Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 50 of 82
Found at i:18351600 original size:4 final size:4
Alignment explanation
Indices: 18351560--18351586 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18351550 GCTAATACTT
18351560 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
18351587 GTGAAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:18353131 original size:13 final size:13
Alignment explanation
Indices: 18353113--18353137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18353103 TCTTTATTAG
18353113 TATATATATATAA
1 TATATATATATAA
18353126 TATATATATATA
1 TATATATATATA
18353138 TAGAACAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATATATATATAA
Found at i:18354282 original size:19 final size:19
Alignment explanation
Indices: 18354255--18354295 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
18354245 ATCGACAACT
* *
18354255 TTACTAACAAAATTTTTGG
1 TTACCAACAAAATTTTTCG
18354274 TTACCAACAAAATTTTTCG
1 TTACCAACAAAATTTTTCG
18354293 TTA
1 TTA
18354296 TCAAAGGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (19 bp):
TTACCAACAAAATTTTTCG
Found at i:18356566 original size:8 final size:8
Alignment explanation
Indices: 18356555--18356604 Score: 66
Period size: 8 Copynumber: 6.2 Consensus size: 8
18356545 AATAAGCATG
18356555 TATGTATA
1 TATGTATA
18356563 TATGTATA
1 TATGTATA
*
18356571 TATATATA
1 TATGTATA
*
18356579 TATATATA
1 TATGTATA
18356587 TATGTATA
1 TATGTATA
18356595 TGA-GTATA
1 T-ATGTATA
18356603 TA
1 TA
18356605 ATTAACTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
7 1 0.03
8 37 0.95
9 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (8 bp):
TATGTATA
Found at i:18356569 original size:12 final size:12
Alignment explanation
Indices: 18356552--18356595 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
18356542 GAAAATAAGC
*
18356552 ATGTATGTATAT
1 ATGTATATATAT
18356564 ATGTATATATAT
1 ATGTATATATAT
*
18356576 ATATATATATAT
1 ATGTATATATAT
18356588 ATGTATAT
1 ATGTATAT
18356596 GAGTATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
ATGTATATATAT
Found at i:18356604 original size:2 final size:2
Alignment explanation
Indices: 18356559--18356595 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
18356549 AGCATGTATG
* *
18356559 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18356596 GAGTATATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18357400 original size:15 final size:15
Alignment explanation
Indices: 18357380--18357432 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
18357370 AATAAGCATG
18357380 TATATATGTATATGA
1 TATATATGTATATGA
*
18357395 TATATATATATAT-A
1 TATATATGTATATGA
18357409 TATCATATCGTATATGA
1 TAT-ATAT-GTATATGA
18357426 GTATATA
1 -TATATA
18357433 ATTAACTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 16 0.50
16 5 0.16
17 4 0.12
18 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (15 bp):
TATATATGTATATGA
Found at i:18357404 original size:19 final size:19
Alignment explanation
Indices: 18357380--18357416 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
18357370 AATAAGCATG
* *
18357380 TATATATGTATATGATATA
1 TATATATATATATCATATA
18357399 TATATATATATATCATAT
1 TATATATATATATCATAT
18357417 CGTATATGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (19 bp):
TATATATATATATCATATA
Found at i:18358479 original size:2 final size:2
Alignment explanation
Indices: 18358472--18358505 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18358462 TTTCTTGGTA
18358472 CT CT CT 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 CT CT CT
18358506 GTGTTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18359138 original size:2 final size:2
Alignment explanation
Indices: 18359131--18359156 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18359121 CTGTGGTCTT
18359131 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
18359157 ACACACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18362454 original size:138 final size:138
Alignment explanation
Indices: 18362206--18362481 Score: 507
Period size: 138 Copynumber: 2.0 Consensus size: 138
18362196 GTAATGAAGG
* * *
18362206 CTTTCATAACATTCAATGATATTCCTGTACCGAAAGTGTGGGTGTTCCTGTTGATTTTTGTATTA
1 CTTTCATAACATTCAATGACATTCCTGTACCGAAAGTGTGGGTGTTCCTGTTGAATTCTGTATTA
18362271 AGTCTAATTAACCAGATTCAATATACCTGTGTAGAACTTCCTTGATTAACTTTAATTTTTATTAC
66 AGTCTAATTAACCAGATTCAATATACCTGTGTAGAACTTCCTTGATTAACTTTAATTTTTATTAC
18362336 AGCATGGA
131 AGCATGGA
*
18362344 CTTTCATAACATTCAATGACATTCCTGTACTGAAAGTGTGGGTGTTCCTGTTGAATTCTGTATTA
1 CTTTCATAACATTCAATGACATTCCTGTACCGAAAGTGTGGGTGTTCCTGTTGAATTCTGTATTA
*
18362409 AGTCTAATTAACCAGATTCAATATACCTGTGTAGAGCTTCCTTGATTAACTTTAATTTTTATTAC
66 AGTCTAATTAACCAGATTCAATATACCTGTGTAGAACTTCCTTGATTAACTTTAATTTTTATTAC
18362474 AGCATGGA
131 AGCATGGA
18362482 AAGGATCCTA
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 133 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (138 bp):
CTTTCATAACATTCAATGACATTCCTGTACCGAAAGTGTGGGTGTTCCTGTTGAATTCTGTATTA
AGTCTAATTAACCAGATTCAATATACCTGTGTAGAACTTCCTTGATTAACTTTAATTTTTATTAC
AGCATGGA
Found at i:18363320 original size:16 final size:16
Alignment explanation
Indices: 18363299--18363333 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
18363289 GTAAAAAACT
18363299 AAATAACCACCAAATA
1 AAATAACCACCAAATA
*
18363315 AAATAACCACTAAATA
1 AAATAACCACCAAATA
18363331 AAA
1 AAA
18363334 GAAACTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.20, G:0.00, T:0.14
Consensus pattern (16 bp):
AAATAACCACCAAATA
Found at i:18363848 original size:106 final size:104
Alignment explanation
Indices: 18363619--18363830 Score: 363
Period size: 106 Copynumber: 2.0 Consensus size: 104
18363609 CTGATGGACA
* *
18363619 CTCATATCTTCTAATTCTTTAGAGTTTATTGACCTCTCGGGATTCTTAGCCATGAATAACACCTC
1 CTCATATCTTCTAATTCTCTAGAGCTTATTGACCTCTCGGGATTCTTAGCCATGAATAACA-C-C
18363684 CTCATTCACCTCATGTTCTTCGGCTACTACAGCTTTTTCTT
64 CTCATTCACCTCATGTTCTTCGGCTACTACAGCTTTTTCTT
18363725 CTCATATCTTCTAATTCTCTAGAGCTTATTGACCTCTCGGGATTCTTAGCCATGAATAACA-CCT
1 CTCATATCTTCTAATTCTCTAGAGCTTATTGACCTCTCGGGATTCTTAGCCATGAATAACACCCT
* *
18363789 CATTCACCTCATTTTCTTTGGCTACTACAGCTTTTTCTT
66 CATTCACCTCATGTTCTTCGGCTACTACAGCTTTTTCTT
18363828 CTC
1 CTC
18363831 CTTGATTGAG
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
103 43 0.42
106 59 0.58
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.41
Consensus pattern (104 bp):
CTCATATCTTCTAATTCTCTAGAGCTTATTGACCTCTCGGGATTCTTAGCCATGAATAACACCCT
CATTCACCTCATGTTCTTCGGCTACTACAGCTTTTTCTT
Found at i:18386079 original size:20 final size:20
Alignment explanation
Indices: 18386051--18386089 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18386041 TAAATTATTT
18386051 TTAAA-TTTTATTATTTTTAA
1 TTAAATTTTTA-TATTTTTAA
*
18386071 TTAAGTTTTTATATTTTTA
1 TTAAATTTTTATATTTTTA
18386090 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
TTAAATTTTTATATTTTTAA
Found at i:18386495 original size:21 final size:21
Alignment explanation
Indices: 18386469--18386520 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
18386459 CTAAGAGCAA
* *
18386469 TTTTTAGATTCTTTTCTTATT
1 TTTTTAAATTCTATTCTTATT
18386490 TTTTTAAATTCTATTCTTATT
1 TTTTTAAATTCTATTCTTATT
18386511 CTTTTCTAAA
1 -TTTT-TAAA
18386521 GAGATTGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 19 0.70
22 4 0.15
23 4 0.15
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAAATTCTATTCTTATT
Found at i:18390527 original size:32 final size:32
Alignment explanation
Indices: 18390486--18390548 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
18390476 TGTCATAAGG
18390486 ACCTATCTGATCCAAAATAAAAATATAAAAAT
1 ACCTATCTGATCCAAAATAAAAATATAAAAAT
18390518 ACCTATCTGATCCAAAATAAAAATATAAAAA
1 ACCTATCTGATCCAAAATAAAAATATAAAAA
18390549 ATTCAATCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.57, C:0.16, G:0.03, T:0.24
Consensus pattern (32 bp):
ACCTATCTGATCCAAAATAAAAATATAAAAAT
Found at i:18391232 original size:35 final size:35
Alignment explanation
Indices: 18391182--18391271 Score: 128
Period size: 35 Copynumber: 2.6 Consensus size: 35
18391172 ACAGAGAACA
* *
18391182 AACT-GAACAAGTGAAGTATTACTTCACGCAAAAT
1 AACTAGAACAAGTGAAGTACTACTTCACGCAAAAC
*
18391216 AACTAGAACAAGTGAAGTGCTACTTCACGCAAAAC
1 AACTAGAACAAGTGAAGTACTACTTCACGCAAAAC
* *
18391251 AACTAGAATAAGTAAAGTACT
1 AACTAGAACAAGTGAAGTACT
18391272 CCATATGGAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
34 4 0.08
35 45 0.92
ACGTcount: A:0.46, C:0.18, G:0.16, T:0.21
Consensus pattern (35 bp):
AACTAGAACAAGTGAAGTACTACTTCACGCAAAAC
Found at i:18391530 original size:29 final size:29
Alignment explanation
Indices: 18391498--18391571 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 29
18391488 TATTCTCGTG
**
18391498 TACCTATTCTTGTACTTCTTCTTCTCTTA
1 TACCTATTCTTGTACAACTTCTTCTCTTA
** *
18391527 TACCTATTCTCATACAACTTCTTCTCTTG
1 TACCTATTCTTGTACAACTTCTTCTCTTA
18391556 TACCTATTCTTGTACA
1 TACCTATTCTTGTACA
18391572 CCTCTTTTCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.19, C:0.28, G:0.04, T:0.49
Consensus pattern (29 bp):
TACCTATTCTTGTACAACTTCTTCTCTTA
Found at i:18391829 original size:18 final size:17
Alignment explanation
Indices: 18391802--18391838 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
18391792 TCTCTTTAAA
18391802 TTCTCTTTTTAATTATC
1 TTCTCTTTTTAATTATC
*
18391819 TTCTACTTTTTAATTCTC
1 TTCT-CTTTTTAATTATC
18391837 TT
1 TT
18391839 TTTATTGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (17 bp):
TTCTCTTTTTAATTATC
Found at i:18392911 original size:50 final size:50
Alignment explanation
Indices: 18392854--18393111 Score: 141
Period size: 50 Copynumber: 5.1 Consensus size: 50
18392844 TTCAGCCGCT
* *
18392854 AGCTTTATCGCTTATATTTTGGCTATAATTATATTATACTATTGGTCGCA
1 AGCTTTATCGCTCATATTTTGGCCATAATTATATTATACTATTGGTCGCA
* * * * **
18392904 AGCTTTATCACTCAT-TCTTTGACCATAGTTCATCATTCTTACT-TCAG-CTGCA
1 AGCTTTATCGCTCATAT-TTTGGCCATAATT-AT-ATT-ATACTATTGGTC-GCA
* * ** * * *
18392956 AGCTTTTTCGCTCGTATTTTGGCCGCAATGATATTTTTCTATTGGTCGCA
1 AGCTTTATCGCTCATATTTTGGCCATAATTATATTATACTATTGGTCGCA
* * * ** *
18393006 AGCTTTATCGCTTAT-TCTTTGACCATAATTGAT-TT-TTCATATTTCATCCGCT
1 AGCTTTATCGCTCATAT-TTTGGCCATAATT-ATATTATAC-TA-TTGGT-CGCA
* ** * * *
18393058 AGCTTTATCGCTCATAATTTGGCTGTAATGATGTTATGCTATTGGTCGCA
1 AGCTTTATCGCTCATATTTTGGCCATAATTATATTATACTATTGGTCGCA
18393108 AGCT
1 AGCT
18393112 ATTCTCACCT
Statistics
Matches: 153, Mismatches: 39, Indels: 32
0.68 0.17 0.14
Matches are distributed among these distances:
49 9 0.06
50 63 0.41
51 16 0.10
52 58 0.38
53 7 0.05
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (50 bp):
AGCTTTATCGCTCATATTTTGGCCATAATTATATTATACTATTGGTCGCA
Found at i:18392990 original size:102 final size:102
Alignment explanation
Indices: 18392839--18393111 Score: 296
Period size: 102 Copynumber: 2.7 Consensus size: 102
18392829 TAAAAAAAAA
* * * *** *
18392839 TCATA-TTCAGCCGCTAGCTTTATCGCTTATATTTTGGCTATAATTATATTATACTATTGGTCGC
1 TCATACTTCAGCCGCAAGCTTTATCGCTCATAATTTGGCCGCAATGATATTATACTATTGGTCGC
*
18392903 AAGCTTTATCACTCATTCTTTGACCATAGTTCATCAT
66 AAGCTTTATCACTCATTCTTTGACCATAATTCATCAT
* * * * * * *
18392940 TCTTACTTCAGCTGCAAGCTTTTTCGCTCGTATTTTGGCCGCAATGATATTTTTCTATTGGTCGC
1 TCATACTTCAGCCGCAAGCTTTATCGCTCATAATTTGGCCGCAATGATATTATACTATTGGTCGC
* * * **
18393005 AAGCTTTATCGCTTATTCTTTGACCATAATTGATTTT
66 AAGCTTTATCACTCATTCTTTGACCATAATTCATCAT
* * * * * * *
18393042 TCATATTTCATCCGCTAGCTTTATCGCTCATAATTTGGCTGTAATGATGTTATGCTATTGGTCGC
1 TCATACTTCAGCCGCAAGCTTTATCGCTCATAATTTGGCCGCAATGATATTATACTATTGGTCGC
18393107 AAGCT
66 AAGCT
18393112 ATTCTCACCT
Statistics
Matches: 140, Mismatches: 31, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
101 4 0.03
102 136 0.97
ACGTcount: A:0.22, C:0.21, G:0.15, T:0.43
Consensus pattern (102 bp):
TCATACTTCAGCCGCAAGCTTTATCGCTCATAATTTGGCCGCAATGATATTATACTATTGGTCGC
AAGCTTTATCACTCATTCTTTGACCATAATTCATCAT
Found at i:18393944 original size:50 final size:50
Alignment explanation
Indices: 18393887--18394050 Score: 136
Period size: 50 Copynumber: 3.2 Consensus size: 50
18393877 TTCAGCCGCT
*
18393887 AGCTTTATCGCTTATATTTTGGCTGTAATTATATTATACTATTGGTCGCA
1 AGCTTTATCGCTCATATTTTGGCTGTAATTATATTATACTATTGGTCGCA
* * ** * * * *
18393937 AGCTTTATCACTCAT-TCTTTGACCATAGTTGATCATTCTCACT-TTAG-CTACA
1 AGCTTTATCGCTCATAT-TTTGGCTGTAATT-AT-ATTAT-ACTATTGGTC-GCA
* * * * *
18393989 AGCTTTTTCGCTCATATTTTGGCTGCAATGATATTTTTCTATTGGTCGCA
1 AGCTTTATCGCTCATATTTTGGCTGTAATTATATTATACTATTGGTCGCA
18394039 AGCTTTATCGCT
1 AGCTTTATCGCT
18394051 TATTCTTTGA
Statistics
Matches: 84, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
49 3 0.04
50 42 0.50
51 6 0.07
52 29 0.35
53 4 0.05
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.44
Consensus pattern (50 bp):
AGCTTTATCGCTCATATTTTGGCTGTAATTATATTATACTATTGGTCGCA
Found at i:18394150 original size:102 final size:102
Alignment explanation
Indices: 18393872--18394150 Score: 323
Period size: 102 Copynumber: 2.7 Consensus size: 102
18393862 TAAAAAAAAA
* * *
18393872 TCATA-TTCAGCCGCTAGCTTTATCGCTTATATTTTGGCTGTAATTATATTATACTATTGGTCGC
1 TCATATTTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATA-TATATTATTGGTCGC
* *
18393936 AAGCTTTATCACTCATTCTTTGACCATAGTTGATCATTC
65 AAGCTTTATCGCTCATTCTTTGACCATAATTGAT-ATTC
* ** * * * * *
18393975 TCA-CTTT-AGCTACAAGCTTTTTCGCTCATATTTTGGCTGCAATGATATTTTTCTATTGGTCGC
1 TCATATTTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATATATAT-TATTGGTCGC
* *
18394038 AAGCTTTATCGCTTATTCTTTGACCATAATTGAT-TTT
65 AAGCTTTATCGCTCATTCTTTGACCATAATTGATATTC
* * * *
18394075 TCATATTTCAGCCGCTAGCTTTATCGCTCATAATTTGGATGTAATGATGTAATGTTATTGGTCGC
1 TCATATTTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATAT-ATATTATTGGTCGC
18394140 AAGCTTTATCG
65 AAGCTTTATCG
18394151 TTAATTTCTT
Statistics
Matches: 145, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
100 5 0.03
101 5 0.03
102 128 0.88
103 7 0.05
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (102 bp):
TCATATTTCAGCCGCTAGCTTTATCGCTCATATTTTGGCTGTAATGATATATATTATTGGTCGCA
AGCTTTATCGCTCATTCTTTGACCATAATTGATATTC
Found at i:18394265 original size:26 final size:27
Alignment explanation
Indices: 18394225--18394276 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
18394215 AAGGTTGAAT
*
18394225 TAATCTCCTTCATATCAAGTT-AGAGC
1 TAATCTCCTTCATATAAAGTTGAGAGC
* *
18394251 TAATCTCTTTGATATAAAGTTGAGAG
1 TAATCTCCTTCATATAAAGTTGAGAG
18394277 TTCCCTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (27 bp):
TAATCTCCTTCATATAAAGTTGAGAGC
Found at i:18395089 original size:19 final size:19
Alignment explanation
Indices: 18395061--18395098 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
18395051 CCATTTAACT
* *
18395061 TATTGGAGTATGATTTGAG
1 TATTGAAGTATAATTTGAG
18395080 TATTGAAGTATAATTTGAG
1 TATTGAAGTATAATTTGAG
18395099 GGTTTTCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTGAAGTATAATTTGAG
Found at i:18397229 original size:11 final size:11
Alignment explanation
Indices: 18397213--18397244 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
18397203 TCAGGCTTGG
18397213 GATAGCCGATA
1 GATAGCCGATA
18397224 GATAGCCGATA
1 GATAGCCGATA
18397235 GATAGCCGAT
1 GATAGCCGAT
18397245 TACATCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.19
Consensus pattern (11 bp):
GATAGCCGATA
Found at i:18400479 original size:11 final size:10
Alignment explanation
Indices: 18400454--18400510 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 10
18400444 TTAATATATA
*
18400454 TAATAAAAAA
1 TAATAAAAAT
18400464 TAATAAAAAT
1 TAATAAAAAT
18400474 TGAATAAAAA-
1 T-AATAAAAAT
18400484 TAA-AAAAA-
1 TAATAAAAAT
18400492 TAA-AAAAAT
1 TAATAAAAAT
*
18400501 CAACTAAAAA
1 TAA-TAAAAA
18400511 AATAATTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 13 0.32
9 4 0.10
10 11 0.27
11 13 0.32
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (10 bp):
TAATAAAAAT
Found at i:18400511 original size:28 final size:28
Alignment explanation
Indices: 18400458--18400510 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
18400448 TATATATAAT
*
18400458 AAAAAATAATAAAAATTGAATAAAAATA
1 AAAAAATAATAAAAATTCAATAAAAATA
18400486 AAAAAATAA-AAAAA-TCAACTAAAAA
1 AAAAAATAATAAAAATTCAA-TAAAAA
18400511 AATAATTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 11 0.48
28 9 0.39
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (28 bp):
AAAAAATAATAAAAATTCAATAAAAATA
Found at i:18401177 original size:2 final size:2
Alignment explanation
Indices: 18401170--18401218 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
18401160 TATCTTGAAC
* *
18401170 AT AT AT AT -T AA AA AT AT AT AT AT AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
18401210 AT AC AT AT A
1 AT AT AT AT A
18401219 AAAAAAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18401200 original size:23 final size:23
Alignment explanation
Indices: 18401170--18401218 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
18401160 TATCTTGAAC
*
18401170 ATATATATTAAAAATATATATAT
1 ATATATATTAAAAATATATACAT
* *
18401193 ATATATATTATATATATATACAT
1 ATATATATTAAAAATATATACAT
18401216 ATA
1 ATA
18401219 AAAAAAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATATATTAAAAATATATACAT
Found at i:18401204 original size:17 final size:17
Alignment explanation
Indices: 18401184--18401217 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18401174 ATATTAAAAA
*
18401184 TATATATATATATATAT
1 TATATATATATACATAT
18401201 TATATATATATACATAT
1 TATATATATATACATAT
18401218 AAAAAAAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TATATATATATACATAT
Found at i:18401543 original size:64 final size:65
Alignment explanation
Indices: 18401463--18401592 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
18401453 TATAAGCCAC
18401463 ATAGAATCAAGA-TTTTTATGAAAAAGATATTAAATATTATTGCATAATCAATAAAATATTACAA
1 ATAGAATCAAGATTTTTTATGAAAAAGATATTAAATATTATTGCATAATCAATAAAATATTACAA
*
18401527 ATAGAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATAATCAATAAAATATTACAA
1 ATAGAATCAAGATTTTTTATGAAAAAGATATTAAATATTATTGCATAATCAATAAAATATTACAA
18401592 A
1 A
18401593 AGATATTGAC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
64 11 0.17
65 53 0.83
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (65 bp):
ATAGAATCAAGATTTTTTATGAAAAAGATATTAAATATTATTGCATAATCAATAAAATATTACAA
Found at i:18401597 original size:41 final size:41
Alignment explanation
Indices: 18401549--18401682 Score: 153
Period size: 41 Copynumber: 3.2 Consensus size: 41
18401539 TTTTTTATGA
*
18401549 AAAAGATATTAAATATTATTGCATAATCAATAAAATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
* * ** * * *
18401590 AAAAGATATTGACAT-TAAAAGAAAAATGCAATCAAATATTAT
1 AAAAGATATT-AAATATTATTGCATAAT-CAATCAAATATTAC
* *
18401632 GAAAGATATTAAATATTATTGCATAATCAATCAAATATCAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
18401673 AAAAGATATT
1 AAAAGATATT
18401683 GACATTACAA
Statistics
Matches: 72, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
41 41 0.57
42 31 0.43
ACGTcount: A:0.54, C:0.08, G:0.07, T:0.31
Consensus pattern (41 bp):
AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
Found at i:18402110 original size:41 final size:41
Alignment explanation
Indices: 18402062--18402195 Score: 162
Period size: 41 Copynumber: 3.2 Consensus size: 41
18402052 TTTTTTATGA
*
18402062 AAAAGATATTAAATATTATTGCATAATCAATAAAATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
* * ** * * *
18402103 AAAAGATATTGACAT-TAAAAGAAAAATGCAATCAAATATTAT
1 AAAAGATATT-AAATATTATTGCATAAT-CAATCAAATATTAC
*
18402145 GAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
1 AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
18402186 AAAAGATATT
1 AAAAGATATT
18402196 GACATTACAA
Statistics
Matches: 73, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
41 42 0.58
42 31 0.42
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.31
Consensus pattern (41 bp):
AAAAGATATTAAATATTATTGCATAATCAATCAAATATTAC
Found at i:18402150 original size:42 final size:41
Alignment explanation
Indices: 18402086--18402212 Score: 130
Period size: 42 Copynumber: 3.0 Consensus size: 41
18402076 ATTATTGCAT
*
18402086 AATCAATAAAATATTACAAAAGATATTGACATTAAAAGAAA
1 AATCAATCAAATATTACAAAAGATATTGACATTAAAAGAAA
** * * ** * *
18402127 AATGCAATCAAATATTATGAAAGATATT-AAATATTATTGCAT
1 AAT-CAATCAAATATTACAAAAGATATTGACAT-TAAAAGAAA
*
18402169 AATCAATCAAATATTACAAAAGATATTGACATTACAAAAAAA
1 AATCAATCAAATATTACAAAAGATATTGACATTA-AAAGAAA
18402211 AA
1 AA
18402213 AATTGGTATT
Statistics
Matches: 64, Mismatches: 18, Indels: 7
0.72 0.20 0.08
Matches are distributed among these distances:
41 29 0.45
42 35 0.55
ACGTcount: A:0.57, C:0.09, G:0.07, T:0.28
Consensus pattern (41 bp):
AATCAATCAAATATTACAAAAGATATTGACATTAAAAGAAA
Found at i:18402478 original size:513 final size:509
Alignment explanation
Indices: 18401510--18402523 Score: 1852
Period size: 513 Copynumber: 2.0 Consensus size: 509
18401500 TATTGCATAA
18401510 TCAATAAAATATTACAAATAGAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATAA
1 TCAATAAAATATTACAAATAGAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATAA
18401575 TCAATAAAATATTACAAAAGATATTGACATTAAAAGAAAAATGCAATCAAATATTATGAAAGATA
66 TCAATAAAATATTACAAAAGATATTGACATTAAAAGAAAAATGCAATCAAATATTATGAAAGATA
18401640 TTAAATATTATTGCATAATCAATCAAATATCACAAAAGATATTGACATTACAAAAAAAAAAAATT
131 TTAAATATTATTGCATAATCAATCAAATATCACAAAAGATATTGACATTACAAAAAAAAAAAATT
*
18401705 GGTATTACACCTTACATAAGGCAGTAACGTGTTACTACCTAAAGCATTACTGGCTAATGTGTTAC
196 GGTATTACACCTTACATAAGGCAGTAACGTGTTACTACCTAAAGCATTACTGGCTAAGGTGTTAC
18401770 TGTCTAAAGTAGTACTGCCCAAGGCATTACTGCTCAAAGTGATATAGTACAATACGTTATAGTAC
261 TGTCTAAAGTAGTACTGCCCAAGGCATTACTGCTCAAAGTGATATAGTACAATACGTTATAGTAC
* * *
18401835 AAAAAAAAATTATATTTTAAATTAATACATAAGAATTATTTTTTTTTAACAATTAATTCTTATGT
326 AAAAAAAAATTATACTTTAAATTAATACATAAGAATTA--TTTTTTTAACAATGAATTCTTATGC
* * * *
18401900 AGGGGGTAAAATGTAGATACTTGATTTTGGTTAATATTTATTCTCTAAAGAATTATGTTACAATA
389 AAGGGGCAAAATGTAGATACTTGATTTTGGTTAATACTTATACTCTAAAGAATTATGTTACAATA
18401965 TAATATTGCACAGAGAACAACCTGAACAAGTGAAAGTACTACTTCACTCAAATCAAC
454 TAATATTGCACAGAGAACAACCTGAACAAGTG-AAGTACTACTTCACTCAAATCAAC
18402022 TNCAATAAAATATTACAAATAGAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATA
1 T-CAATAAAATATTACAAATAGAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATA
18402087 ATCAATAAAATATTACAAAAGATATTGACATTAAAAGAAAAATGCAATCAAATATTATGAAAGAT
65 ATCAATAAAATATTACAAAAGATATTGACATTAAAAGAAAAATGCAATCAAATATTATGAAAGAT
*
18402152 ATTAAATATTATTGCATAATCAATCAAATATTACAAAAGATATTGACATTAC-AAAAAAAAAAAT
130 ATTAAATATTATTGCATAATCAATCAAATATCACAAAAGATATTGACATTACAAAAAAAAAAAAT
18402216 TGGTATTACACCTTACATAAGGCAGTAACGTGTTACTACCTAAAGCATTACTGGCTAAGGTGTTA
195 TGGTATTACACCTTACATAAGGCAGTAACGTGTTACTACCTAAAGCATTACTGGCTAAGGTGTTA
18402281 CTGTCTAAAGTAGTACTGCCCAAGGCATTACTGCTCAAAGTGATATAGTACAATACGTTATAGTA
260 CTGTCTAAAGTAGTACTGCCCAAGGCATTACTGCTCAAAGTGATATAGTACAATACGTTATAGTA
18402346 CAAAAAAAAAGAATTTATACTTTAAATTAATACATAAGAATTA-TTTTTTAACAATGAATTCTTA
325 C--AAAAAAA-AA-TTATACTTTAAATTAATACATAAGAATTATTTTTTTAACAATGAATTCTTA
*
18402410 TGCAAGGGGCAAAATGTAGATACTTGATTTTGGTTAATACTTCTACTCTAAAGAATTATGTTACA
386 TGCAAGGGGCAAAATGTAGATACTTGATTTTGGTTAATACTTATACTCTAAAGAATTATGTTACA
18402475 ATATAATATTGCACAGAGAACAACCTGAACAAGTGAAGTACTACTTCAC
451 ATATAATATTGCACAGAGAACAACCTGAACAAGTGAAGTACTACTTCAC
18402524 GCAGAATAAC
Statistics
Matches: 487, Mismatches: 10, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
512 157 0.32
513 293 0.60
514 7 0.01
515 2 0.00
516 28 0.06
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (509 bp):
TCAATAAAATATTACAAATAGAATCAAGGTTTTTTATGAAAAAGATATTAAATATTATTGCATAA
TCAATAAAATATTACAAAAGATATTGACATTAAAAGAAAAATGCAATCAAATATTATGAAAGATA
TTAAATATTATTGCATAATCAATCAAATATCACAAAAGATATTGACATTACAAAAAAAAAAAATT
GGTATTACACCTTACATAAGGCAGTAACGTGTTACTACCTAAAGCATTACTGGCTAAGGTGTTAC
TGTCTAAAGTAGTACTGCCCAAGGCATTACTGCTCAAAGTGATATAGTACAATACGTTATAGTAC
AAAAAAAAATTATACTTTAAATTAATACATAAGAATTATTTTTTTAACAATGAATTCTTATGCAA
GGGGCAAAATGTAGATACTTGATTTTGGTTAATACTTATACTCTAAAGAATTATGTTACAATATA
ATATTGCACAGAGAACAACCTGAACAAGTGAAGTACTACTTCACTCAAATCAAC
Found at i:18402547 original size:35 final size:35
Alignment explanation
Indices: 18402493--18402608 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
18402483 TTGCACAGAG
* *
18402493 AACAACCT-GAACAAGTGAAGTACTACTTCACGCAG
1 AACAA-CTAGAACAAGTGAAGTATTACTTCACGCAA
* * *
18402528 AATAACTAGAACAAGTGAAGTGTTACTTCACGTAA
1 AACAACTAGAACAAGTGAAGTATTACTTCACGCAA
* * *
18402563 AACAACTAGAACAAGTAAAGTATTACTTAAAGCAA
1 AACAACTAGAACAAGTGAAGTATTACTTCACGCAA
18402598 AACAACTAGAA
1 AACAACTAGAA
18402609 TAATGAAAGC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
34 2 0.03
35 67 0.97
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (35 bp):
AACAACTAGAACAAGTGAAGTATTACTTCACGCAA
Found at i:18402886 original size:29 final size:29
Alignment explanation
Indices: 18402854--18402929 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
18402844 CTTATTCTTA
* ***
18402854 TGTACCTATTCTTGTACCTTTTCTTCTCT
1 TGTACCTATTCTTATACAGCTTCTTCTCT
*
18402883 TGTACCTATTCTCATACAGCTTCTTCTCT
1 TGTACCTATTCTTATACAGCTTCTTCTCT
*
18402912 TGTACTTATTCTTATACA
1 TGTACCTATTCTTATACA
18402930 CCTCTTTTCT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.17, C:0.26, G:0.07, T:0.50
Consensus pattern (29 bp):
TGTACCTATTCTTATACAGCTTCTTCTCT
Found at i:18405053 original size:20 final size:20
Alignment explanation
Indices: 18405028--18405065 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
18405018 TTGTAGATTT
* *
18405028 TTTTAATTGGTTAAAGTTTA
1 TTTTAATCGATTAAAGTTTA
18405048 TTTTAATCGATTAAAGTT
1 TTTTAATCGATTAAAGTT
18405066 AAAGAAAGAG
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:0.32, C:0.03, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTTAATCGATTAAAGTTTA
Found at i:18405094 original size:21 final size:21
Alignment explanation
Indices: 18405070--18405116 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
18405060 AAAGTTAAAG
*
18405070 AAAGAGAAGCTTTAATCAATT
1 AAAGAGAAGCATTAATCAATT
* *
18405091 AAAG-GGAGGATTAATCAATT
1 AAAGAGAAGCATTAATCAATT
18405111 ACAAGA
1 A-AAGA
18405117 AAGTTGTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (21 bp):
AAAGAGAAGCATTAATCAATT
Found at i:18408726 original size:32 final size:30
Alignment explanation
Indices: 18408684--18408742 Score: 91
Period size: 32 Copynumber: 1.9 Consensus size: 30
18408674 AAAGAGAAAG
18408684 AAAGGATTTAGAAAGAGAGAGAGTTCAAAGGA
1 AAAGGATTTAGAAAGAGAGA-A-TTCAAAGGA
*
18408716 AAAGGTTTTAGAAAGAGAGAATTCAAA
1 AAAGGATTTAGAAAGAGAGAATTCAAA
18408743 AAGAAGAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 1 0.04
32 19 0.73
ACGTcount: A:0.51, C:0.03, G:0.27, T:0.19
Consensus pattern (30 bp):
AAAGGATTTAGAAAGAGAGAATTCAAAGGA
Found at i:18408735 original size:30 final size:32
Alignment explanation
Indices: 18408684--18408742 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
18408674 AAAGAGAAAG
*
18408684 AAAGGATTTAGAAAGAGAGAGAGTTCAAAGGA
1 AAAGGATTTAGAAAGAGAGAGAATTCAAAGGA
*
18408716 AAAGGTTTTAG-AA-AGAGAGAATTCAAA
1 AAAGGATTTAGAAAGAGAGAGAATTCAAA
18408743 AAGAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 13 0.52
31 2 0.08
32 10 0.40
ACGTcount: A:0.51, C:0.03, G:0.27, T:0.19
Consensus pattern (32 bp):
AAAGGATTTAGAAAGAGAGAGAATTCAAAGGA
Found at i:18410214 original size:6 final size:6
Alignment explanation
Indices: 18410203--18410261 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
18410193 TAATGCATGC
* * *
18410203 AAAAGA AAAAGA AAAA-A AAAA-A AAAAG- -AAAGG AAAAGG AAAAGG
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
18410247 AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAA
18410262 CCCACCACGG
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
4 4 0.08
5 10 0.20
6 35 0.71
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:18410888 original size:18 final size:19
Alignment explanation
Indices: 18410857--18410898 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
18410847 GGGAATTTGG
18410857 GGAAA-GAGGAGGGGAGGA
1 GGAAAGGAGGAGGGGAGGA
*
18410875 GTAAAGGAGG-GGGGAGGA
1 GGAAAGGAGGAGGGGAGGA
18410893 GGAAAG
1 GGAAAG
18410899 AGAAGGTGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.38, C:0.00, G:0.60, T:0.02
Consensus pattern (19 bp):
GGAAAGGAGGAGGGGAGGA
Found at i:18421004 original size:2 final size:2
Alignment explanation
Indices: 18420997--18421027 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18420987 TGACAATGTC
18420997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18421028 AGAATAAACC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18421515 original size:10 final size:11
Alignment explanation
Indices: 18421491--18421517 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
18421481 GGTAAAAACC
18421491 AAAAAAAAAGA
1 AAAAAAAAAGA
18421502 AAAAAAAAAGA
1 AAAAAAAAAGA
18421513 AAAAA
1 AAAAA
18421518 TTGAATTGCT
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:18422290 original size:15 final size:16
Alignment explanation
Indices: 18422272--18422301 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18422262 TAAAAAGTGG
18422272 AAATAATAA-AATGAT
1 AAATAATAACAATGAT
18422287 AAATAATAACAATGA
1 AAATAATAACAATGA
18422302 GCATATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.03, G:0.07, T:0.23
Consensus pattern (16 bp):
AAATAATAACAATGAT
Found at i:18426777 original size:2 final size:2
Alignment explanation
Indices: 18426765--18426801 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
18426755 TTGTACAAAT
*
18426765 TA TA CA 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 T
18426802 TAATTCTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18433232 original size:13 final size:12
Alignment explanation
Indices: 18433209--18433248 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
18433199 TTAATAATGT
*
18433209 ATTAACATATTA
1 ATTAACTTATTA
18433221 ATGTAACTTATTA
1 AT-TAACTTATTA
18433234 TATTAACTTATTA
1 -ATTAACTTATTA
18433247 AT
1 AT
18433249 ATATTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 19 0.76
14 2 0.08
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (12 bp):
ATTAACTTATTA
Found at i:18435206 original size:15 final size:16
Alignment explanation
Indices: 18435186--18435223 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
18435176 TATAGAATAA
*
18435186 TGATAATT-CGTAATT
1 TGATAATTAAGTAATT
18435201 TGATAATTAAGTAATT
1 TGATAATTAAGTAATT
*
18435217 TGGTAAT
1 TGATAAT
18435224 ATTCGTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.45
Consensus pattern (16 bp):
TGATAATTAAGTAATT
Found at i:18446176 original size:2 final size:2
Alignment explanation
Indices: 18446169--18446217 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
18446159 NNNNNNNNNN
18446169 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18446211 AT AT AT A
1 AT AT AT A
18446218 AAAGAAAGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18446472 original size:59 final size:59
Alignment explanation
Indices: 18446422--18446818 Score: 555
Period size: 59 Copynumber: 6.7 Consensus size: 59
18446412 AATTTATAAG
* * * * * *
18446422 CTTGATTTAGGCACGACCGATCTCAAAATAAGTTCGATTTAAAAATTGAAATTCATAGA
1 CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
* * *
18446481 CTTAATCTAGGCTCGACCGATTTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
1 CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
* *
18446540 CTTGATCTAGGCTCGACTTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAAA
1 CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
* *
18446599 CTTGATCTAGGCTCAACCTATCTCAAAATAGGTTCGATTTAAAAATTGAAATTCCTAGA
1 CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
* * *
18446658 CTTGATCTAGGCTCGACCCATCTCAAAACAAGTTCGATTTAAAAATTGAAATTTCTAGA
1 CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
* * *
18446717 CTAT-ATCTAGGCTCGACCTATCTCATAACAGGTTCGATTTAAAAAATTAAAATGT-CTAAA
1 CT-TGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTT-AAAAATTGAAAT-TCCTAGA
* * *
18446777 CTTAATCTAGGCTCAACCTATCTCACAACAGGTTCGATTTAA
1 CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAA
18446819 TTCTCTAATG
Statistics
Matches: 306, Mismatches: 28, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
59 253 0.83
60 52 0.17
61 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (59 bp):
CTTGATCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTGAAATTCCTAGA
Found at i:18450657 original size:448 final size:448
Alignment explanation
Indices: 18449822--18450689 Score: 1475
Period size: 448 Copynumber: 1.9 Consensus size: 448
18449812 CATGAATTTC
* * * *
18449822 TTACTCAAGTAGTATATGACCTGTTCTTTCTTTCCTATTTCATCATGTTACCCTAGTACATATCT
1 TTACTCAAGTAGTATATGACCTGTTCTCTCTTTCCTATTTCATCATGTTACCCCAATACACATCT
18449887 CATGGAATTCTTGTTCATAGTTAAATACAAAATAAGAGGTTTTTCAGCCGTTGGTGGTACCAATA
66 CATGGAATTCTTGTTCATAGTTAAATACAAAATAAGAGGTTTTTCAGCCGTTGGTGGTACCAATA
*
18449952 CCGGTGGATTTGTGAGATACTTTTTTATTTTATCAAAAACTATCTGACATTCTTCATTCCACTCT
131 CCGGTGGATTTGTGAGATACTTTTTGATTTTATCAAAAACTATCTGACATTCTTCATTCCACTCT
* * *
18450017 TTTAGGTCTCGCTTTCGAAGTAGCTTGAAGATTGGATCGCGTTTAAAGGTGAGTTAGGATATAAA
196 TTTAGGTCTCGCTTTCGAAGCAGCTTGAAGATTGGATCACGTTTAAAGATGAGTTAGGATATAAA
18450082 TCGAGCAATGTAATTCAACCTCCTTAAAAATCCTCTCACTTCTTTTTGCATTTTAGGAGGTGGCA
261 TCGAGCAATGTAATTCAACCTCCTTAAAAATCCTCTCACTTCTTTTTGCATTTTAGGAGGTGGCA
*
18450147 ACTCTTGAATAGCTCGTATTTTATCCGGGTCCACTTCAATTCTTTTTTCACTTACTACAAACCCC
326 ACTCTTGAATAACTCGTATTTTATCCGGGTCCACTTCAATTCTTTTTTCACTTACTACAAACCCC
18450212 AACAATTTCCAAGAAGTAACACAAAAAGTAGTATATGGCATGTTCTTTCTTTTTTCAT
391 AACAATTTCCAAGAAGTAACACAAAAAGTAGTATATGGCATGTTCTTTCTTTTTTCAT
* * * *
18450270 TTACTCAAGTAGTATATGGCCTGTTCTCTCTTTCTTGTTTCATCATGTTGCCCCAATACACATCT
1 TTACTCAAGTAGTATATGACCTGTTCTCTCTTTCCTATTTCATCATGTTACCCCAATACACATCT
* *
18450335 CATGGAATTCTTGTTCATAGTTAAATACAAACTAAGAGGTTTTTCAGTCGTTGGTGGTACCAATA
66 CATGGAATTCTTGTTCATAGTTAAATACAAAATAAGAGGTTTTTCAGCCGTTGGTGGTACCAATA
* ** *
18450400 TCGGTGGATTTGTGAGATACTTTTTGATTTTATCAAAGGCTATCTGACATTCTTCATTCCATTCT
131 CCGGTGGATTTGTGAGATACTTTTTGATTTTATCAAAAACTATCTGACATTCTTCATTCCACTCT
* * * *
18450465 TTTGGGTCTTGCTTTCGAAGCAGCTTGAAGATTGGATCACTTTTAAAGATGAGTTGGGATATAAA
196 TTTAGGTCTCGCTTTCGAAGCAGCTTGAAGATTGGATCACGTTTAAAGATGAGTTAGGATATAAA
* *
18450530 TCGAGCAATGTAATTCAACCTCCTTAAAAATCCTTTCACTTCTTTTTGCTTTTTAGGAGGTGGCA
261 TCGAGCAATGTAATTCAACCTCCTTAAAAATCCTCTCACTTCTTTTTGCATTTTAGGAGGTGGCA
*
18450595 ACTCTTGAATAACTTGTATTTTATCCGGGTCCACTTCAATTCTTTTTTCACTTACTACAAACCCC
326 ACTCTTGAATAACTCGTATTTTATCCGGGTCCACTTCAATTCTTTTTTCACTTACTACAAACCCC
* * *
18450660 AACAATTTTCAGGAAGTAACACCAAAAGTA
391 AACAATTTCCAAGAAGTAACACAAAAAGTA
18450690 CATTTTATAG
Statistics
Matches: 391, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
448 391 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (448 bp):
TTACTCAAGTAGTATATGACCTGTTCTCTCTTTCCTATTTCATCATGTTACCCCAATACACATCT
CATGGAATTCTTGTTCATAGTTAAATACAAAATAAGAGGTTTTTCAGCCGTTGGTGGTACCAATA
CCGGTGGATTTGTGAGATACTTTTTGATTTTATCAAAAACTATCTGACATTCTTCATTCCACTCT
TTTAGGTCTCGCTTTCGAAGCAGCTTGAAGATTGGATCACGTTTAAAGATGAGTTAGGATATAAA
TCGAGCAATGTAATTCAACCTCCTTAAAAATCCTCTCACTTCTTTTTGCATTTTAGGAGGTGGCA
ACTCTTGAATAACTCGTATTTTATCCGGGTCCACTTCAATTCTTTTTTCACTTACTACAAACCCC
AACAATTTCCAAGAAGTAACACAAAAAGTAGTATATGGCATGTTCTTTCTTTTTTCAT
Found at i:18457099 original size:16 final size:14
Alignment explanation
Indices: 18457066--18457112 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
18457056 TTTATAAGCT
18457066 TCTCTCACTTTCTC
1 TCTCTCACTTTCTC
18457080 TCTCTTCACTTTCT-
1 TCTC-TCACTTTCTC
18457094 TCTCTCACTTTCTC
1 TCTCTCACTTTCTC
18457108 TCTCT
1 TCTCT
18457113 AGCGATGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.29
14 13 0.42
15 9 0.29
ACGTcount: A:0.06, C:0.40, G:0.00, T:0.53
Consensus pattern (14 bp):
TCTCTCACTTTCTC
Found at i:18457179 original size:17 final size:18
Alignment explanation
Indices: 18457153--18457188 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18457143 GATTTTTTCC
*
18457153 CTTTTTTTTTTCT-TCTT
1 CTTTTATTTTTCTCTCTT
18457170 CTTTTATTTTTCTCTCTT
1 CTTTTATTTTTCTCTCTT
18457188 C
1 C
18457189 CTTTCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (18 bp):
CTTTTATTTTTCTCTCTT
Found at i:18458432 original size:217 final size:217
Alignment explanation
Indices: 18458040--18458478 Score: 779
Period size: 217 Copynumber: 2.0 Consensus size: 217
18458030 AGTGTTGGAC
* ** *
18458040 AAAGAAAAACAGAAGTATGCTAATCGGTTAAGGCATGTGGTTAATCGATTAGAGCACAAGACTTG
1 AAAGAAAAACAAAAGTATGCTAATCGGTTAAGGCATACGGTTAATCAATTAGAGCACAAGACTTG
*
18458105 AAGAATATCCAAAGCTCCAAAATTTAAATTTAAAATGAAGATGAACGTTGAATGGAGTCAAAATA
66 AAGAATATCCAAAGCTCCAAAATTTAAATTTAAAATGAAGATGAAAGTTGAATGGAGTCAAAATA
18458170 AAGAAGTGCAAATTCGAAGAATTTTTAATTGATTAGAGCTTGTGTTAATCAGTTAAGGCTAAAGG
131 AAGAAGTGCAAATTCGAAGAATTTTTAATTGATTAGAGCTTGTGTTAATCAGTTAAGGCTAAAGG
18458235 AAGTGAAGCTCCAATCAGTTAA
196 AAGTGAAGCTCCAATCAGTTAA
* * * *
18458257 AAAGGAAAACAAAAGTGTGCTAATTGGTTAAGGCATACGGTTAATCAATTAGAGCGCAAGACTTG
1 AAAGAAAAACAAAAGTATGCTAATCGGTTAAGGCATACGGTTAATCAATTAGAGCACAAGACTTG
*
18458322 AAGAATATCCAAAGCTCCAAAATTTAAATTTAAAGTGAAGATGAAAGTTGAATGGAGTCAAAATA
66 AAGAATATCCAAAGCTCCAAAATTTAAATTTAAAATGAAGATGAAAGTTGAATGGAGTCAAAATA
*
18458387 AAGAAGTGTAAATTCGAAGAATTTTTAATTGATTAGAGCTTGTGTTAATCAGTTAAGGCTAAAGG
131 AAGAAGTGCAAATTCGAAGAATTTTTAATTGATTAGAGCTTGTGTTAATCAGTTAAGGCTAAAGG
18458452 AAGTGAAGCTCCAATCAGTTAA
196 AAGTGAAGCTCCAATCAGTTAA
18458474 AAAGA
1 AAAGA
18458479 GAGTTAACCA
Statistics
Matches: 210, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 210 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.26
Consensus pattern (217 bp):
AAAGAAAAACAAAAGTATGCTAATCGGTTAAGGCATACGGTTAATCAATTAGAGCACAAGACTTG
AAGAATATCCAAAGCTCCAAAATTTAAATTTAAAATGAAGATGAAAGTTGAATGGAGTCAAAATA
AAGAAGTGCAAATTCGAAGAATTTTTAATTGATTAGAGCTTGTGTTAATCAGTTAAGGCTAAAGG
AAGTGAAGCTCCAATCAGTTAA
Found at i:18462159 original size:18 final size:19
Alignment explanation
Indices: 18462116--18462168 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
18462106 TTAATATATT
*
18462116 ATTAAATAAATTTAAAAAAC
1 ATTAAA-AAAGTTAAAAAAC
*
18462136 A-AAAAAAAGTTAAAAAA-
1 ATTAAAAAAGTTAAAAAAC
*
18462153 ATTAAAATAGTTAAAA
1 ATTAAAAAAGTTAAAA
18462169 TCGATTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.04
18 23 0.82
19 3 0.11
20 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.25
Consensus pattern (19 bp):
ATTAAAAAAGTTAAAAAAC
Found at i:18464707 original size:66 final size:66
Alignment explanation
Indices: 18464614--18464896 Score: 539
Period size: 66 Copynumber: 4.3 Consensus size: 66
18464604 CCCATCCTGA
* * *
18464614 CTCCAAACCCTTTTCAGCTACCTCCCCTGCTTCCTCCAAACCCCATTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
18464679 C
66 C
18464680 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
18464745 C
66 C
18464746 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
18464811 C
66 C
18464812 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
18464877 C
66 C
18464878 CTCCCAACCCTTTTCAGCC
1 CTCCCAACCCTTTTCAGCC
18464897 GCCACCAGCT
Statistics
Matches: 214, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 214 1.00
ACGTcount: A:0.13, C:0.52, G:0.06, T:0.29
Consensus pattern (66 bp):
CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
C
Found at i:18464896 original size:33 final size:33
Alignment explanation
Indices: 18464614--18464896 Score: 406
Period size: 33 Copynumber: 8.6 Consensus size: 33
18464604 CCCATCCTGA
18464614 CTCCAAACCCTTTTCAG-CTACCTCCCCTGCTTC
1 CTCCAAACCCTTTTCAGCCT-CCTCCCCTGCTTC
** *
18464647 CTCCAAACCCCATTCAGCCTCCTCCCTTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
* *
18464680 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
* *
18464713 CTCCAAACCCCTTTCAGCCTCCTCCCTTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
* *
18464746 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
* *
18464779 CTCCAAACCCCTTTCAGCCTCCTCCCTTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
* *
18464812 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
* *
18464845 CTCCAAACCCCTTTCAGCCTCCTCCCTTGCTTC
1 CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
*
18464878 CTCCCAACCCTTTTCAGCC
1 CTCCAAACCCTTTTCAGCC
18464897 GCCACCAGCT
Statistics
Matches: 219, Mismatches: 30, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
33 217 0.99
34 2 0.01
ACGTcount: A:0.13, C:0.52, G:0.06, T:0.29
Consensus pattern (33 bp):
CTCCAAACCCTTTTCAGCCTCCTCCCCTGCTTC
Found at i:18464930 original size:36 final size:38
Alignment explanation
Indices: 18464878--18465124 Score: 308
Period size: 36 Copynumber: 6.6 Consensus size: 38
18464868 CCCTTGCTTC
* * * *
18464878 CTCCCAACCCTTTTCAGCCGCCACCAGCTCCAC-TTAT
1 CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
*
18464915 -TCCAAACCCGTTTCAGCCTCCTCCAGCTCCAC-TTAT
1 CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
* *
18464951 -TCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTTTT
1 CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
* *
18464988 CCTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTTTT
1 -CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
*
18465027 CCTCCAAACCCGTTTCAGCCTCCTCCAGCTCCAC-TTAT
1 -CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
* *
18465065 -TCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTTTT
1 CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
*
18465102 CCTCCAAACCCGTTTCGGCCTCC
1 -CTCCAAACCCGTTTCAGCCTCC
18465125 TCGAGCACCT
Statistics
Matches: 190, Mismatches: 14, Indels: 10
0.89 0.07 0.05
Matches are distributed among these distances:
36 92 0.48
37 6 0.03
38 3 0.02
39 89 0.47
ACGTcount: A:0.16, C:0.47, G:0.10, T:0.27
Consensus pattern (38 bp):
CTCCAAACCCGTTTCAGCCTCCCCCAGCTCCACTTTAT
Found at i:18464935 original size:66 final size:64
Alignment explanation
Indices: 18464614--18464932 Score: 395
Period size: 66 Copynumber: 4.8 Consensus size: 64
18464604 CCCATCCTGA
* * ** *
18464614 CTCCAAACCCTTTTCAGCTACCTCCCCTGCTTCCTCCAAACCCCATTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCCACTTCCTCCAAACCCCTTTCAG-C-CCTCCCTTGCTT
18464679 C
64 C
**
18464680 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCCACTTCCTCCAAACCCCTTTCAG-C-CCTCCCTTGCTT
18464745 C
64 C
**
18464746 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCCACTTCCTCCAAACCCCTTTCAG-C-CCTCCCTTGCTT
18464811 C
64 C
**
18464812 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCTCCCCCACTTCCTCCAAACCCCTTTCAG-C-CCTCCCTTGCTT
18464877 C
64 C
* * ** *
18464878 CTCCCAACCCTTTTCAGCCGCCACCAGCTCCACTTATTCCAAACCCGTTTCAGCC
1 CTCCCAACCCTTTTCAGCCACCTCC--C-CCACTTCCTCCAAACCCCTTTCAGCC
18464933 TCCTCCAGCT
Statistics
Matches: 240, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
66 218 0.91
67 1 0.00
68 2 0.01
69 19 0.08
ACGTcount: A:0.14, C:0.51, G:0.07, T:0.28
Consensus pattern (64 bp):
CTCCCAACCCTTTTCAGCCACCTCCCCCACTTCCTCCAAACCCCTTTCAGCCCTCCCTTGCTTC
Found at i:18464935 original size:132 final size:130
Alignment explanation
Indices: 18464614--18464932 Score: 449
Period size: 132 Copynumber: 2.4 Consensus size: 130
18464604 CCCATCCTGA
* * * ** * *
18464614 CTCCAAACCCTTTTCAGCTACCTCCCCTGCTTCCTCCAAACCCCATTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCACCCCCACTTACTCCAAACCCCTTTCAG-C-CCTCCCTTGCTT
18464679 CCTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCT
64 CCTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCT
18464744 TC
129 TC
* ** *
18464746 CTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTT
1 CTCCCAACCCTTTTCAGCCACCACCCCCACTTACTCCAAACCCCTTTCAG-C-CCTCCCTTGCTT
18464811 CCTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCT
64 CCTCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCT
18464876 TC
129 TC
* * *
18464878 CTCCCAACCCTTTTCAGCCGCCACCAGCTCCACTTATTCCAAACCCGTTTCAGCC
1 CTCCCAACCCTTTTCAGCCACCACC--C-CCACTTACTCCAAACCCCTTTCAGCC
18464933 TCCTCCAGCT
Statistics
Matches: 174, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
132 152 0.87
133 1 0.01
134 2 0.01
135 19 0.11
ACGTcount: A:0.14, C:0.51, G:0.07, T:0.28
Consensus pattern (130 bp):
CTCCCAACCCTTTTCAGCCACCACCCCCACTTACTCCAAACCCCTTTCAGCCCTCCCTTGCTTCC
TCCCAACCCTTTTCAGCCACCTCCCCTGCTTCCTCCAAACCCCTTTCAGCCTCCTCCCTTGCTTC
Found at i:18465072 original size:114 final size:111
Alignment explanation
Indices: 18464875--18465124 Score: 410
Period size: 114 Copynumber: 2.2 Consensus size: 111
18464865 CCTCCCTTGC
* * *
18464875 TTCCTCCCAACCCTTTTCAGCCGCCACCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCTCCA
1 TTCCTCCAAACCCGTTTCAGCCTCCACCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCTCCA
18464940 GCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTT
66 GCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTT
* * *
18464986 TTCCTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTTTTCCTCCAAACCCGTTTCAGCCTCCT
1 TTCCTCCAAACCCGTTTCAGCCTCCACCAGCTCCAC-TTAT--TCCAAACCCGTTTCAGCCTCCT
18465051 CCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTT
63 CCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTT
*
18465100 TTCCTCCAAACCCGTTTCGGCCTCC
1 TTCCTCCAAACCCGTTTCAGCCTCC
18465125 TCGAGCACCT
Statistics
Matches: 129, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
111 31 0.24
112 3 0.02
114 95 0.74
ACGTcount: A:0.16, C:0.47, G:0.10, T:0.28
Consensus pattern (111 bp):
TTCCTCCAAACCCGTTTCAGCCTCCACCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCTCCA
GCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTT
Found at i:18465125 original size:75 final size:75
Alignment explanation
Indices: 18464875--18465126 Score: 357
Period size: 75 Copynumber: 3.4 Consensus size: 75
18464865 CCTCCCTTGC
* * * * * *
18464875 TTCCTCCCAACCCTTTTCAGCCGCCACCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCTCCA
1 TTCCTCCAAACCCGTTTCAGCCTCCTCCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCG
18464940 GCTCCAC-TT
66 GCTCCACTTT
* * * *
18464949 AT--TCCAAACCCGTTTCAGCCTCCCCCGGCTCCACTTTTTCCTCCAAACCCGTTTCAGCCTCCC
1 TTCCTCCAAACCCGTTTCAGCCTCCTCCAGCTCCAC-TTAT--TCCAAACCCGTTTCAGCCTCCC
18465012 CCGGCTCCACTTT
63 CCGGCTCCACTTT
18465025 TTCCTCCAAACCCGTTTCAGCCTCCTCCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCG
1 TTCCTCCAAACCCGTTTCAGCCTCCTCCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCG
18465090 GCTCCACTTT
66 GCTCCACTTT
*
18465100 TTCCTCCAAACCCGTTTCGGCCTCCTC
1 TTCCTCCAAACCCGTTTCAGCCTCCTC
18465127 GAGCACCTCC
Statistics
Matches: 158, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
72 27 0.17
73 3 0.02
74 1 0.01
75 91 0.58
76 3 0.02
77 3 0.02
78 30 0.19
ACGTcount: A:0.15, C:0.47, G:0.10, T:0.28
Consensus pattern (75 bp):
TTCCTCCAAACCCGTTTCAGCCTCCTCCAGCTCCACTTATTCCAAACCCGTTTCAGCCTCCCCCG
GCTCCACTTT
Found at i:18465192 original size:3 final size:3
Alignment explanation
Indices: 18465177--18465206 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
18465167 AGGGCTAACT
*
18465177 CCA CCA TCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA
18465207 TTCTTCCCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.63, G:0.00, T:0.03
Consensus pattern (3 bp):
CCA
Found at i:18470078 original size:37 final size:39
Alignment explanation
Indices: 18470015--18470099 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 39
18470005 GCAATTGTCC
*
18470015 ATTTTTTATTATTAATTATTATTTTCATTT-T-ATT-TT
1 ATTTTTTATTATCAATTATTATTTTCATTTCTAATTATT
*
18470051 ATTTTTTATTATCATATT-TTCTATTTCATTTCTAATTATT
1 ATTTTTTATTATCA-ATTATTAT-TTTCATTTCTAATTATT
18470091 ATTTTTTAT
1 ATTTTTTAT
18470100 ACTTTACAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
36 16 0.38
37 11 0.26
38 1 0.02
39 3 0.07
40 11 0.26
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (39 bp):
ATTTTTTATTATCAATTATTATTTTCATTTCTAATTATT
Found at i:18472002 original size:17 final size:18
Alignment explanation
Indices: 18471981--18472022 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
18471971 TTCTTTTTTC
18471981 ATTTTTTCATTATT-ATTT
1 ATTTTTTCATT-TTCATTT
*
18471999 -TTTTGTCATTTTCATTT
1 ATTTTTTCATTTTCATTT
18472016 ATTTTTT
1 ATTTTTT
18472023 GTTTATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTTTTCATTTTCATTT
Found at i:18472010 original size:24 final size:21
Alignment explanation
Indices: 18471974--18472022 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
18471964 TTTTTTTTTC
18471974 TTTTTTCATTTTTTCATTATTATT
1 TTTTTTCA-TTTTTCA-T-TTATT
18471998 TTTTTGTCA-TTTTCATTTATT
1 TTTTT-TCATTTTTCATTTATT
18472019 TTTT
1 TTTT
18472023 GTTTATGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 6 0.25
24 5 0.21
25 3 0.12
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTTCATTTTTCATTTATT
Found at i:18472033 original size:24 final size:24
Alignment explanation
Indices: 18471984--18472040 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
18471974 TTTTTTCATT
*
18471984 TTTTCA-TTATTATTTTTTTGTCA
1 TTTTCATTTATTATTTTTTTATCA
*
18472007 TTTTCATTTATT-TTTTGTTTATGA
1 TTTTCATTTATTATTTT-TTTATCA
*
18472031 TTTTTATTTA
1 TTTTCATTTA
18472041 ATAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTTCATTTATTATTTTTTTATCA
Found at i:18472289 original size:36 final size:38
Alignment explanation
Indices: 18472212--18472290 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 38
18472202 AAGAGATTTT
* *
18472212 TCAAAGCTGAGGCAACGAAACTTCTAAAAATGAACTTC
1 TCAAAGCTGAGGCAACGAAACTTCTAAAAATAAACTCC
*
18472250 TCAAAGCTGAGGCAACG-AACTT-TTAAAATAAACTCC
1 TCAAAGCTGAGGCAACGAAACTTCTAAAAATAAACTCC
18472286 TCAAA
1 TCAAA
18472291 ACTTAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 16 0.42
37 5 0.13
38 17 0.45
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.22
Consensus pattern (38 bp):
TCAAAGCTGAGGCAACGAAACTTCTAAAAATAAACTCC
Found at i:18472293 original size:23 final size:23
Alignment explanation
Indices: 18472267--18472315 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
18472257 TGAGGCAACG
*
18472267 AACTTTTAAAATAAACTCCTCAA
1 AACTTTAAAAATAAACTCCTCAA
* *
18472290 AAC-TTAAAAATGAACTCTTCAA
1 AACTTTAAAAATAAACTCCTCAA
18472312 AACT
1 AACT
18472316 GAGACAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (23 bp):
AACTTTAAAAATAAACTCCTCAA
Found at i:18472305 original size:22 final size:22
Alignment explanation
Indices: 18472274--18472315 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18472264 ACGAACTTTT
18472274 AAAATAAACTCCTCAAAACTTA
1 AAAATAAACTCCTCAAAACTTA
* *
18472296 AAAATGAACTCTTCAAAACT
1 AAAATAAACTCCTCAAAACT
18472316 GAGACAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.21, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAACTCCTCAAAACTTA
Found at i:18472347 original size:60 final size:58
Alignment explanation
Indices: 18472236--18472353 Score: 157
Period size: 58 Copynumber: 2.0 Consensus size: 58
18472226 ACGAAACTTC
* *
18472236 TAAAAATGAACTTCTCAAAGCTGAGGCAACGAACTTTTAAAATAAACTCCTCAAAACT
1 TAAAAATGAACTTCTCAAAACTGAGACAACGAACTTTTAAAATAAACTCCTCAAAACT
* * *
18472294 TAAAAATGAAC-TCTTCAAAACTGAGACAACTAGGCTTTTGAAAATGAACTCCTCAAAACT
1 TAAAAATGAACTTC-TCAAAACTGAGACAACGA-ACTTTT-AAAATAAACTCCTCAAAACT
18472354 GAGGTAATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 2 0.04
58 26 0.50
59 5 0.10
60 19 0.37
ACGTcount: A:0.44, C:0.20, G:0.11, T:0.25
Consensus pattern (58 bp):
TAAAAATGAACTTCTCAAAACTGAGACAACGAACTTTTAAAATAAACTCCTCAAAACT
Found at i:18472664 original size:38 final size:38
Alignment explanation
Indices: 18472293--18472666 Score: 387
Period size: 38 Copynumber: 9.9 Consensus size: 38
18472283 TCCTCAAAAC
* * * **
18472293 TTAAAAATGAACTCTTCAAAACTGAGACAACTAGGCTT
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
* * * **
18472331 TTGAAAATGAACTCCTCAAAACTGAGGTAATGGGACTT
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
* * * **
18472369 TAAAAAATGAACTCCTCAAAACTGAGGTAATGGGACTT
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
* *
18472407 TAAAAAATGAACTCCTCAAAACTGAGGCAATGAAAC-T
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
* * *
18472444 TTAAAAATGAACTCTTCAAAATTGAGGCAATGAAAC-T
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
* * *
18472481 TGAAAAATGAACTCCTCAAAGCTGAGGCAACGAGACTT
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
*
18472519 TTAAAAATGAACTCCTCAAAGCTTGAGGCAACGAAACTT
1 TTAAAAATGAACTCCTCAAAAC-TGAGGCAACGAAACTT
* * * ** *
18472558 CTT-TAAACGAACTCGTCAAAGTTGAGGCAATGAAACTT
1 -TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
* *
18472596 CTAAAAATGAACTCCTCAAAA-TCAAGGCAACGAAACTT
1 TTAAAAATGAACTCCTCAAAACT-GAGGCAACGAAACTT
* *
18472634 TTAAAAATGAACTACTCAAAATTGAGGCAACGA
1 TTAAAAATGAACTCCTCAAAACTGAGGCAACGA
18472667 GACCCCTTTT
Statistics
Matches: 291, Mismatches: 39, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
37 67 0.23
38 191 0.66
39 31 0.11
40 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (38 bp):
TTAAAAATGAACTCCTCAAAACTGAGGCAACGAAACTT
Found at i:18484508 original size:16 final size:19
Alignment explanation
Indices: 18484473--18484518 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
18484463 AATTGTCCAT
18484473 TTTTTATTATTAATTATTA
1 TTTTTATTATTAATTATTA
18484492 TTTTTATT-TT-ATT-TTA
1 TTTTTATTATTAATTATTA
18484508 TTTTTTATTAT
1 -TTTTTATTAT
18484519 CATATTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.12
17 11 0.44
18 3 0.12
19 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTATTATTAATTATTA
Found at i:18485837 original size:78 final size:78
Alignment explanation
Indices: 18485687--18485930 Score: 294
Period size: 82 Copynumber: 3.1 Consensus size: 78
18485677 CGGCTTTTCT
* * * *
18485687 TTCTCC-CTCTACCCAGGTTAACCAACGGCAACTCAAGCACCAGATCCAGCGCCGGTAGGGCTTC
1 TTCTCCTCTCTACCCACGTTAACCGACGGCAACCCAAGCACCAGATCCAGCGCCGGTAGCGCTTC
18485751 CTCTCTCTCACTC
66 CTCTCTCTCACTC
* ** * *
18485764 TTCTCCTCTCTACCCACGCTAACCGGTGGCAACCCAAGCACCAGATCCAGCGCCGGCT-TCTCTC
1 TTCTCCTCTCTACCCACGTTAACCGACGGCAACCCAAGCACCAGATCCAGCGCCGG-TAGCGCT-
*
18485828 TCCTCCTCTCTCTCTC
64 TCCT-CTCTCTCACTC
* ** * *
18485844 TCGCTCTCTCTCTACCCACGTTAACCGACGGCAACCCAAGCACCAGATCCAGCATCGGTCGGGCT
1 T-TCTC-CTCTCTACCCACGTTAACCGACGGCAACCCAAGCACCAGATCCAGCGCCGGTAGCGCT
18485909 TCCTCTCTCTCACTC
64 TCCTCTCTCTCACTC
18485924 TTCTCCT
1 TTCTCCT
18485931 GTCGACGCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
77 6 0.04
78 47 0.34
79 8 0.06
80 22 0.16
81 8 0.06
82 48 0.35
ACGTcount: A:0.18, C:0.43, G:0.15, T:0.24
Consensus pattern (78 bp):
TTCTCCTCTCTACCCACGTTAACCGACGGCAACCCAAGCACCAGATCCAGCGCCGGTAGCGCTTC
CTCTCTCTCACTC
Found at i:18485841 original size:14 final size:14
Alignment explanation
Indices: 18485822--18485856 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
18485812 AGCGCCGGCT
18485822 TCTCTCTC-CTC-C
1 TCTCTCTCTCTCGC
18485834 TCTCTCTCTCTCGC
1 TCTCTCTCTCTCGC
18485848 TCTCTCTCT
1 TCTCTCTCT
18485857 ACCCACGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 3 0.14
14 10 0.48
ACGTcount: A:0.00, C:0.51, G:0.03, T:0.46
Consensus pattern (14 bp):
TCTCTCTCTCTCGC
Found at i:18486301 original size:15 final size:14
Alignment explanation
Indices: 18486281--18486314 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
18486271 CTCCACCCTT
*
18486281 TTTTTTCTTTTTTCA
1 TTTTTTCTTTATT-A
18486296 TTTTTTCTTTATTA
1 TTTTTTCTTTATTA
18486310 TTTTT
1 TTTTT
18486315 GTGTCACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTTATTA
Found at i:18487771 original size:35 final size:34
Alignment explanation
Indices: 18487713--18487819 Score: 104
Period size: 35 Copynumber: 3.3 Consensus size: 34
18487703 ATTCAAAGGT
* *
18487713 CTTCGCTTCAAGGTATTTTATGACTTGATCTTGAA
1 CTTCGCTTCAAGG-GTCTTATGACTTGATCTTGAA
18487748 CTTCGCTTCAAGGGTC-T-TGA--TGA-CTTGAA
1 CTTCGCTTCAAGGGTCTTATGACTTGATCTTGAA
* *
18487777 ---CGATTCAAGAGTCTTGATGACTTGATCTTGAA
1 CTTCGCTTCAAGGGTCTT-ATGACTTGATCTTGAA
18487809 CTTCGCTTCAA
1 CTTCGCTTCAA
18487820 TGAACAATAT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
26 11 0.19
27 1 0.02
29 9 0.16
30 3 0.05
31 3 0.05
32 9 0.16
33 1 0.02
34 1 0.02
35 20 0.34
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (34 bp):
CTTCGCTTCAAGGGTCTTATGACTTGATCTTGAA
Found at i:18488244 original size:79 final size:80
Alignment explanation
Indices: 18488106--18488271 Score: 196
Period size: 79 Copynumber: 2.1 Consensus size: 80
18488096 AATATGGATT
*
18488106 TTATCTCTTAAATTATCTTAATTTATTTAGAAATAAATTGGATAACCAATAAGTAAATTTTAATT
1 TTATCTCTTAAATTATCTTAATTTATTTAGAAATAAATTGGACAACCAATAAGTAAATTTTAATT
*
18488171 GGTCAAATTTAA-ATA
66 GATCAAA-TTAATATA
* * * * **
18488186 TTATCTC-TAAATTATCTTGATTTATTTAGAGATAACA-TGGACAACCAAT-GGATGAATTTTTG
1 TTATCTCTTAAATTATCTTAATTTATTTAGAAATAA-ATTGGACAACCAATAAG-TAAATTTTAA
*
18488248 TTGATCCAATTAATATA
64 TTGATCAAATTAATATA
18488265 TTATCTC
1 TTATCTC
18488272 AAAAGATAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
78 5 0.07
79 61 0.82
80 8 0.11
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (80 bp):
TTATCTCTTAAATTATCTTAATTTATTTAGAAATAAATTGGACAACCAATAAGTAAATTTTAATT
GATCAAATTAATATA
Found at i:18493833 original size:4 final size:4
Alignment explanation
Indices: 18493824--18493854 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
18493814 CATAGCTATT
18493824 TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
18493855 CATTTTGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:18494655 original size:2 final size:2
Alignment explanation
Indices: 18494648--18494695 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
18494638 TTGCTTGTTT
18494648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18494690 TA TA TA
1 TA TA TA
18494696 CTCAGNAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18495246 original size:2 final size:2
Alignment explanation
Indices: 18495239--18495267 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18495229 TTAAAGTTAA
18495239 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18495268 AATCTGCTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18496482 original size:2 final size:2
Alignment explanation
Indices: 18496475--18496502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18496465 TTTAAACAAA
18496475 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
18496503 TTTAGCTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18499443 original size:18 final size:17
Alignment explanation
Indices: 18499395--18499444 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
18499385 AATGAGATAG
* *
18499395 ATAGAAGAAGAGTAGAA
1 ATAGAAGAAGGGAAGAA
18499412 ATAGAAGAAGGGAAGAA
1 ATAGAAGAAGGGAAGAA
18499429 A-AGAGAGACAGGGAAG
1 ATAGA-AGA-AGGGAAG
18499445 GGGCATGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 19 0.66
18 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.36, T:0.06
Consensus pattern (17 bp):
ATAGAAGAAGGGAAGAA
Found at i:18503895 original size:30 final size:30
Alignment explanation
Indices: 18503852--18503922 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
18503842 AATTATTAGT
* *
18503852 TATAAGGATTTATTTAATTCAAAATAAAAA
1 TATAAAGACTTATTTAATTCAAAATAAAAA
** *
18503882 TATAAAGACTTATTTGGTTCAAAATAAAAG
1 TATAAAGACTTATTTAATTCAAAATAAAAA
*
18503912 TATAAAAACTT
1 TATAAAGACTT
18503923 GATTGAACGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (30 bp):
TATAAAGACTTATTTAATTCAAAATAAAAA
Found at i:18509598 original size:39 final size:39
Alignment explanation
Indices: 18509555--18509634 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
18509545 ACCATAGGTA
*
18509555 CTTTCAGTTTTGGTTAACCTGTGTCTTTCTCTCTTAAAG
1 CTTTCAGTTTTGGTTAACCTGTCTCTTTCTCTCTTAAAG
18509594 CTTTCAGTTTTGGTTAACCTGTCTCTTTCTCTCTTAAAG
1 CTTTCAGTTTTGGTTAACCTGTCTCTTTCTCTCTTAAAG
18509633 CT
1 CT
18509635 ATCATCCCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.15, C:0.23, G:0.14, T:0.49
Consensus pattern (39 bp):
CTTTCAGTTTTGGTTAACCTGTCTCTTTCTCTCTTAAAG
Found at i:18520361 original size:29 final size:29
Alignment explanation
Indices: 18520313--18520384 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
18520303 ATTAAAGTAT
* * * *
18520313 AACAAAATGTTTTTGAATATGTCGTGTAAC
1 AACAATAT-TTTTTCAATATGGCATGTAAC
18520343 AACAATATTTTTTCAATATGGCATGTAAC
1 AACAATATTTTTTCAATATGGCATGTAAC
18520372 AACAATATTTTTT
1 AACAATATTTTTT
18520385 TTTTTAACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 31 0.82
30 7 0.18
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (29 bp):
AACAATATTTTTTCAATATGGCATGTAAC
Found at i:18520529 original size:45 final size:45
Alignment explanation
Indices: 18520465--18520569 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
18520455 AATAGTATTT
* **
18520465 TTTTTTCA-ACATGGTGTGTAACAACCTAACCATGGCTTGTCACAG
1 TTTTTT-ATACATGGCGTGTAACAACCTAACCATAACTTGTCACAG
*
18520510 TTTTTTATACATGGCGTGTAACAAGCTAACCATAACTTGTCACAG
1 TTTTTTATACATGGCGTGTAACAACCTAACCATAACTTGTCACAG
** *
18520555 GCTTTTGTACATGGC
1 TTTTTTATACATGGC
18520570 ATGTCACATA
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (45 bp):
TTTTTTATACATGGCGTGTAACAACCTAACCATAACTTGTCACAG
Found at i:18520529 original size:77 final size:79
Alignment explanation
Indices: 18520360--18520533 Score: 201
Period size: 77 Copynumber: 2.2 Consensus size: 79
18520350 TTTTTTCAAT
* * *
18520360 ATGGCATGTAACAACAATATTTTTTTTTTTAACATGGTGTGTAACAACCTTTTTTAACTATGACT
1 ATGGCGTGTAACAACAATATTTTTTTTTTCAACATGGTGTGTAACAACC----TTAACCATGACT
*
18520425 TGTAACATATTTTTTTAC
62 TGTAACATATTTTTATAC
* * * * *
18520443 ATAGCGTGTAACAATAGTA-TTTTTTTTTCAACATGGTGTGTAACAACC-TAACCATGGCTTGTC
1 ATGGCGTGTAACAACAATATTTTTTTTTTCAACATGGTGTGTAACAACCTTAACCATGACTTGTA
18520506 ACAGT-TTTTTATAC
66 ACA-TATTTTTATAC
18520520 ATGGCGTGTAACAA
1 ATGGCGTGTAACAA
18520534 GCTAACCATA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
77 36 0.45
78 1 0.01
82 28 0.35
83 15 0.19
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (79 bp):
ATGGCGTGTAACAACAATATTTTTTTTTTCAACATGGTGTGTAACAACCTTAACCATGACTTGTA
ACATATTTTTATAC
Found at i:18520681 original size:69 final size:68
Alignment explanation
Indices: 18520495--18520716 Score: 266
Period size: 69 Copynumber: 3.2 Consensus size: 68
18520485 ACAACCTAAC
* * * * * * *
18520495 CATGGCTTGTCACAGT-TTTTTATACATGGCGTGTAACAAGCTAACCATAACTTGTCACAGGCTT
1 CATGGCGTGTCACA-TATTTTTGTACATAGCGTGTAACACGCTAACCATGATTTGTCACA-GTTT
18520559 TTGTA
64 TTGTA
* * *
18520564 CATGGCATGTCACATATTTTTGTACATAACGTGTAACACGCTAACCATGATTTGTCATACGTTTT
1 CATGGCGTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGATTTGTCACA-GTTTT
18520629 TGTA
65 TGTA
* *
18520633 CATGGCGTGTCACTTATTTTTGTACATAGCGTGTAACACGCTAACCATGGTTTGTCACAGATTTT
1 CATGGCGTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGATTTGTCACAG-TTTT
18520698 TGTA
65 TGTA
* * *
18520702 TATAGCGTGTAACAT
1 CATGGCGTGTCACAT
18520717 CATAACATGT
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
68 2 0.02
69 130 0.98
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.36
Consensus pattern (68 bp):
CATGGCGTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGATTTGTCACAGTTTTT
GTA
Found at i:18526183 original size:25 final size:25
Alignment explanation
Indices: 18526127--18526201 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
18526117 TTTAATTTTC
*
18526127 AATTATAATTTAG-TTATTTTTAGTTT
1 AATTATAA-TTAGTTTATTTTTA-TTA
**
18526153 GTTTATAATTAGTTTATTTTTATTA
1 AATTATAATTAGTTTATTTTTATTA
*
18526178 AATTATTTATTA-TTTATTTTTATT
1 AATTA-TAATTAGTTTATTTTTATT
18526202 TCCTTTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
25 21 0.51
26 20 0.49
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (25 bp):
AATTATAATTAGTTTATTTTTATTA
Found at i:18526193 original size:19 final size:19
Alignment explanation
Indices: 18526159--18526195 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
18526149 GTTTGTTTAT
18526159 AATTAGTTTATTTTTATTA
1 AATTAGTTTATTTTTATTA
18526178 AATTA-TTTATTATTTATT
1 AATTAGTTTATT-TTTATT
18526196 TTTATTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
AATTAGTTTATTTTTATTA
Found at i:18527145 original size:13 final size:13
Alignment explanation
Indices: 18527127--18527164 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
18527117 TCAGGAGACC
18527127 TTATAAATAATTA
1 TTATAAATAATTA
*
18527140 TTATAAATAATAA
1 TTATAAATAATTA
*
18527153 TAATAAATAATT
1 TTATAAATAATT
18527165 GAGAACTCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TTATAAATAATTA
Found at i:18527858 original size:16 final size:15
Alignment explanation
Indices: 18527834--18527872 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
18527824 AACATTTAAT
18527834 TTTTAAATTAAAATA
1 TTTTAAATTAAAATA
18527849 TTTTATAATTAAAATA
1 TTTTA-AATTAAAATA
18527865 -TTTAAATT
1 TTTTAAATT
18527873 TATTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.17
15 9 0.39
16 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTTTAAATTAAAATA
Found at i:18527934 original size:56 final size:56
Alignment explanation
Indices: 18527827--18527935 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 56
18527817 TTATTATAAC
*
18527827 ATTTAATTTTTAAATTAAAATATTTTATAATTAAAATATTTAAATTTATTTTTTAT
1 ATTTAATTTTTAAATTAAAATATTTTATAATTAAAATATTTAAATTAATTTTTTAT
*
18527883 ATTTTATTTTTAAAATATAAAA-ATTTTATAATTAAAAT-TTT-AATTCAATTTTT
1 ATTTAATTTTT-AAAT-TAAAATATTTTATAATTAAAATATTTAAATT-AATTTTT
18527936 AAGTATAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
55 4 0.08
56 19 0.40
57 20 0.42
58 5 0.10
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (56 bp):
ATTTAATTTTTAAATTAAAATATTTTATAATTAAAATATTTAAATTAATTTTTTAT
Found at i:18529599 original size:19 final size:18
Alignment explanation
Indices: 18529575--18529626 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
18529565 AATTGATTTT
18529575 ATTTAAATATTTTTAAATA
1 ATTTAAATATTTTTAAA-A
*
18529594 ATTTAAGA-ATTTTTTAAA
1 ATTTAA-ATATTTTTAAAA
*
18529612 ATATTATATATTTTT
1 AT-TTAAATATTTTT
18529627 CTTTTTATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 4 0.14
19 23 0.82
20 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTAAATATTTTTAAAA
Found at i:18530985 original size:3 final size:3
Alignment explanation
Indices: 18530977--18531008 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18530967 TTTCTTTCAA
18530977 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
18531009 TCAGATTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18550895 original size:4 final size:4
Alignment explanation
Indices: 18550886--18550910 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
18550876 AGATGGGTGT
18550886 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
18550911 TTTGGTTGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:18553967 original size:2 final size:2
Alignment explanation
Indices: 18553960--18554022 Score: 94
Period size: 2 Copynumber: 32.0 Consensus size: 2
18553950 AACTTTTCAT
*
18553960 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TNC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
18554001 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
18554023 GTTATTAAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
1 2 0.04
2 54 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18554542 original size:20 final size:20
Alignment explanation
Indices: 18554514--18554552 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18554504 TTTAAAATAA
18554514 AAAAATTATCTCTTCATATG
1 AAAAATTATCTCTTCATATG
* *
18554534 AAAAGTTATCTTTTCATAT
1 AAAAATTATCTCTTCATAT
18554553 TGTGTTTTAT
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:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAAATTATCTCTTCATATG
Found at i:18561111 original size:3 final size:3
Alignment explanation
Indices: 18561103--18561136 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
18561093 CCTAAACCCT
18561103 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18561137 AATTAATCTC
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):
ATA
Found at i:18574222 original size:12 final size:12
Alignment explanation
Indices: 18574205--18574243 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
18574195 GAAAAGATAA
*
18574205 GATGAAGACGAT
1 GATGAAGATGAT
*
18574217 GATGAAAATGAT
1 GATGAAGATGAT
*
18574229 GATGATGATGAT
1 GATGAAGATGAT
18574241 GAT
1 GAT
18574244 AAGTGCCATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.03, G:0.31, T:0.26
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:18579276 original size:50 final size:48
Alignment explanation
Indices: 18579219--18579317 Score: 180
Period size: 50 Copynumber: 2.0 Consensus size: 48
18579209 GGTCAGGTTT
18579219 TGCAGAGAGAAGGAACGGAGAAATAGTAGGATATATATATATATATATA
1 TGCAGAGAGAAGGAACGGAGAAATAGTA-GATATATATATATATATATA
18579268 TNGCAGAGAGAAGGAACGGAGAAATAGTAGATATATATATATATATATA
1 T-GCAGAGAGAAGGAACGGAGAAATAGTAGATATATATATATATATATA
18579317 T
1 T
18579318 ATTTTTTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
49 22 0.45
50 27 0.55
ACGTcount: A:0.46, C:0.04, G:0.23, T:0.25
Consensus pattern (48 bp):
TGCAGAGAGAAGGAACGGAGAAATAGTAGATATATATATATATATATA
Found at i:18581199 original size:34 final size:34
Alignment explanation
Indices: 18581160--18581227 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
18581150 TTTTTTTTTT
18581160 AAGCTTTTCCAACCTTTGATTTGTTGATTTGCAA
1 AAGCTTTTCCAACCTTTGATTTGTTGATTTGCAA
18581194 AAGCTTTTCCAACCTTTGATTTGTTGATTTGCAA
1 AAGCTTTTCCAACCTTTGATTTGTTGATTTGCAA
18581228 TGCCTCCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.44
Consensus pattern (34 bp):
AAGCTTTTCCAACCTTTGATTTGTTGATTTGCAA
Found at i:18581513 original size:14 final size:15
Alignment explanation
Indices: 18581489--18581518 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
18581479 TTTATATTTT
18581489 TTTTATTTCTAACAA
1 TTTTATTTCTAACAA
18581504 TTTT-TTTCTAACAA
1 TTTTATTTCTAACAA
18581518 T
1 T
18581519 ATAACTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTATTTCTAACAA
Found at i:18602246 original size:44 final size:44
Alignment explanation
Indices: 18602183--18602271 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
18602173 GTTCACTGTC
18602183 ATAAGATGAATACATTATTATATCCATTGCAAAGAAATCAAACA
1 ATAAGATGAATACATTATTATATCCATTGCAAAGAAATCAAACA
* *
18602227 ATAAGATGAATATATTATTATATCCATTTCAAAGAAATCAAACA
1 ATAAGATGAATACATTATTATATCCATTGCAAAGAAATCAAACA
18602271 A
1 A
18602272 CAAAAAGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (44 bp):
ATAAGATGAATACATTATTATATCCATTGCAAAGAAATCAAACA
Found at i:18610312 original size:31 final size:34
Alignment explanation
Indices: 18610276--18610338 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
18610266 ATAATTGATT
18610276 TTAAATATA-A-AATATTAATTG-TTAAAAATCA
1 TTAAATATATATAATATTAATTGATTAAAAATCA
*
18610307 TTAAATATATATTATTATTAATTGATTAAAAA
1 TTAAATATATA-TAATATTAATTGATTAAAAA
18610339 AATAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 9 0.33
32 1 0.04
34 10 0.37
35 7 0.26
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (34 bp):
TTAAATATATATAATATTAATTGATTAAAAATCA
Found at i:18610434 original size:23 final size:23
Alignment explanation
Indices: 18610408--18610452 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
18610398 ATTTTAATTT
*
18610408 TTAT-CTATTTTTAATAAAATTAA
1 TTATACTATTGTT-ATAAAATTAA
*
18610431 TTATATTATTGTTATAAAATTA
1 TTATACTATTGTTATAAAATTA
18610453 TAAGAGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATACTATTGTTATAAAATTAA
Found at i:18617831 original size:78 final size:78
Alignment explanation
Indices: 18617702--18617897 Score: 250
Period size: 78 Copynumber: 2.5 Consensus size: 78
18617692 AAGATGTTAA
* * * * *
18617702 ATTTACATATTGGCACCATTATACC-TACATGTATAATAGGAATGCCACATGTCCACCTATTACA
1 ATTTATATATTGGCATCATTATACCTTA-ATGTATAATAGAAATACCACATGTCCACCTATCACA
* * *
18617766 TGGATTTTGATGGT
65 AGGACTTTGATAGT
* * *
18617780 ATTTATATATTGGCATCATTATACCTTAATCTATATTAGAAATACCACATGTCCACTTATCACAA
1 ATTTATATATTGGCATCATTATACCTTAATGTATAATAGAAATACCACATGTCCACCTATCACAA
18617845 GGACTTTGATAGT
66 GGACTTTGATAGT
* *
18617858 ATTTATATAGTGACATCATTATACCTTTAATGTATAATAG
1 ATTTATATATTGGCATCATTATACC-TTAATGTATAATAG
18617898 GAGTGCCACA
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
78 87 0.86
79 14 0.14
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (78 bp):
ATTTATATATTGGCATCATTATACCTTAATGTATAATAGAAATACCACATGTCCACCTATCACAA
GGACTTTGATAGT
Found at i:18620609 original size:19 final size:19
Alignment explanation
Indices: 18620585--18620621 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
18620575 GGTGATGATG
18620585 AAAATT-TGGAAAGGAAAAA
1 AAAATTATGGAAA-GAAAAA
18620604 AAAATTATGGAAAGAAAA
1 AAAATTATGGAAAGAAAA
18620622 TTCTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.65, C:0.00, G:0.19, T:0.16
Consensus pattern (19 bp):
AAAATTATGGAAAGAAAAA
Found at i:18620937 original size:41 final size:42
Alignment explanation
Indices: 18620880--18620962 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 42
18620870 GGTAACATTG
* *
18620880 GCAATTTAATTTCAATCAAATAATTAAAA-GGTTCTTACCTT
1 GCAATTTAATTCCAATCAAACAATTAAAAGGGTTCTTACCTT
* * *
18620921 GCAATTTAATTCCAATCAGACAGTTAAAAGGGTTTTTACCTT
1 GCAATTTAATTCCAATCAAACAATTAAAAGGGTTCTTACCTT
18620963 ACTTACCTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 25 0.69
42 11 0.31
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (42 bp):
GCAATTTAATTCCAATCAAACAATTAAAAGGGTTCTTACCTT
Found at i:18622380 original size:24 final size:25
Alignment explanation
Indices: 18622353--18622405 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
18622343 ATAAAATATT
* *
18622353 TTTTTCTTATTTTCT-TTTTTTTCC
1 TTTTTATTATTTTCTAATTTTTTCC
18622377 TTTTTATTATTTTCTAAATTTTTTCC
1 TTTTTATTATTTTCT-AATTTTTTCC
18622403 TTT
1 TTT
18622406 CTAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 14 0.56
26 11 0.44
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTTATTATTTTCTAATTTTTTCC
Found at i:18622406 original size:16 final size:16
Alignment explanation
Indices: 18622387--18622421 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
18622377 TTTTTATTAT
18622387 TTTCTAAATTTTTTCC
1 TTTCTAAATTTTTTCC
* *
18622403 TTTCTAATTTTTTTTC
1 TTTCTAAATTTTTTCC
18622419 TTT
1 TTT
18622422 ACTTGAGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCTAAATTTTTTCC
Found at i:18647756 original size:22 final size:20
Alignment explanation
Indices: 18647730--18647772 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
18647720 GTTTTTTTTT
18647730 TTTTTATTTATTTTTCCTGTTG
1 TTTTT-TTT-TTTTTCCTGTTG
18647752 -TTTTTTTTTTTTCCTGTTG
1 TTTTTTTTTTTTTCCTGTTG
18647771 TT
1 TT
18647773 AATAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.05, C:0.09, G:0.09, T:0.77
Consensus pattern (20 bp):
TTTTTTTTTTTTTCCTGTTG
Found at i:18648130 original size:2 final size:2
Alignment explanation
Indices: 18648125--18648154 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18648115 ACACACACAC
18648125 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
18648155 NNNNNNNNNN
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18648268 original size:2 final size:2
Alignment explanation
Indices: 18648226--18648257 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18648216 ACACACACAC
18648226 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
18648258 GTTTTATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18649853 original size:2 final size:2
Alignment explanation
Indices: 18649846--18649873 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18649836 CTTCTGTTGG
18649846 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
18649874 TATTTGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18650529 original size:15 final size:15
Alignment explanation
Indices: 18650505--18650534 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18650495 ATTTGAGATT
18650505 ATCATAATTTTAATG
1 ATCATAATTTTAATG
*
18650520 ATCATGATTTTAATG
1 ATCATAATTTTAATG
18650535 TGGATTTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (15 bp):
ATCATAATTTTAATG
Found at i:18650553 original size:69 final size:69
Alignment explanation
Indices: 18650477--18650607 Score: 244
Period size: 69 Copynumber: 1.9 Consensus size: 69
18650467 TCATTTCGTG
* *
18650477 AAAAATTAAATAAATATTATTTGAGATTATCATAATTTTAATGATCATGATTTTAATGTGGATTT
1 AAAAATTAAATAAATATTACTTGAGATTATCATAAATTTAATGATCATGATTTTAATGTGGATTT
18650542 CATA
66 CATA
18650546 AAAAATTAAATAAATATTACTTGAGATTATCATAAATTTAATGATCATGATTTTAATGTGGA
1 AAAAATTAAATAAATATTACTTGAGATTATCATAAATTTAATGATCATGATTTTAATGTGGA
18650608 AGATTGTAGG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (69 bp):
AAAAATTAAATAAATATTACTTGAGATTATCATAAATTTAATGATCATGATTTTAATGTGGATTT
CATA
Done.