Indices: 51931255--51931350 Score: 64
Period size: 11 Copynumber: 9.2 Consensus size: 11
51931245 TTTTTATTTT
51931255 AAAAATTTT-A
1 AAAAATTTTAA
*
51931265 AAAAA-TTAAA
1 AAAAATTTTAA
51931275 AAAAGTATTTTAA
1 AAAA--ATTTTAA
*
51931288 AAATATTTT-A
1 AAAAATTTTAA
*
51931298 AAATATTTT--
1 AAAAATTTTAA
51931307 -AAAA--TTAA
1 AAAAATTTTAA
51931315 AAAAATTTTAA
1 AAAAATTTTAA
*
51931326 AAAAGTATTTAA
1 AAAAAT-TTTAA
*
51931338 AAAAAATTTAA
1 AAAAATTTTAA
51931349 AA
1 AA
51931351 TTAAAAAAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
6 2 0.03
8 3 0.04
9 6 0.09
10 20 0.29
11 21 0.30
12 10 0.14
13 7 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AAAAATTTTAA
Done.