Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 16 of 356
Found at i:5687668 original size:62 final size:62
Alignment explanation
Indices: 5687547--5687669 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
5687537 TAAAATATTG
* * *** * **
5687547 AATATATTAAAATTTTAAAATTAGTTATATTTAACTTTTTTTAATATTTTTAATTTTTTAAA
1 AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAAA
5687609 AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAA
1 AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAA
5687670 TATATTTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (62 bp):
AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAAA
Found at i:5687713 original size:17 final size:17
Alignment explanation
Indices: 5687644--5687711 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
5687634 TATACTTAAC
5687644 AAATTTTAATATATTTA
1 AAATTTTAATATATTTA
5687661 AAATTTTAATATATTTA
1 AAATTTTAATATATTTA
** *
5687678 ATTTTTTTAAGT-TTTTTA
1 A-AATTTTAA-TATATTTA
5687696 AAATTTTAAATATATT
1 AAATTTT-AATATATT
5687712 AAGAACTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
17 23 0.56
18 17 0.41
19 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
AAATTTTAATATATTTA
Found at i:5687797 original size:18 final size:17
Alignment explanation
Indices: 5687751--5687789 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5687741 AAAATATATA
* *
5687751 TTAAGTATATTAAAATT
1 TTAAATATATTAAACTT
5687768 TTAAATATATTAAACTT
1 TTAAATATATTAAACTT
5687785 TTAAA
1 TTAAA
5687790 ATTAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAACTT
Found at i:5691240 original size:40 final size:40
Alignment explanation
Indices: 5691185--5691266 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
5691175 AGGAGAATTC
5691185 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
1 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
5691225 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
1 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
5691265 TA
1 TA
5691267 TAACGAGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (40 bp):
TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
Found at i:5694240 original size:73 final size:73
Alignment explanation
Indices: 5694153--5694300 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
5694143 CATACAATGT
5694153 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
1 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
5694218 AACCCCAC
66 AACCCCAC
*
5694226 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTTTAATTTGACT
1 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
5694291 AACCCCAC
66 AACCCCAC
5694299 TG
1 TG
5694301 GACACTTATC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (73 bp):
TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
AACCCCAC
Found at i:5699719 original size:27 final size:26
Alignment explanation
Indices: 5699636--5699726 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
5699626 AACCCCAAAC
5699636 TCGAGGTTCAA-AGTTCA-AGTTTGAGGT
1 TCGAGGTTCAATA-TT-AGAGTTT-AGGT
* * * *
5699663 TCAAGGTCCAATGTTAGGGTTTAGGGT
1 TCGAGGTTCAATATTAGAGTTTA-GGT
5699690 TCGAGGTTCAATATTAGAGTTTAGGAT
1 TCGAGGTTCAATATTAGAGTTTAGG-T
*
5699717 TCGAGATTCA
1 TCGAGGTTCA
5699727 TGATTTAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 4 0.08
27 47 0.92
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (26 bp):
TCGAGGTTCAATATTAGAGTTTAGGT
Found at i:5701990 original size:3 final size:3
Alignment explanation
Indices: 5701984--5702012 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5701974 TGTTGTTGTT
5701984 TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5702013 GAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5705151 original size:25 final size:25
Alignment explanation
Indices: 5705122--5705173 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
5705112 AAGAATAATT
**
5705122 TGAATATTGGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
5705147 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
5705172 TG
1 TG
5705174 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:5706487 original size:12 final size:12
Alignment explanation
Indices: 5706470--5706494 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5706460 AAAGTAAAAT
5706470 TATGAATTGAAA
1 TATGAATTGAAA
5706482 TATGAATTGAAA
1 TATGAATTGAAA
5706494 T
1 T
5706495 TGAGATATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TATGAATTGAAA
Found at i:5716020 original size:10 final size:12
Alignment explanation
Indices: 5716002--5716030 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5715992 CCCTTCTTTC
5716002 ACTTTTTT-TTA
1 ACTTTTTTATTA
5716013 ACTTTTTTATTA
1 ACTTTTTTATTA
5716025 ACTTTT
1 ACTTTT
5716031 GTCTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (12 bp):
ACTTTTTTATTA
Found at i:5716038 original size:20 final size:19
Alignment explanation
Indices: 5716014--5716060 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5716004 TTTTTTTTAA
5716014 CTTTTTTATT-AACTTTTGT
1 CTTTTTT-TTAAACTTTTGT
* *
5716033 CTTTTTCTTTAAATTTTTTT
1 CTTTTT-TTTAAACTTTTGT
5716053 CTTTTTTT
1 CTTTTTTT
5716061 GAGTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (19 bp):
CTTTTTTTTAAACTTTTGT
Found at i:5716112 original size:23 final size:24
Alignment explanation
Indices: 5716069--5716115 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5716059 TTGAGTTTTA
*
5716069 TATTTTTTCTTATTTTATTTTGTT
1 TATTTCTTCTTATTTTATTTTGTT
5716093 TATTTCTT-TTATTTCT-TTTTGTT
1 TATTTCTTCTTATTT-TATTTTGTT
5716116 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (24 bp):
TATTTCTTCTTATTTTATTTTGTT
Found at i:5716156 original size:23 final size:21
Alignment explanation
Indices: 5716130--5716178 Score: 53
Period size: 24 Copynumber: 2.2 Consensus size: 21
5716120 ATTTTAAAAA
*
5716130 ATTTGAAATGTTTTATAATATAT
1 ATTTGAAATATTTTA-AATAT-T
*
5716153 ATTTTTAAATATTTTAAATATT
1 A-TTTGAAATATTTTAAATATT
5716175 ATTT
1 ATTT
5716179 TTAAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 3 0.13
22 2 0.09
23 6 0.26
24 12 0.52
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
ATTTGAAATATTTTAAATATT
Found at i:5716162 original size:24 final size:22
Alignment explanation
Indices: 5716135--5716210 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 22
5716125 AAAAAATTTG
*
5716135 AAATGTTTTATAATATATATTTTT
1 AAATATTTTA-AATAT-TATTTTT
5716159 AAATATTTTAAATATTATTTTT
1 AAATATTTTAAATATTATTTTT
*
5716181 AAATTATTTTTAA-A--ATTTTT
1 AAA-TATTTTAAATATTATTTTT
5716201 AAATTATTTT
1 AAA-TATTTT
5716211 TAAAATGTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
20 16 0.33
22 11 0.22
23 13 0.27
24 9 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (22 bp):
AAATATTTTAAATATTATTTTT
Found at i:5716188 original size:11 final size:11
Alignment explanation
Indices: 5716152--5716214 Score: 87
Period size: 11 Copynumber: 5.9 Consensus size: 11
5716142 TTATAATATA
5716152 TATTTTTAAA-
1 TATTTTTAAAT
*
5716162 TATTTTAAATAT
1 TATTTTTAA-AT
5716174 TATTTTTAAAT
1 TATTTTTAAAT
5716185 TATTTTTAAA-
1 TATTTTTAAAT
5716195 -ATTTTTAAAT
1 TATTTTTAAAT
5716205 TATTTTTAAA
1 TATTTTTAAA
5716215 ATGTTGAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
9 9 0.19
10 8 0.17
11 22 0.47
12 8 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:5716189 original size:33 final size:31
Alignment explanation
Indices: 5716152--5716214 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
5716142 TTATAATATA
5716152 TATTTTTAAATATTTTAAATATTATTTTTAAAT
1 TATTTTTAAA-ATTTTAAA-ATTATTTTTAAAT
*
5716185 TATTTTTAAAATTTTTAAATTATTTTTAAA
1 TATTTTTAAAATTTTAAAATTATTTTTAAA
5716215 ATGTTGAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 12 0.41
32 7 0.24
33 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TATTTTTAAAATTTTAAAATTATTTTTAAAT
Found at i:5716211 original size:21 final size:20
Alignment explanation
Indices: 5716153--5716232 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
5716143 TATAATATAT
*
5716153 ATTTTTAAA-TATTTTAAATA
1 ATTTTTAAATTATTTTTAA-A
5716173 TTATTTTTAAATTATTTTTAAA
1 --ATTTTTAAATTATTTTTAAA
5716195 ATTTTTAAATTATTTTTAAA
1 ATTTTTAAATTATTTTTAAA
* *
5716215 ATGTTGAATATTATTTTT
1 ATTTTTAA-ATTATTTTT
5716233 TTAAATTATG
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
20 26 0.49
21 9 0.17
22 10 0.19
23 8 0.15
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (20 bp):
ATTTTTAAATTATTTTTAAA
Found at i:5716257 original size:54 final size:52
Alignment explanation
Indices: 5716152--5716254 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 52
5716142 TTATAATATA
* *
5716152 TATTTTTAAATATTTTAAATATTATTTTTAAATTATTTTTAAAATTTTTAAAT
1 TATTTTTAAATATGTTAAATATTATTTTTAAATTATTCTTAAAA-TTTTAAAT
*
5716205 TATTTTTAAA-ATGTTGAATATTATTTTTTTAAATTATGTCTTATAAATTT
1 TATTTTTAAATATGTTAAATATTA--TTTTTAAATTAT-TCTTA-AAATTT
5716255 AAAAAAATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
52 11 0.26
53 10 0.23
54 12 0.28
55 7 0.16
56 3 0.07
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (52 bp):
TATTTTTAAATATGTTAAATATTATTTTTAAATTATTCTTAAAATTTTAAAT
Found at i:5716317 original size:14 final size:14
Alignment explanation
Indices: 5716300--5716328 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5716290 TTTAAATTTT
5716300 AAATATATTTTTAA
1 AAATATATTTTTAA
5716314 AAATATATTTTTAA
1 AAATATATTTTTAA
5716328 A
1 A
5716329 CAAAATAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:5716364 original size:21 final size:22
Alignment explanation
Indices: 5716340--5716386 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
5716330 AAAATAAAAC
5716340 AATTTCAAAAATATATTTTT-A
1 AATTTCAAAAATATATTTTTGA
*
5716361 AATTTTAAAAATATATTTTTGA
1 AATTTCAAAAATATATTTTTGA
5716383 AATT
1 AATT
5716387 ATTTCTTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTTCAAAAATATATTTTTGA
Found at i:5716399 original size:36 final size:34
Alignment explanation
Indices: 5716355--5716452 Score: 139
Period size: 36 Copynumber: 2.9 Consensus size: 34
5716345 CAAAAATATA
5716355 TTTTTAAATTTTAAAAATATATTTTTGAAATTAT
1 TTTTTAAATTTTAAAAATATATTTTTGAAATTAT
*
5716389 TTCTTATAAATTTTAAAAATATATTTTAGAAATTAT
1 TT-TT-TAAATTTTAAAAATATATTTTTGAAATTAT
*
5716425 TTTTT-AATTTTAAATAT-TATTTTT-AAAT
1 TTTTTAAATTTTAAAAATATATTTTTGAAAT
5716453 ATTAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
31 4 0.07
32 6 0.10
33 11 0.19
34 3 0.05
35 4 0.07
36 31 0.53
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTTTAAATTTTAAAAATATATTTTTGAAATTAT
Found at i:5716436 original size:20 final size:20
Alignment explanation
Indices: 5716411--5716469 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
5716401 TTAAAAATAT
5716411 ATTTTAGAA-ATTATTTTTTA
1 ATTTTA-AATATTATTTTTTA
*
5716431 ATTTTAAATATTATTTTTAA
1 ATTTTAAATATTATTTTTTA
*
5716451 ATATTAAATATATATTTTT
1 ATTTTAAATAT-TATTTTT
5716470 AATAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 26 0.74
21 7 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
ATTTTAAATATTATTTTTTA
Found at i:5716450 original size:13 final size:13
Alignment explanation
Indices: 5716432--5716456 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5716422 TATTTTTTAA
5716432 TTTTAAATATTAT
1 TTTTAAATATTAT
5716445 TTTTAAATATTA
1 TTTTAAATATTA
5716457 AATATATATT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:5716466 original size:21 final size:20
Alignment explanation
Indices: 5716420--5716471 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
5716410 TATTTTAGAA
* *
5716420 ATTATTTTTTAATTTTAAAT
1 ATTATTTTTAAATATTAAAT
5716440 ATTATTTTTAAATATTAAAT
1 ATTATTTTTAAATATTAAAT
5716460 ATATATTTTTAA
1 AT-TATTTTTAA
5716472 TAATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATTTTTAAATATTAAAT
Found at i:5716566 original size:13 final size:13
Alignment explanation
Indices: 5716550--5716575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5716540 TTAAAAATCA
5716550 TAATTTCAAAAAT
1 TAATTTCAAAAAT
5716563 TAATTTCAAAAAT
1 TAATTTCAAAAAT
5716576 AAAGAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTTCAAAAAT
Found at i:5716608 original size:33 final size:31
Alignment explanation
Indices: 5716571--5716639 Score: 84
Period size: 33 Copynumber: 2.2 Consensus size: 31
5716561 ATTAATTTCA
*
5716571 AAAATAAAGAAAAATAATATATTTTTAAATTTT
1 AAAATAAAGAAAAATAATATA--TTTAAAATTT
** *
5716604 AAAATTTATAAAAATAATATATTTAAAATTT
1 AAAATAAAGAAAAATAATATATTTAAAATTT
5716635 AAAAT
1 AAAAT
5716640 TTAGAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 14 0.44
33 18 0.56
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
AAAATAAAGAAAAATAATATATTTAAAATTT
Found at i:5716636 original size:31 final size:32
Alignment explanation
Indices: 5716578--5716647 Score: 106
Period size: 31 Copynumber: 2.2 Consensus size: 32
5716568 TCAAAAATAA
*
5716578 AGAAAAATAATATATTTTTAAATTTTAAAATTT
1 AGAAAAATAATATA-TTTTAAAATTTAAAATTT
*
5716611 ATAAAAATAATATA-TTTAAAATTTAAAATTT
1 AGAAAAATAATATATTTTAAAATTTAAAATTT
5716642 AGAAAA
1 AGAAAA
5716648 TTTAATTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 21 0.62
33 13 0.38
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (32 bp):
AGAAAAATAATATATTTTAAAATTTAAAATTT
Found at i:5716675 original size:36 final size:32
Alignment explanation
Indices: 5716631--5716753 Score: 122
Period size: 36 Copynumber: 3.6 Consensus size: 32
5716621 TATATTTAAA
5716631 ATTTAAAATTTAGAAAATTTAATTTCAAAAATATAT
1 ATTTAAAATTTA-AAAA--TAATTTCAAAAATA-AT
* *
5716667 TTTTAAAATTTATAAGACATAATTTAAAAAATAAT
1 ATTTAAAATTTA-AA-A-ATAATTTCAAAAATAAT
*
5716702 ATTCAAAATTTTAAAAATAATTTC-AAAATAAT
1 ATTTAAAA-TTTAAAAATAATTTCAAAAATAAT
5716734 ATTTAAAATTTTTAAAAATA
1 ATTTAAAA--TTTAAAAATA
5716754 TATATTATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
32 15 0.20
33 18 0.24
34 1 0.01
35 10 0.13
36 30 0.39
37 1 0.01
38 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (32 bp):
ATTTAAAATTTAAAAATAATTTCAAAAATAAT
Found at i:5716726 original size:20 final size:21
Alignment explanation
Indices: 5716687--5716730 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5716677 TATAAGACAT
5716687 AATTTAAAAAATAATATTCAA
1 AATTTAAAAAATAATATTCAA
*
5716708 AATTTTAAAAATAAT-TTCAA
1 AATTTAAAAAATAATATTCAA
5716728 AAT
1 AAT
5716731 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTTAAAAAATAATATTCAA
Found at i:5716758 original size:23 final size:22
Alignment explanation
Indices: 5716726--5716792 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
5716716 AAATAATTTC
5716726 AAAATA-ATATTTAAAATTTTT
1 AAAATATATATTTAAAATTTTT
**
5716747 AAAAATATATATTATAAAACATTT
1 -AAAATATATATT-TAAAATTTTT
* * *
5716771 CAAATATACATTTCAAATTTTT
1 AAAATATATATTTAAAATTTTT
5716793 TAATATTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 13 0.36
23 15 0.42
24 8 0.22
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATATATTTAAAATTTTT
Found at i:5716827 original size:16 final size:17
Alignment explanation
Indices: 5716808--5716844 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
5716798 TTAATAACAA
5716808 AAAATAA-ATAAAAA-AT
1 AAAATAAGA-AAAAATAT
5716824 AAAATAAGAAAAAATAT
1 AAAATAAGAAAAAATAT
5716841 AAAA
1 AAAA
5716845 CTTAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAAATAAGAAAAAATAT
Found at i:5716835 original size:24 final size:24
Alignment explanation
Indices: 5716806--5716860 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
5716796 TATTAATAAC
*
5716806 AAAAAATAAATAAAAAATAAAATAAG
1 AAAAAAT--ATAAAAAATAAAAAAAG
**
5716832 AAAAAATATAAAACTTAAAAAAAG
1 AAAAAATATAAAAAATAAAAAAAG
5716856 AAAAA
1 AAAAA
5716861 GATTTAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 19 0.73
26 7 0.27
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.15
Consensus pattern (24 bp):
AAAAAATATAAAAAATAAAAAAAG
Found at i:5716875 original size:20 final size:19
Alignment explanation
Indices: 5716849--5716902 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 19
5716839 ATAAAACTTA
5716849 AAAAAAGAAAAAGATTTAA-
1 AAAAAAGAAAAAGA-TTAAT
5716868 AGAAAAAGACAAAAG-TTAAT
1 A-AAAAAGA-AAAAGATTAAT
5716888 AAAAAAGTAAAAAGA
1 AAAAAAG-AAAAAGA
5716903 AAAAAAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
19 16 0.53
20 9 0.30
21 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAAAAGAAAAAGATTAAT
Found at i:5717206 original size:27 final size:27
Alignment explanation
Indices: 5717174--5717226 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5717164 TATAGTTGAA
5717174 TGGTTATTTAGTGTTTAATTAAGTGAT
1 TGGTTATTTAGTGTTTAATTAAGTGAT
5717201 TGGTTATTTAGTGTTTAATTAAGTGA
1 TGGTTATTTAGTGTTTAATTAAGTGA
5717227 AGTAGCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (27 bp):
TGGTTATTTAGTGTTTAATTAAGTGAT
Found at i:5729026 original size:16 final size:16
Alignment explanation
Indices: 5729007--5729039 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5728997 ATATAAATTT
5729007 AAAAATTAAAAAAATA
1 AAAAATTAAAAAAATA
*
5729023 AAAAATTAAATAAATA
1 AAAAATTAAAAAAATA
5729039 A
1 A
5729040 CTAAAATAAC
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:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAAAAATA
Found at i:5739880 original size:28 final size:28
Alignment explanation
Indices: 5739849--5739938 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
5739839 TATTTCAGAA
5739849 AATAGAGTATTAAAAATGATTAAATTGT
1 AATAGAGTATTAAAAATGATTAAATTGT
* * * *
5739877 AATAGAGAAACTAAATCCAAAGA--AAA---C
1 AATAGAG-TATTAAA---AATGATTAAATTGT
5739904 AATAGAGTATTAAAAATGATTAAATTGT
1 AATAGAGTATTAAAAATGATTAAATTGT
5739932 AATAGAG
1 AATAGAG
5739939 AAACTAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 18
0.63 0.11 0.25
Matches are distributed among these distances:
23 4 0.09
25 3 0.07
26 5 0.11
27 7 0.16
28 14 0.31
29 5 0.11
30 3 0.07
32 4 0.09
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.27
Consensus pattern (28 bp):
AATAGAGTATTAAAAATGATTAAATTGT
Found at i:5739909 original size:55 final size:55
Alignment explanation
Indices: 5739849--5739959 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
5739839 TATTTCAGAA
5739849 AATAGAGTATTAAAAATGATTAAATTGTAATAGAGAAACTAAATCCAAAGAAAAC
1 AATAGAGTATTAAAAATGATTAAATTGTAATAGAGAAACTAAATCCAAAGAAAAC
5739904 AATAGAGTATTAAAAATGATTAAATTGTAATAGAGAAACTAAATCCAAAGAAAAC
1 AATAGAGTATTAAAAATGATTAAATTGTAATAGAGAAACTAAATCCAAAGAAAAC
5739959 A
1 A
5739960 CATTGTACAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (55 bp):
AATAGAGTATTAAAAATGATTAAATTGTAATAGAGAAACTAAATCCAAAGAAAAC
Found at i:5757199 original size:28 final size:27
Alignment explanation
Indices: 5757159--5757235 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 27
5757149 AATTCTTTCT
5757159 ATTTTTTATAGTTTATATATATATTAGA
1 ATTTTTTATAGTTTATATATAT-TTAGA
* * *
5757187 TTTTTTTCTAGTTT-TAT-TATTTATA
1 ATTTTTTATAGTTTATATATATTTAGA
* *
5757212 ATTTTTTAAAATTTATATATATTT
1 ATTTTTTATAGTTTATATATATTT
5757236 TTAGTAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 14 0.35
26 6 0.15
27 8 0.20
28 12 0.30
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTTTATAGTTTATATATATTTAGA
Found at i:5760901 original size:51 final size:51
Alignment explanation
Indices: 5760821--5760977 Score: 205
Period size: 51 Copynumber: 3.1 Consensus size: 51
5760811 GACGAAGCTC
* * * *
5760821 CTGCTGCCGCTGAAGTTCCAACTGCCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
5760872 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
* * *
5760923 CTGCTGCCGCTGATGCTCCAACTG-C--TGCTGCCT-CTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATG-CTGCTGAAGCTCCAACTG
*
5760971 ATGCTGC
1 CTGCTGC
5760978 TGCCGTTGTA
Statistics
Matches: 97, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
48 25 0.26
49 2 0.02
50 1 0.01
51 69 0.71
ACGTcount: A:0.18, C:0.32, G:0.25, T:0.25
Consensus pattern (51 bp):
CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
Found at i:5760975 original size:27 final size:24
Alignment explanation
Indices: 5760821--5761004 Score: 170
Period size: 24 Copynumber: 7.3 Consensus size: 24
5760811 GACGAAGCTC
*
5760821 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* * *
5760845 CCGTTGATGCTGCTGAAGTTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
*
5760872 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
5760896 ACGTTGATGCTGCTGAAGCTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
*
5760923 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
5760947 CTGCTGCCTCTGAAGCTCCAACTGATG
1 CTGCTGCCGCTGAAGCTCCAAC---TG
* * *
5760974 CTGCTGCCGTTGTAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
5760998 CCGCTGC
1 CTGCTGC
5761005 TGTTCAAATT
Statistics
Matches: 132, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
24 67 0.51
25 2 0.02
26 2 0.02
27 61 0.46
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.26
Consensus pattern (24 bp):
CTGCTGCCGCTGAAGCTCCAACTG
Found at i:5761005 original size:27 final size:27
Alignment explanation
Indices: 5760821--5761006 Score: 117
Period size: 27 Copynumber: 7.2 Consensus size: 27
5760811 GACGAAGCTC
* * *
5760821 CTGCTGCCGCTGAAGTTCCAACTGCCG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* * *
5760848 TTGATG-CTGCTGAAGTTCCAACT---G
1 CTGCTGCCT-CTGAAGCTCCAACTGACG
* *
5760872 CTGCTGCCGCTGAAGCTCCAACAGACG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* *
5760899 TTGATG-CTGCTGAAGCTCCAACT---G
1 CTGCTGCCT-CTGAAGCTCCAACTGACG
* *
5760923 CTGCTGCCGCTGATGCTCCAACT---G
1 CTGCTGCCTCTGAAGCTCCAACTGACG
*
5760947 CTGCTGCCTCTGAAGCTCCAACTGATG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* * *
5760974 CTGCTGCCGT-TGTAGTTCCAACTGCCG
1 CTGCTGCC-TCTGAAGCTCCAACTGACG
5761001 CTGCTG
1 CTGCTG
5761007 TTCAAATTGA
Statistics
Matches: 126, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
24 57 0.45
25 2 0.02
26 2 0.02
27 64 0.51
28 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.26
Consensus pattern (27 bp):
CTGCTGCCTCTGAAGCTCCAACTGACG
Found at i:5772321 original size:46 final size:45
Alignment explanation
Indices: 5772269--5772588 Score: 369
Period size: 46 Copynumber: 7.0 Consensus size: 45
5772259 GCTATCTGAA
* *
5772269 ATGAAATATGTAAGATCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATA-GTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
5772315 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACGTGAC
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
5772361 ATGAAA-AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATAG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
5772407 GA-GAAATGAATAAGACCATAGTTGAAAGATACCATGGCAGCGTGAC
1 -ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
5772453 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGGAACATGAC
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
5772499 ATGAAA-AGAATAAGACCATGGTTGAAAGATACCATGGTAACATGAC
1 ATGAAATAG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
5772545 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATG
5772589 TCAAAGATAA
Statistics
Matches: 239, Mismatches: 23, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
46 231 0.97
47 1 0.00
48 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (45 bp):
ATGAAATAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:5772431 original size:92 final size:92
Alignment explanation
Indices: 5772279--5772588 Score: 435
Period size: 92 Copynumber: 3.4 Consensus size: 92
5772269 ATGAAATATG
* * **
5772279 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
*
5772344 TATCATGGCAACGTGACATGAAAAGAA
66 TACCATGGCAACGTGACATGAAAAGAA
*
5772371 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGA-GAAATGAATAAGACCATAGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-ATGAAATGAATAAGACCATGGTTGAAAG
* *
5772435 ATACCATGGCAGCGTGACATGAAATGAA
65 ATACCATGGCAACGTGACATGAAAAGAA
* *
5772463 TAAGACCATGGTTGAAAGATACCATGGGAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* * *
5772528 TACCATGGTAACATGACA-GAAAATGAG
66 TACCATGGCAACGTGACATGAAAA-GAA
* * * *
5772555 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATG
5772589 TCAAAGATAA
Statistics
Matches: 194, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
91 5 0.03
92 188 0.97
93 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACGTGACATGAAAAGAA
Found at i:5772519 original size:138 final size:138
Alignment explanation
Indices: 5772279--5772588 Score: 469
Period size: 138 Copynumber: 2.2 Consensus size: 138
5772269 ATGAAATATG
* * * **
5772279 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* *
5772344 TATCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC-G
66 TACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
5772408 AGAAATGAA
131 A-AAATGAA
* *
5772417 TAAGACCATAGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* *
5772482 TACCATGGGAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGTAACATGACAG
66 TACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
5772547 AAAATGAG
131 AAAATGAA
* * *
5772555 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATAGTTGAAAGATACCATGGCAACATG
5772589 TCAAAGATAA
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
138 153 0.99
139 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (138 bp):
TAAGACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
AAAATGAA
Found at i:5774499 original size:93 final size:93
Alignment explanation
Indices: 5774370--5774542 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
5774360 CACCCATAAG
* * *
5774370 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTTA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
5774435 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* * *
5774463 CGAACTTGGACTCAACTCAATGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
5774528 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
5774543 CAAATATCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:5774538 original size:46 final size:46
Alignment explanation
Indices: 5774363--5774538 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
5774353 TGTAACCCAC
* * *
5774363 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
5774409 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** * * *
5774455 ACATCTCTCGAACTTGGACTCAACTCAATGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
5774502 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
5774539 TGCCCAAATA
Statistics
Matches: 104, Mismatches: 19, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 66 0.63
47 29 0.28
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:5776254 original size:14 final size:14
Alignment explanation
Indices: 5776235--5776340 Score: 68
Period size: 13 Copynumber: 8.1 Consensus size: 14
5776225 GTACAATCAC
5776235 TTCATATAACT-ATT
1 TTCATATAACTCA-T
5776249 TTCATATAA-TCAT
1 TTCATATAACTCAT
5776262 TTCATAT-ACTCAT
1 TTCATATAACTCAT
*
5776275 TT-ATATAAC-AAT
1 TTCATATAACTCAT
** *
5776287 TTTGTAT-ACCCAT
1 TTCATATAACTCAT
* *
5776300 CTCATATTAC-CAT
1 TTCATATAACTCAT
* *
5776313 TTCGTAGAA-TCAT
1 TTCATATAACTCAT
5776326 TTCATATAAC-CAT
1 TTCATATAACTCAT
5776339 TT
1 TT
5776341 TGAGTAACCA
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
12 11 0.15
13 49 0.68
14 12 0.17
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (14 bp):
TTCATATAACTCAT
Found at i:5776314 original size:26 final size:26
Alignment explanation
Indices: 5776277--5776356 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
5776267 ATACTCATTT
* * *
5776277 ATATAACAATTTTGTATACCCATCTC
1 ATATAACCATTTTGTAGAACCATCTC
* * * *
5776303 ATATTACCATTTCGTAGAATCATTTC
1 ATATAACCATTTTGTAGAACCATCTC
*
5776329 ATATAACCATTTTG-AGTAACCATTTC
1 ATATAACCATTTTGTAG-AACCATCTC
5776355 AT
1 AT
5776357 TTTACACATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (26 bp):
ATATAACCATTTTGTAGAACCATCTC
Found at i:5776816 original size:17 final size:18
Alignment explanation
Indices: 5776790--5776835 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5776780 TTTTCAACAT
*
5776790 AATCATAATTTAGT-CAA
1 AATCACAATTTAGTACAA
*
5776807 TATCACAATTTAGTACAA
1 AATCACAATTTAGTACAA
5776825 AATCACCAATT
1 AATCA-CAATT
5776836 GTCATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 12 0.50
18 7 0.29
19 5 0.21
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (18 bp):
AATCACAATTTAGTACAA
Found at i:5781700 original size:24 final size:24
Alignment explanation
Indices: 5781424--5781693 Score: 378
Period size: 24 Copynumber: 11.0 Consensus size: 24
5781414 GATGAAGCTC
* *
5781424 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
* * * *
5781448 TCTTTGATGCTGCTGAAGTTCCAACTG
1 -C--TGCTGCCGCTGATGCTCCAACTG
* *
5781475 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGATGCTCCAACTG
* *
5781499 ACGTTGCTGCTGCTGAAGCTCCAACTG
1 -C--TGCTGCCGCTGATGCTCCAACTG
5781526 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5781550 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5781574 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5781598 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5781622 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5781646 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
* *
5781670 CTGCTGCCTCTGAAGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5781694 ACGCTGCTGG
Statistics
Matches: 228, Mismatches: 12, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
24 182 0.80
25 2 0.01
26 2 0.01
27 42 0.18
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (24 bp):
CTGCTGCCGCTGATGCTCCAACTG
Found at i:5788525 original size:13 final size:13
Alignment explanation
Indices: 5788507--5788570 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
5788497 AGTTCTTTAT
5788507 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
5788520 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
5788533 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
* *
5788546 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
5788559 TG-TTTTGGAAAA
1 TGCTTTT-GAAAA
5788571 ATTTAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
12 4 0.10
13 38 0.90
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5798021 original size:26 final size:26
Alignment explanation
Indices: 5797969--5798023 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
5797959 CTGATTGCAG
* *
5797969 TAATTGGTTTGACCAGCTAATTTTAT
1 TAATTGATTTGACCAGCTAATTCTAT
*
5797995 TAATTGATTTGACCAAG-TGATTCTAT
1 TAATTGATTTGACC-AGCTAATTCTAT
5798021 TAA
1 TAA
5798024 CTGTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.44
Consensus pattern (26 bp):
TAATTGATTTGACCAGCTAATTCTAT
Found at i:5800560 original size:22 final size:22
Alignment explanation
Indices: 5800532--5800575 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5800522 AGCATATCAG
5800532 ATTGCTTCCTTGCTGCACGTTT
1 ATTGCTTCCTTGCTGCACGTTT
5800554 ATTGCTTCCTTGCTGCACGTTT
1 ATTGCTTCCTTGCTGCACGTTT
5800576 GTGAGCAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.27, G:0.18, T:0.45
Consensus pattern (22 bp):
ATTGCTTCCTTGCTGCACGTTT
Found at i:5801103 original size:44 final size:45
Alignment explanation
Indices: 5801045--5801141 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 45
5801035 CAAGCTGAAG
* * * *
5801045 TGGCGGACAGTCTAAATGCAAGC-CTGAGTGGGTGCAAGCCAAAAA
1 TGGCAGACAATCTAAATGCAAGCTC-AAGAGGGTGCAAGCCAAAAA
*
5801090 -GGCAGACAATCTAAATGTAAGCTCAAGAGGGTGCAAGCCAAAAA
1 TGGCAGACAATCTAAATGCAAGCTCAAGAGGGTGCAAGCCAAAAA
5801134 TGGCAGAC
1 TGGCAGAC
5801142 TAAAGGCAAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 37 0.82
45 8 0.18
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.14
Consensus pattern (45 bp):
TGGCAGACAATCTAAATGCAAGCTCAAGAGGGTGCAAGCCAAAAA
Found at i:5804501 original size:23 final size:23
Alignment explanation
Indices: 5804475--5804525 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
5804465 TACTATTTCA
5804475 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5804498 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5804521 TATTT
1 TATTT
5804526 GAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:5804781 original size:42 final size:42
Alignment explanation
Indices: 5804720--5804881 Score: 191
Period size: 42 Copynumber: 3.7 Consensus size: 42
5804710 TCGTTTTCTC
** *
5804720 GATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAAT
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAAT
* *
5804762 GATGCCATAGCCCAGCTATGGTCTTACACATATTCATAT-AT
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAAT
*
5804803 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATT
1 -GATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATAAT
5804853 GATGCCATAGCCCAGCTATGGTCTTACAC
1 GATGCCATAGCCCAGCTATGGTCTTACAC
5804882 GAATCACATA
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.02
42 63 0.61
45 2 0.02
48 1 0.01
49 34 0.33
50 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAAT
Found at i:5804974 original size:47 final size:46
Alignment explanation
Indices: 5804803--5804971 Score: 194
Period size: 47 Copynumber: 3.6 Consensus size: 46
5804793 ATTCATATAT
* *
5804803 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATAT
1 CGATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCAC--AC
* * * *
5804852 TGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACAC
* * * * *
5804898 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACAC
*
5804945 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATAGCCCAGATATGGTCTTA
5804972 TACGGAAATC
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
46 28 0.26
47 38 0.36
48 11 0.10
49 30 0.28
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (46 bp):
CGATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACAC
Found at i:5804983 original size:95 final size:94
Alignment explanation
Indices: 5804762--5804971 Score: 236
Period size: 95 Copynumber: 2.3 Consensus size: 94
5804752 TTCACATAAT
* * * *
5804762 GATGCCATAGCCCAGCTATGGTCTTACAC-ATAT-TCATATAT--C-GATGCCATAGCCCAGCTA
1 GATGCCATAGCCCAGATATGGTCTTACACGA-ATCACATATCTCACTGATGCCATAGCCCAGATA
* **
5804822 TGGTCTTACACGTAATCACATATCACATATT
65 TGGTCTTACACGTAAGCACATATCACA-ACC
* *
5804853 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
* *
5804918 GGTCTTATACAGT-AGCATATATCAC-ACC
66 GGTCTTACAC-GTAAGCACATATCACAACC
*
5804946 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
5804972 TACGGAAATC
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
91 31 0.30
92 7 0.07
93 25 0.25
94 1 0.01
95 36 0.35
96 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (94 bp):
GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
GGTCTTACACGTAAGCACATATCACAACC
Found at i:5805028 original size:31 final size:31
Alignment explanation
Indices: 5804993--5805110 Score: 175
Period size: 31 Copynumber: 3.8 Consensus size: 31
5804983 CTTGTCACTT
*
5804993 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
5805024 GTAGCC-AGAGCTACCATTTTTCACTGATTAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
5805055 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5805086 GTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
5805111 TGTTATTTGT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.01
31 76 0.99
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:5805090 original size:62 final size:62
Alignment explanation
Indices: 5804993--5805110 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
5804983 CTTGTCACTT
*
5804993 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCAG-AGCTACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAG-CAGAAGCTACCACTTTTCACTGATTAG
* *
5805055 GTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
5805111 TGTTATTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 3 0.06
62 49 0.94
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (62 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATTAG
Found at i:5805190 original size:50 final size:50
Alignment explanation
Indices: 5805086--5805268 Score: 240
Period size: 56 Copynumber: 3.5 Consensus size: 50
5805076 CACTGATCAG
* * * * *
5805086 GTAGCAGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
5805137 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGTGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAA--GT
*
5805189 AGCCGTAGCCGAAGCTATTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 ----GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
5805243 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
5805269 GTTGCCATGG
Statistics
Matches: 117, Mismatches: 9, Indels: 13
0.84 0.06 0.09
Matches are distributed among these distances:
50 44 0.38
51 23 0.20
52 2 0.02
54 2 0.02
56 46 0.39
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:5808139 original size:19 final size:19
Alignment explanation
Indices: 5808115--5808159 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5808105 AAAGAAAGAT
5808115 GAAGATGTGTGTAGAGAGA
1 GAAGATGTGTGTAGAGAGA
5808134 GAAGATGTGTGTAGAGAGA
1 GAAGATGTGTGTAGAGAGA
5808153 GAAGATG
1 GAAGATG
5808160 AAAGGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (19 bp):
GAAGATGTGTGTAGAGAGA
Found at i:5810127 original size:68 final size:65
Alignment explanation
Indices: 5810041--5810261 Score: 214
Period size: 67 Copynumber: 3.4 Consensus size: 65
5810031 TAATACGGGA
* * *
5810041 TGTATACCATGTGTACAAGAGAGCTACGAGACATTATGAGGTAGCTAGGTTGCATGGGTGATACT
1 TGTACACCATGTATACAAGAGAGCTACGAGA-A-TA-GAAGTAGCTAGGTTGCATGGGTGATACT
5810106 ATG
63 ATG
* * * * * *
5810109 TGTACACCATGTATACAAGAGAGCTACAAG-ATAGATGTAGCTAGGTTGCATGTGTGGTTCCAGG
1 TGTACACCATGTATACAAGAGAGCTACGAGAATAGAAGTAGCTAGGTTGCATGGGTGATACTA--
5810173 TG
64 TG
* * * * * **
5810175 AAGGACACCATGTAAACAAGAGAGCTACGAG-ATA-AAGTGGCTAGATCACATGGGTGATACTAT
1 -TGTACACCATGTATACAAGAGAGCTACGAGAATAGAAGTAGCTAGGTTGCATGGGTGATACTAT
5810238 G
65 G
*
5810239 TGTACACCATGTGTACAAGAGAG
1 TGTACACCATGTATACAAGAGAG
5810262 ACAAAATTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
63 19 0.15
64 26 0.21
65 2 0.02
66 22 0.18
67 29 0.23
68 27 0.22
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (65 bp):
TGTACACCATGTATACAAGAGAGCTACGAGAATAGAAGTAGCTAGGTTGCATGGGTGATACTATG
Found at i:5813916 original size:21 final size:21
Alignment explanation
Indices: 5813884--5813924 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
5813874 AGGCTCGAGG
5813884 GGCCTGTTTTAGGCC-ATACAA
1 GGCCTGTTTTA-GCCTATACAA
5813905 GGCCT-TTCTTAGCCTATACA
1 GGCCTGTT-TTAGCCTATACA
5813925 CCAATTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GGCCTGTTTTAGCCTATACAA
Found at i:5825469 original size:23 final size:23
Alignment explanation
Indices: 5825443--5825494 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
5825433 TATAATTTTA
5825443 TAAAA-ATTCAAAATCCTAAATTC
1 TAAAATATT-AAAATCCTAAATTC
* *
5825466 TAAAATATTAAAATCCTAGATTT
1 TAAAATATTAAAATCCTAAATTC
5825489 TAAAAT
1 TAAAAT
5825495 TATCTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAATATTAAAATCCTAAATTC
Found at i:5831342 original size:114 final size:114
Alignment explanation
Indices: 5831216--5831439 Score: 369
Period size: 114 Copynumber: 2.0 Consensus size: 114
5831206 TTTTTTTTTA
* *
5831216 AATTTAAATAAACAACTATTTATG-ATTTTTTTATATGTTATATTTTGGATTTTAGATTTGAATT
1 AATTTAAATAAACAAC-ATTTATGCATTTTTTCATATGTTATACTTTGGATTTTAGATTTGAATT
* * * *
5831280 TTTAAAGATATATTTGTAAATGATAAAATTTTGAAGAGTTTTGTAATTTC
65 TTTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAATTTC
*
5831330 AATTTAAATAAACAACGTTTATGCATTTTTTCATATGTTATACTTTGGATTTTAGATTTGAATTT
1 AATTTAAATAAACAACATTTATGCATTTTTTCATATGTTATACTTTGGATTTTAGATTTGAATTT
5831395 TTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAA
66 TTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAA
5831440 GTGCTTTAAC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 6 0.06
114 96 0.94
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.47
Consensus pattern (114 bp):
AATTTAAATAAACAACATTTATGCATTTTTTCATATGTTATACTTTGGATTTTAGATTTGAATTT
TTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAATTTC
Found at i:5833222 original size:3 final size:3
Alignment explanation
Indices: 5833214--5833245 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5833204 ATTACATCCA
5833214 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5833246 AACATGTGAT
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:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5837550 original size:73 final size:73
Alignment explanation
Indices: 5837463--5837648 Score: 363
Period size: 73 Copynumber: 2.5 Consensus size: 73
5837453 ACAACTTGAC
5837463 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5837528 CACTAACA
66 CACTAACA
5837536 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
5837601 CACTAACA
66 CACTAACA
*
5837609 AACTTAGTTGGAATACAACTAAGTTACATCATTACATCCA
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCA
5837649 AATAATAATA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCCACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:5837657 original size:3 final size:3
Alignment explanation
Indices: 5837649--5837689 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
5837639 ATTACATCCA
5837649 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5837690 AACATGTGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5843304 original size:30 final size:29
Alignment explanation
Indices: 5843270--5843337 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
5843260 AATTTATATA
5843270 TTTATTATTTCTAAAAGATTAAAAT-AAATT
1 TTTATTATTTCTAAAAG-TTAAAATGAAA-T
* * * *
5843300 TTTATCATTTTTGAAAGTTAAAATGTAAT
1 TTTATTATTTCTAAAAGTTAAAATGAAAT
5843329 TTTATTATT
1 TTTATTATT
5843338 AAAATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (29 bp):
TTTATTATTTCTAAAAGTTAAAATGAAAT
Found at i:5847176 original size:30 final size:30
Alignment explanation
Indices: 5847140--5847197 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5847130 GATTAAAGAT
*
5847140 GAGTAATTTTATCTCGTATCTTAATAATGA
1 GAGTAATTTAATCTCGTATCTTAATAATGA
*
5847170 GAGTAATTTAATCTCGTATCTTATTAAT
1 GAGTAATTTAATCTCGTATCTTAATAAT
5847198 AATGGGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (30 bp):
GAGTAATTTAATCTCGTATCTTAATAATGA
Found at i:5848463 original size:21 final size:20
Alignment explanation
Indices: 5848439--5848484 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5848429 TACAAATGTG
5848439 TTAATATTTAATTGAAAATAT
1 TTAATATTTAATT-AAAATAT
* *
5848460 TTAATGATTTTATTTAAATAT
1 TTAAT-ATTTAATTAAAATAT
5848481 TTAA
1 TTAA
5848485 AATATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTAATATTTAATTAAAATAT
Found at i:5852492 original size:19 final size:18
Alignment explanation
Indices: 5852452--5852492 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
5852442 TTGATTGCAC
*
5852452 AAAAAAAATTAACTTTTA
1 AAAAAAAATTAAATTTTA
5852470 AAAAAAAATTAAAATTTGTA
1 AAAAAAAATT-AAATTT-TA
5852490 AAA
1 AAA
5852493 GAAGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 5 0.25
20 5 0.25
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAAAAATTAAATTTTA
Found at i:5852933 original size:30 final size:31
Alignment explanation
Indices: 5852898--5852958 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
5852888 TATTTTATTA
*
5852898 TTAA-TTTTGTTATTATTTTAAAGACATTTG
1 TTAATTTTTATTATTATTTTAAAGACATTTG
5852928 TTAATTTTTATTATTATTTTAAAGACATTTG
1 TTAATTTTTATTATTATTTTAAAGACATTTG
5852959 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.57
Consensus pattern (31 bp):
TTAATTTTTATTATTATTTTAAAGACATTTG
Found at i:5853102 original size:12 final size:12
Alignment explanation
Indices: 5853081--5853114 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5853071 TATATATTTT
*
5853081 AAAATTATATAA
1 AAAATAATATAA
5853093 AAAATAATATAA
1 AAAATAATATAA
*
5853105 AAATTAATAT
1 AAAATAATAT
5853115 CGATGGGCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:5853877 original size:20 final size:18
Alignment explanation
Indices: 5853849--5853894 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 18
5853839 ATTGAATGAT
5853849 AAATGAAAAGAAAATAATA
1 AAATGAAAAGAAAATAA-A
* *
5853868 AAATTGAAAATATAATAAA
1 AAA-TGAAAAGAAAATAAA
5853887 AAATGAAA
1 AAATGAAA
5853895 TTCTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 7 0.29
20 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
AAATGAAAAGAAAATAAA
Found at i:5853948 original size:8 final size:8
Alignment explanation
Indices: 5853898--5853929 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
5853888 AATGAAATTC
5853898 TAAATTAT
1 TAAATTAT
5853906 TAAATTAT
1 TAAATTAT
5853914 TAAATTAT
1 TAAATTAT
5853922 TAAATTAT
1 TAAATTAT
5853930 ACTTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
TAAATTAT
Found at i:5854668 original size:90 final size:89
Alignment explanation
Indices: 5854363--5854949 Score: 307
Period size: 89 Copynumber: 6.6 Consensus size: 89
5854353 TATTTATTTT
** *
5854363 TTTATTTTCCAGAATAATTATAATAATTACTATTTATTTTATTT-TGTTTTCTG-GGCATTTAAG
1 TTTATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTAT-TTTTC-GAGACATTTAAG
* * * **
5854426 TTTAAGTAT-AG-TGCTGCAATA--A
64 TTTGAGCATGAGATACAACAATATTA
** * * *
5854448 -AAATTTTTCAGACTAATTATAATAATTGCTATTTATTTTATTTATTTTTCGAGACATTTAAGTT
1 TTTATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGTT
* *
5854512 TGAGTATGATGTTACAACAATATTA
66 TGAGCATGA-GATACAACAATATTA
* * *
5854537 TTT-TTTTTTAGAATAATTATTATAATTACTATTTATTTTATTTCTTTTTCGAGACATTTGGAG-
1 TTTATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTT-AAGT
* * * *
5854600 TTGAGCATGCA-ATA-ATATATTTGTTT
65 TTGAGCATG-AGATACA-ACA-ATATTA
** * *
5854626 TTTATTTTTTAGAATAATTATAATAATTTTTATTTATTTTATTTATTTTTCAGGGTACTGAGGCT
1 TTTATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTC-GAG-AC--A--TT
* * *
5854691 TAAGTTT-AG--T--GCTACAACATTTTTA
60 TAAGTTTGAGCATGAGATACAACAATATTA
* * * * * * * * *
5854716 TTTTATTTTTTCGTAATATTTATAACAATTATTATTTATTTTATTTCTTTTTCGGGGCACTTAAC
1 -TTTATTTTTTAG-AATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAG
* * * *
5854781 CTTGAGTC-TAATGTTGCAACAATATT-
64 TTTGAG-CATGA-GATACAACAATATTA
* * * ** * * *
5854807 TTT-CTTTTTAGAATATTTATAATAATTACTATTCATTTTATTTCGTTTTC-AGATACTTAAGCT
1 TTTATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGTT
* * * **
5854870 TAAGTATGATGTTGTAACAATATT-
66 TGAGCATGA-GATACAACAATATTA
** *
5854894 TTTATTATTGTCCGAAATAATTATAATAATTACTATGTATTTTATTTCATTTTTCG
1 TTTATT-TT-TTAG-AATAATTATAATAATTACTATTTATTTTATTT-ATTTTTCG
5854950 GATTAATTGA
Statistics
Matches: 396, Mismatches: 69, Indels: 66
0.75 0.13 0.12
Matches are distributed among these distances:
83 1 0.00
84 60 0.15
85 2 0.01
86 8 0.02
87 41 0.10
88 41 0.10
89 75 0.19
90 56 0.14
91 49 0.12
92 53 0.13
93 1 0.00
94 1 0.00
95 4 0.01
96 4 0.01
ACGTcount: A:0.30, C:0.09, G:0.10, T:0.51
Consensus pattern (89 bp):
TTTATTTTTTAGAATAATTATAATAATTACTATTTATTTTATTTATTTTTCGAGACATTTAAGTT
TGAGCATGAGATACAACAATATTA
Found at i:5854801 original size:92 final size:88
Alignment explanation
Indices: 5854625--5854948 Score: 247
Period size: 92 Copynumber: 3.6 Consensus size: 88
5854615 TATATTTGTT
* * * * **
5854625 TTTTATTTTTTAGAATAATTATAATAATTTTTATTTATTTTATTTATTTTTCAGGGTACTGAGGC
1 TTTTATTTTTTAGAATATTTATAATAATTATTATTTATTTTATTTCTTTTTCAGGGCACTGAACC
* * *
5854690 TTAAGTTTAGTGCTACAACATTTTTA
66 TTAAGTCTAATGCTACAACA---ATA
* * * *
5854716 TTTTATTTTTTCGTAATATTTATAACAATTATTATTTATTTTATTTCTTTTTCGGGGCACTTAAC
1 TTTTATTTTTTAG-AATATTTATAATAATTATTATTTATTTTATTTCTTTTTCAGGGCACTGAAC
* * *
5854781 CTTGAGTCTAATGTTGCAACAATA
65 CTTAAGTCTAATGCTACAACAATA
* * * ** * *
5854805 TTTT-TCTTTTTAGAATATTTATAATAATTACTATTCATTTTATTTCGTTTTCA-GATACTTAAG
1 TTTTAT-TTTTTAGAATATTTATAATAATTATTATTTATTTTATTTCTTTTTCAGGGCACTGAAC
* * * **
5854868 CTTAAGTATGATGTTGTAACAATA
65 CTTAAGTCTAATGCTACAACAATA
** * * *
5854892 TTTTTATTATTGTCCGAAATAATTATAATAATTACTATGTATTTTATTTCATTTTTC
1 -TTTTATT-TT-TTAG-AATATTTATAATAATTATTATTTATTTTATTTC-TTTTTC
5854949 GGATTAATTG
Statistics
Matches: 190, Mismatches: 35, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
87 27 0.14
88 41 0.22
89 15 0.08
90 2 0.01
91 42 0.22
92 63 0.33
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.52
Consensus pattern (88 bp):
TTTTATTTTTTAGAATATTTATAATAATTATTATTTATTTTATTTCTTTTTCAGGGCACTGAACC
TTAAGTCTAATGCTACAACAATA
Found at i:5854939 original size:91 final size:87
Alignment explanation
Indices: 5854361--5854946 Score: 242
Period size: 84 Copynumber: 6.6 Consensus size: 87
5854351 ACTATTTATT
* * ** * *
5854361 TTTTTATTTTCCAGAATAATTATAATAATTACTATTTATTTTATTTTGTTTTCTG-GGCATTTAA
1 TTTTTATTTT-TAGAATATTTATAATAATTACTA-TTATTTTATTTCATTTTC-GAGACACTTAA
** * * *
5854425 GTTTAAGTATAGTGCTGCAATAA-A
63 CCTTAAGTATAATGTTGCAACAATA
* * * * *
5854449 ----AATTTTTCAGACTAATTATAATAATTGCTATTTATTTTATTT-ATTTTTCGAGACATTTAA
1 TTTTTATTTTT-AGAATATTTATAATAATTACTA-TTATTTTATTTCA-TTTTCGAGACACTTAA
** * * *
5854509 GTTTGAGTATGATGTTACAACAATA
63 CCTTAAGTATAATGTTGCAACAATA
* * * * * *
5854534 TTATTTTTTTTTAGAATAATTATTATAATTACTATTTATTTTATTTCTTTTTCGAGACATTTGGA
1 TT-TTTATTTTTAGAATATTTATAATAATTACTA-TTATTTTATTTCATTTTCGAGACACTT-AA
* * * ** ** ****
5854599 -GTTGAGCATGCAATAATATATTTGT-
63 CCTTAAGTAT--AATGTTGCAACAATA
* ** ** *
5854624 TTTTTATTTTTTAGAATAATTATAATAATTTTTATTTATTTTATTT-ATTTTTC-AGGGTACTGA
1 TTTTTA-TTTTTAGAATATTTATAATAATTACTA-TTATTTTATTTCA-TTTTCGA-GACACTTA
** * * * * * *
5854687 GGCTTAAGTTTAGTGCTACAACATTTT
62 ACCTTAAGTATAATGTTGCAACA-ATA
* * * * * *
5854714 TATTTTATTTTTTCGTAATATTTATAACAATTATTATTTATTTTATTTCTTTTTCGGGGCACTTA
1 T-TTTTA-TTTTTAG-AATATTTATAATAATTACTA-TTATTTTATTTCATTTTCGAGACACTTA
* *
5854779 ACCTTGAGTCTAATGTTGCAACAATA
62 ACCTTAAGTATAATGTTGCAACAATA
* * * *
5854805 TTTTTCTTTTTAGAATATTTATAATAATTACTATTCATTTTATTTCGTTTTC-AGATACTTAAGC
1 TTTTTATTTTTAGAATATTTATAATAATTACTATT-ATTTTATTTCATTTTCGAGACACTTAACC
* *
5854869 TTAAGTATGATGTTGTAACAATA
65 TTAAGTATAATGTTGCAACAATA
* *
5854892 TTTTTATTATTGTCCGAAATAATTATAATAATTACTATGTATTTTATTTCATTTT
1 TTTTTATT-TT-T-AG-AATATTTATAATAATTACTAT-TATTTTATTTCATTTT
5854947 TCGGATTAAT
Statistics
Matches: 383, Mismatches: 86, Indels: 55
0.73 0.16 0.10
Matches are distributed among these distances:
83 1 0.00
84 67 0.17
85 1 0.00
87 36 0.09
88 40 0.10
89 64 0.17
90 63 0.16
91 54 0.14
92 57 0.15
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (87 bp):
TTTTTATTTTTAGAATATTTATAATAATTACTATTATTTTATTTCATTTTCGAGACACTTAACCT
TAAGTATAATGTTGCAACAATA
Found at i:5866453 original size:14 final size:14
Alignment explanation
Indices: 5866412--5866468 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
5866402 GTCGGAGTCG
*
5866412 AGATTCAAGGTTTA
1 AGATTCAAGATTTA
*
5866426 AG-TTCAAAATTTA
1 AGATTCAAGATTTA
*
5866439 AGATTCGAGATTTA
1 AGATTCAAGATTTA
* *
5866453 AGATTGAAGGTTTA
1 AGATTCAAGATTTA
5866467 AG
1 AG
5866469 TTTAAATTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
13 11 0.31
14 24 0.69
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (14 bp):
AGATTCAAGATTTA
Found at i:5868835 original size:21 final size:20
Alignment explanation
Indices: 5868791--5868828 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5868781 ATTGCAATTC
5868791 TAAAAATATAAATAATTTTA
1 TAAAAATATAAATAATTTTA
*
5868811 TAAAAA-ATTAATAATTTT
1 TAAAAATATAAATAATTTT
5868829 GATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAAATATAAATAATTTTA
Found at i:5875626 original size:22 final size:22
Alignment explanation
Indices: 5875598--5875641 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5875588 AAGGTGAAAG
5875598 TTGATTCTTAAACAACACTAAA
1 TTGATTCTTAAACAACACTAAA
5875620 TTGATTCTTAAACAACACTAAA
1 TTGATTCTTAAACAACACTAAA
5875642 AAAAAGAGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (22 bp):
TTGATTCTTAAACAACACTAAA
Found at i:5878669 original size:20 final size:21
Alignment explanation
Indices: 5878630--5878669 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5878620 CGTGTTTGCT
* *
5878630 TTCCGTTCAGCTCTTATGAGC
1 TTCCGTTCAACTCATATGAGC
5878651 TTCCGTT-AACTCATATGAG
1 TTCCGTTCAACTCATATGAG
5878670 TTTCAGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TTCCGTTCAACTCATATGAGC
Found at i:5879785 original size:81 final size:81
Alignment explanation
Indices: 5879650--5879893 Score: 418
Period size: 81 Copynumber: 3.0 Consensus size: 81
5879640 ACTAAACTAA
* *
5879650 ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGACATGAATATAGTATGAACCAT
1 ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCAT
5879715 GCTATGTGATATTGGG
66 GCTATGTGATATTGGG
* *
5879731 ATGAAGTAGAAAATAGCATGATATAGTTGATGCATGATATGTGATATGACTATAGAATGAACCAT
1 ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCAT
*
5879796 GCTTTGTGATATTGGG
66 GCTATGTGATATTGGG
*
5879812 ATGAAGTAGAAAATAGTATGATGTAGTTGATGCGA-GATATGTGATATGAATATAGAATGAACCA
1 ATGAAGTAGAAAATAGTATGATATAGTTGATGC-ATGATATGTGATATGAATATAGAATGAACCA
5879876 TGCTATGTGATATTGGG
65 TGCTATGTGATATTGGG
5879893 A
1 A
5879894 ATATATGAAG
Statistics
Matches: 153, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
81 152 0.99
82 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (81 bp):
ATGAAGTAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCAT
GCTATGTGATATTGGG
Found at i:5881808 original size:13 final size:13
Alignment explanation
Indices: 5881790--5881819 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
5881780 TGCTTTCACA
5881790 AAGAGTGTATAAT
1 AAGAGTGTATAAT
5881803 AAGAGTGTATAAT
1 AAGAGTGTATAAT
5881816 AAGA
1 AAGA
5881820 AGTTTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (13 bp):
AAGAGTGTATAAT
Found at i:5893332 original size:6 final size:6
Alignment explanation
Indices: 5893321--5893347 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5893311 TTGGGTTCTA
5893321 TTTTGT TTTTGT TTTTGT TTTTGT TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTT
5893348 CTTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:5894435 original size:6 final size:6
Alignment explanation
Indices: 5894424--5894454 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5894414 AATGCTGAGA
*
5894424 GTTGCT GTTGCT GTTGCT GTTGCT GCTGCT G
1 GTTGCT GTTGCT GTTGCT GTTGCT GTTGCT G
5894455 ACTGCATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.35, T:0.45
Consensus pattern (6 bp):
GTTGCT
Found at i:5896555 original size:114 final size:116
Alignment explanation
Indices: 5896419--5896650 Score: 432
Period size: 117 Copynumber: 2.0 Consensus size: 116
5896409 AAAAATCTTT
5896419 GATTTTTATGCATAAATATGTATATT-AA-ATTATTATTTATTATTATGGTTTTATATTTGATAT
1 GATTTTTATGCATAAATATGTATATTAAATATTATTATTTATTATTATGGTTTTATATTTGATAT
*
5896482 TTATTAATGTTATTTTTATTAAATTGATAGTTTATTATGAAATAAATTAAA
66 TTATTAATGTTATTTTTATTAAATTGATAGTATATTATGAAATAAATTAAA
5896533 GATTTTTATGCATAAATATGTATATTAAATTATTATTATTTATTATTATGGTTTTATATTTGATA
1 GATTTTTATGCATAAATATGTATATTAAA-TATTATTATTTATTATTATGGTTTTATATTTGATA
5896598 TTTATTAATGTTATTTTTATTAAATTGATAGTATATTATGAAATAAATTAAA
65 TTTATTAATGTTATTTTTATTAAATTGATAGTATATTATGAAATAAATTAAA
5896650 G
1 G
5896651 TAAAGACAAA
Statistics
Matches: 114, Mismatches: 1, Indels: 3
0.97 0.01 0.03
Matches are distributed among these distances:
114 26 0.23
115 2 0.02
117 86 0.75
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.53
Consensus pattern (116 bp):
GATTTTTATGCATAAATATGTATATTAAATATTATTATTTATTATTATGGTTTTATATTTGATAT
TTATTAATGTTATTTTTATTAAATTGATAGTATATTATGAAATAAATTAAA
Found at i:5901208 original size:21 final size:21
Alignment explanation
Indices: 5901184--5901227 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5901174 CAAAGGTTAA
*
5901184 TCGATAGCTACTCACAATCTT
1 TCGATAACTACTCACAATCTT
5901205 TCGATAACTACTCACAATCTT
1 TCGATAACTACTCACAATCTT
5901226 TC
1 TC
5901228 AATATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.34
Consensus pattern (21 bp):
TCGATAACTACTCACAATCTT
Found at i:5903477 original size:25 final size:23
Alignment explanation
Indices: 5903402--5903529 Score: 120
Period size: 25 Copynumber: 5.4 Consensus size: 23
5903392 CACTAATGAA
*
5903402 CAGAGAGCACTGAAGTGCT-ATA-
1 CAGAGAGCACT-ACGTGCTAATAT
* *
5903424 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCAC-TACGTGCTAATAT
5903446 CAGAGAGCACTCACGTGCTAAATAT
1 CAGAGAGCACT-ACGTGCT-AATAT
5903471 CAGAGAGCACTAGCGTGCTAATAAT
1 CAGAGAGCACTA-CGTGCTAAT-AT
*
5903496 CAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACT-ACGTGCTAATA-T
5903521 CAGAGAGCA
1 CAGAGAGCA
5903530 TGCTGAGGTC
Statistics
Matches: 91, Mismatches: 5, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.01
22 33 0.36
24 6 0.07
25 51 0.56
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (23 bp):
CAGAGAGCACTACGTGCTAATAT
Found at i:5907874 original size:16 final size:16
Alignment explanation
Indices: 5907850--5907883 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5907840 TTATTAATTT
5907850 ATGTGATTAATT-GAA
1 ATGTGATTAATTGGAA
5907865 ATGTGTATTAATTGGAA
1 ATGTG-ATTAATTGGAA
5907882 AT
1 AT
5907884 TGAAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 7 0.41
17 5 0.29
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (16 bp):
ATGTGATTAATTGGAA
Found at i:5908207 original size:18 final size:18
Alignment explanation
Indices: 5908184--5908271 Score: 113
Period size: 18 Copynumber: 4.9 Consensus size: 18
5908174 TAAAAGTACT
* *
5908184 GAATAACTGACTGTTACA
1 GAATAATTGATTGTTACA
*
5908202 GAATAATTAATTGTTACA
1 GAATAATTGATTGTTACA
**
5908220 GAATAATTGATTGCCACA
1 GAATAATTGATTGTTACA
* *
5908238 GAATAATTGATTGCTACT
1 GAATAATTGATTGTTACA
5908256 GAATAATTGATTGTTA
1 GAATAATTGATTGTTA
5908272 TTGAGTAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (18 bp):
GAATAATTGATTGTTACA
Found at i:5910763 original size:21 final size:21
Alignment explanation
Indices: 5910739--5910791 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5910729 GACACATAAA
*
5910739 GTGCCTAAAATGACACACGAG
1 GTGCCTGAAATGACACACGAG
* *
5910760 GTGCCTGATACGACACACGAG
1 GTGCCTGAAATGACACACGAG
5910781 GTGCCTGAAAT
1 GTGCCTGAAAT
5910792 ACGACACATA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (21 bp):
GTGCCTGAAATGACACACGAG
Found at i:5910777 original size:23 final size:22
Alignment explanation
Indices: 5910750--5910799 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
5910740 TGCCTAAAAT
5910750 GACACACGAGGTGCCTG-ATAC
1 GACACACGAGGTGCCTGAATAC
5910771 GACACACGAGGTGCCTGAAATAC
1 GACACACGAGGTGCCTG-AATAC
5910794 GACACA
1 GACACA
5910800 TAAAGTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.34, C:0.28, G:0.26, T:0.12
Consensus pattern (22 bp):
GACACACGAGGTGCCTGAATAC
Found at i:5910811 original size:23 final size:23
Alignment explanation
Indices: 5910725--5910811 Score: 74
Period size: 21 Copynumber: 4.0 Consensus size: 23
5910715 CCTGATCAGT
*
5910725 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* * *
5910747 A-ATGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
5910767 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
* *
5910790 ATACGACACATAAAGTGTCTGA
1 ATACGACACACAAAGTGCCTGA
5910812 TCAGTAAAGC
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
20 1 0.02
21 32 0.62
22 1 0.02
23 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:5911328 original size:22 final size:22
Alignment explanation
Indices: 5911285--5911328 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5911275 TTCTGTTCTC
* * *
5911285 TTTTCTCTATTCTTTTTGTTTT
1 TTTTCTCTACTCTGTTTCTTTT
*
5911307 TTTTCTTTACTCTGTTTCTTTT
1 TTTTCTCTACTCTGTTTCTTTT
5911329 ATTCACTTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.05, T:0.75
Consensus pattern (22 bp):
TTTTCTCTACTCTGTTTCTTTT
Found at i:5917657 original size:21 final size:22
Alignment explanation
Indices: 5917633--5917681 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
5917623 GCCTAAAACC
*
5917633 ACACACGAGGTGTCTG-ATACG
1 ACACACGAGGTGCCTGAATACG
5917654 ACACACGAGGTGCCTGAAATACG
1 ACACACGAGGTGCCTG-AATACG
5917677 ACACA
1 ACACA
5917682 TAAAGTGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 15 0.60
23 10 0.40
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (22 bp):
ACACACGAGGTGCCTGAATACG
Found at i:5917689 original size:23 final size:23
Alignment explanation
Indices: 5917611--5917693 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 23
5917601 ATCAGTATAT
*
5917611 GACACATAAAGTGCCT-AAA-AC
1 GACACACAAAGTGCCTGAAATAC
* * * *
5917632 CACACACGAGGTGTCTG--ATAC
1 GACACACAAAGTGCCTGAAATAC
* *
5917653 GACACACGAGGTGCCTGAAATAC
1 GACACACAAAGTGCCTGAAATAC
*
5917676 GACACATAAAGTGCCTGA
1 GACACACAAAGTGCCTGA
5917694 TCAGTAAAGC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.02
21 28 0.58
23 19 0.40
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
GACACACAAAGTGCCTGAAATAC
Found at i:5926683 original size:5 final size:5
Alignment explanation
Indices: 5926657--5926714 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
5926647 ATGTGTTAAA
* *
5926657 ATATAT ATATT AAATT ATTATT ATATT ATAGT ATATT ATATTAT ATATT
1 ATAT-T ATATT ATATT A-TATT ATATT ATATT ATATT ATA-T-T ATATT
5926706 ATATT ATAT
1 ATATT ATAT
5926715 AAATAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
5 31 0.69
6 10 0.22
7 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:5926693 original size:10 final size:9
Alignment explanation
Indices: 5926658--5926715 Score: 61
Period size: 8 Copynumber: 6.7 Consensus size: 9
5926648 TGTGTTAAAA
5926658 TATATATAT
1 TATATATAT
*
5926667 TAAAT-TAT
1 TATATATAT
5926675 TAT-TATAT
1 TATATATAT
5926683 TATAGTATAT
1 TATA-TATAT
5926693 TATAT-TA-
1 TATATATAT
5926700 TATATTATAT
1 TATA-TATAT
5926710 TATATA
1 TATATA
5926716 AATAAGTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.34
9 9 0.22
10 13 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (9 bp):
TATATATAT
Found at i:5926705 original size:12 final size:12
Alignment explanation
Indices: 5926660--5926715 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5926650 TGTTAAAATA
*
5926660 TATATATTAAAT
1 TATATATTATAT
5926672 TAT-TATTATATT
1 TATATATTATA-T
5926684 ATAGTATATTATAT
1 -TA-TATATTATAT
5926698 TATATATTATAT
1 TATATATTATAT
5926710 TATATA
1 TATATA
5926716 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5927089 original size:18 final size:19
Alignment explanation
Indices: 5927066--5927104 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5927056 ATATATAGAT
5927066 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5927084 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5927103 AT
1 AT
5927105 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5927453 original size:39 final size:40
Alignment explanation
Indices: 5927343--5927453 Score: 100
Period size: 38 Copynumber: 2.8 Consensus size: 40
5927333 GACCTCGAGT
* * **
5927343 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGATAGAGC
** ** * *
5927384 CGATGAGGTACTGGGTACCAACT-TTACTTCGGTTAG-GC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAGC
*
5927422 CGATGAGACACTGGGTGTCAAATATTGCTTCG
1 CGATGAGACACTGGGTGTCAAATATTACTTCG
5927454 AACTATCCGA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
38 18 0.34
39 18 0.34
40 1 0.02
41 16 0.30
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGATAGAGC
Found at i:5927621 original size:18 final size:19
Alignment explanation
Indices: 5927600--5927640 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
5927590 AATGAAATGA
5927600 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
5927618 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
5927637 GAAA
1 GAAA
5927641 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:5928965 original size:13 final size:13
Alignment explanation
Indices: 5928947--5928984 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
5928937 TACAACAATT
5928947 AAATTAAATAAAA
1 AAATTAAATAAAA
*
5928960 AAATTAAAT-ATA
1 AAATTAAATAAAA
*
5928972 AAATTATATAAAA
1 AAATTAAATAAAA
5928985 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATTAAATAAAA
Found at i:5928976 original size:12 final size:12
Alignment explanation
Indices: 5928947--5928999 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
5928937 TACAACAATT
*
5928947 AAATTAAATAAAA
1 AAATTAAAT-ATA
5928960 AAATTAAATATA
1 AAATTAAATATA
5928972 AAATT--ATATA
1 AAATTAAATATA
5928982 AAATTAAA-ATTA
1 AAATTAAATA-TA
5928994 AAATTA
1 AAATTA
5929000 TATAAGCGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 10 0.28
11 1 0.03
12 16 0.44
13 9 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTAAATATA
Found at i:5928987 original size:22 final size:22
Alignment explanation
Indices: 5928959--5929004 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5928949 ATTAAATAAA
5928959 AAAATT-AAATATAAAATTATAT
1 AAAATTAAAAT-TAAAATTATAT
5928981 AAAATTAAAATTAAAATTATAT
1 AAAATTAAAATTAAAATTATAT
5929003 AA
1 AA
5929005 GCGAGGCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAATTAAAATTAAAATTATAT
Found at i:5929586 original size:17 final size:19
Alignment explanation
Indices: 5929550--5929588 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
5929540 TTTTGCTTTG
*
5929550 TTTGTTGATTCAATGTGTT
1 TTTGTTGATTCAATGGGTT
5929569 TTTGTT-ATTC-ATGGGTT
1 TTTGTTGATTCAATGGGTT
5929586 TTT
1 TTT
5929589 TTTTGTCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 4 0.21
19 6 0.32
ACGTcount: A:0.13, C:0.05, G:0.21, T:0.62
Consensus pattern (19 bp):
TTTGTTGATTCAATGGGTT
Found at i:5936667 original size:99 final size:99
Alignment explanation
Indices: 5936496--5936690 Score: 345
Period size: 99 Copynumber: 2.0 Consensus size: 99
5936486 TTTCAAAGTG
* *
5936496 TGAAACAAATAGTCCCTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCATAATTGCTG
1 TGAAACAAATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCAAAATTGCTG
5936561 CATATCATATACTGCTATTACTTACAATCAAATT
66 CATATCATATACTGCTATTACTTACAATCAAATT
* *
5936595 TGAAACAGATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCTTCACCAAAATTGCTG
1 TGAAACAAATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCAAAATTGCTG
*
5936660 CATATCATATACTTCTATTACTTACAATCAA
66 CATATCATATACTGCTATTACTTACAATCAA
5936691 CCTATCATCT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 91 1.00
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (99 bp):
TGAAACAAATAGTCACTGCCACATTTGACAATTTTGCAGTAATAATGTCATCACCAAAATTGCTG
CATATCATATACTGCTATTACTTACAATCAAATT
Found at i:5942845 original size:21 final size:21
Alignment explanation
Indices: 5942807--5942849 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
5942797 AATGTTATTT
*
5942807 TAACATGAATTTTGATTATAA
1 TAACATGAAATTTGATTATAA
5942828 TAACAT-AAATTTGAATTATAA
1 TAACATGAAATTTG-ATTATAA
5942849 T
1 T
5942850 TGAATCAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
TAACATGAAATTTGATTATAA
Found at i:5943239 original size:35 final size:35
Alignment explanation
Indices: 5943193--5943273 Score: 153
Period size: 35 Copynumber: 2.3 Consensus size: 35
5943183 AGGTTTGCTC
*
5943193 GAAAAATGAGAGGATTTGGGTAAAAATATAAGCTT
1 GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
5943228 GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
1 GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
5943263 GAAAAATGAGA
1 GAAAAATGAGA
5943274 TTAAACAAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.23
Consensus pattern (35 bp):
GAAAAATGAGAGGATTTGGGTAAAAATATAAACTT
Found at i:5949550 original size:23 final size:23
Alignment explanation
Indices: 5949507--5949551 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5949497 TTTCAATTTT
*
5949507 TTATTTTAATAAGTGTCATCTCC
1 TTATTTTAATAAGTCTCATCTCC
* *
5949530 TTATTTTACTAAGTCTTATCTC
1 TTATTTTAATAAGTCTCATCTC
5949552 AATTGATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (23 bp):
TTATTTTAATAAGTCTCATCTCC
Found at i:5956020 original size:14 final size:14
Alignment explanation
Indices: 5955987--5956021 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5955977 TATAATATCT
*
5955987 AAATAATAACAATA
1 AAATAGTAACAATA
5956001 AAATAGTAACAATA
1 AAATAGTAACAATA
*
5956015 TAATAGT
1 AAATAGT
5956022 GAAATAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
AAATAGTAACAATA
Found at i:5956483 original size:9 final size:10
Alignment explanation
Indices: 5956460--5956485 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5956450 TTGAATAGTG
5956460 TTTTTAATTA
1 TTTTTAATTA
5956470 TTTTTAATTA
1 TTTTTAATTA
5956480 TTTTTA
1 TTTTTA
5956486 TATAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTAATTA
Found at i:5959637 original size:106 final size:105
Alignment explanation
Indices: 5959475--5959688 Score: 401
Period size: 106 Copynumber: 2.0 Consensus size: 105
5959465 TCTTTTTAGT
5959475 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
1 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
5959540 ATATTCCTACTTTTCCTCCTAAAATGAAAAAAACGAAAAGA
66 ATATTCCTACTTTTCCTCCTAAAATG-AAAAAACGAAAAGA
5959581 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
1 AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
* *
5959646 ATATTCCTTCTTTTCCTCCTAACATGAAAAAACGAAAAGA
66 ATATTCCTACTTTTCCTCCTAAAATGAAAAAACGAAAAGA
5959686 AAA
1 AAA
5959689 AAAGGAGGAA
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
105 17 0.16
106 89 0.84
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (105 bp):
AAATGAATTAACGTTATCTATGGAGGAAATGATGTCATGATTTTTAATCAATGAGCAGGAGCCCT
ATATTCCTACTTTTCCTCCTAAAATGAAAAAACGAAAAGA
Found at i:5961613 original size:7 final size:7
Alignment explanation
Indices: 5961601--5961626 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
5961591 GTCCTTTAAA
5961601 AAATTTT
1 AAATTTT
5961608 AAATTTT
1 AAATTTT
5961615 AAATTTT
1 AAATTTT
5961622 AAATT
1 AAATT
5961627 AGTAAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AAATTTT
Found at i:5962874 original size:16 final size:16
Alignment explanation
Indices: 5962853--5962883 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5962843 AAATTAATAT
5962853 AAAATAACATAAATTC
1 AAAATAACATAAATTC
*
5962869 AAAATAACCTAAATT
1 AAAATAACATAAATT
5962884 TGAAACAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACATAAATTC
Found at i:5963097 original size:14 final size:14
Alignment explanation
Indices: 5963078--5963117 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5963068 TTGATTGGCT
5963078 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5963092 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5963106 GAAAAATGTTTT
1 GTAAAATGTTTT
5963118 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5963130 original size:34 final size:35
Alignment explanation
Indices: 5963086--5963152 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
5963076 CTGTAAAATG
* *
5963086 TTTTCCGTAAAATGA-TTTCTGAAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
* *
5963120 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGAAAAATATTTT
5963153 CTGGTGTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.50
35 14 0.50
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGAAAAATATTTTAC
Done.