Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 11 of 26
Found at i:3946285 original size:25 final size:28
Alignment explanation
Indices: 3946249--3946313 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
3946239 GAGAATTAAG
*
3946249 AATAATCATTTC-TT-C-ATGGAGTAGT
1 AATAATCTTTTCTTTCCAATGGAGTAGT
3946274 AATAATCTTTTCTTTCCTAATGGAGTAGT
1 AATAATCTTTTCTTTCC-AATGGAGTAGT
3946303 AATAATCTTTT
1 AATAATCTTTT
3946314 TTCCTAATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 11 0.31
26 2 0.06
27 1 0.03
29 21 0.60
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (28 bp):
AATAATCTTTTCTTTCCAATGGAGTAGT
Found at i:3946299 original size:29 final size:27
Alignment explanation
Indices: 3946264--3946321 Score: 98
Period size: 29 Copynumber: 2.1 Consensus size: 27
3946254 TCATTTCTTC
3946264 ATGGAGTAGTAATAATCTTTTCTTTCCTA
1 ATGGAGTAGTAATAATC-TTT-TTTCCTA
3946293 ATGGAGTAGTAATAATCTTTTTTCCTA
1 ATGGAGTAGTAATAATCTTTTTTCCTA
3946320 AT
1 AT
3946322 TGTGTAATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 9 0.31
28 3 0.10
29 17 0.59
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (27 bp):
ATGGAGTAGTAATAATCTTTTTTCCTA
Found at i:3948981 original size:18 final size:19
Alignment explanation
Indices: 3948944--3948982 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3948934 TTCCACTGTG
*
3948944 AATAAAGAAATTCTTGATT
1 AATAAAGAAATTATTGATT
*
3948963 AATAAA-AAATTATTTATT
1 AATAAAGAAATTATTGATT
3948981 AA
1 AA
3948983 AAACCCTTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (19 bp):
AATAAAGAAATTATTGATT
Found at i:3963697 original size:48 final size:48
Alignment explanation
Indices: 3963645--3963738 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
3963635 TCCTAATATC
* * * *
3963645 AAAGTTGATGTTGGAGCTACTCCGAATGTT-GAGATTGTTCATGATGGT
1 AAAGTTGATGCTGAAGCCACTCCGAATGTTCAAG-TTGTTCATGATGGT
**
3963693 AAAGTTGATGCTGAAGCCACTTTGAATGTTCAAGTTGTTCATGATG
1 AAAGTTGATGCTGAAGCCACTCCGAATGTTCAAGTTGTTCATGATG
3963739 TTGGAGCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (48 bp):
AAAGTTGATGCTGAAGCCACTCCGAATGTTCAAGTTGTTCATGATGGT
Found at i:3971097 original size:27 final size:27
Alignment explanation
Indices: 3971059--3971257 Score: 134
Period size: 27 Copynumber: 7.3 Consensus size: 27
3971049 TAATTGTTAT
* * *
3971059 ACATCATGTTAAAAATGTAGTTATTCC
1 ACATCATATTAAAAATTTAGTTATTAC
*
3971086 ACATCATATTAAAAATTTAATTATTAC
1 ACATCATATTAAAAATTTAGTTATTAC
* * ** * *
3971113 ATATTACGTTGAAAAATATAGTTGTTAC
1 ACATCATATT-AAAAATTTAGTTATTAC
*
3971141 ACGTCATATTAAAAATTTAGTTATTAC
1 ACATCATATTAAAAATTTAGTTATTAC
** * * * *
3971168 ATGTCATGTTGAAAAGTTAGTTGTT--
1 ACATCATATTAAAAATTTAGTTATTAC
* *
3971193 ACATGCTATATTAAAAAATATAATTATTAC
1 ACAT-C-ATATT-AAAAATTTAGTTATTAC
* *
3971223 A-AGTCATATTGAAAAATTTAATTGTTAC
1 ACA-TCATATT-AAAAATTTAGTTATTAC
3971251 ACATCAT
1 ACATCAT
3971258 GAAAAAAAAG
Statistics
Matches: 130, Mismatches: 34, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 68 0.52
28 54 0.42
29 3 0.02
30 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (27 bp):
ACATCATATTAAAAATTTAGTTATTAC
Found at i:3971129 original size:55 final size:53
Alignment explanation
Indices: 3971061--3971257 Score: 175
Period size: 55 Copynumber: 3.6 Consensus size: 53
3971051 ATTGTTATAC
* *
3971061 ATCATGTT-AAAAATGTAGTTATTCCACATCATATTAAAAATTTAATTATTACAT
1 ATCACGTTGAAAAAT-TAGTTGTT-CACATCATATTAAAAATTTAATTATTACAT
* * *
3971115 ATTACGTTGAAAAATATAGTTGTTACACGTCATATTAAAAATTTAGTTATTACAT
1 ATCACGTTGAAAAAT-TAGTTGTT-CACATCATATTAAAAATTTAATTATTACAT
* * * *
3971170 GTCATGTTGAAAAGTTAGTTGTT-ACATGCTATATTAAAAAATATAATTATTACA-
1 ATCACGTTGAAAAATTAGTTGTTCACAT-C-ATATT-AAAAATTTAATTATTACAT
** *
3971224 AGTCATATTGAAAAATTTAATTGTTACACATCAT
1 A-TCACGTTGAAAAA-TTAGTTGTT-CACATCAT
3971258 GAAAAAAAAG
Statistics
Matches: 117, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
52 3 0.03
53 1 0.01
54 19 0.16
55 79 0.68
56 10 0.09
57 1 0.01
58 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (53 bp):
ATCACGTTGAAAAATTAGTTGTTCACATCATATTAAAAATTTAATTATTACAT
Found at i:3971162 original size:82 final size:82
Alignment explanation
Indices: 3971048--3971257 Score: 213
Period size: 82 Copynumber: 2.5 Consensus size: 82
3971038 CATGTTAGAA
* * * * * *
3971048 ATAATTGTTATACATCATGTTAAAAATGTAGTTATTCCACATCATATTAAAAATTTAATTATTAC
1 ATAATTGTTACACGTCATATTAAAAATTTAGTTATTACACATCATATTAAAAAGTTAATTATTAC
* * *
3971113 ATATTACGTTGAAAAAT
66 ATACTACATTAAAAAAT
* ** * * * *
3971130 ATAGTTGTTACACGTCATATTAAAAATTTAGTTATTACATGTCATGTTGAAAAGTTAGTTGTTAC
1 ATAATTGTTACACGTCATATTAAAAATTTAGTTATTACACATCATATTAAAAAGTTAATTATTAC
* *
3971195 ATGCTATATTAAAAAAT
66 ATACTACATTAAAAAAT
* * * *
3971212 ATAATTATTACAAGTCATATTGAAAAATTTAATTGTTACACATCAT
1 ATAATTGTTACACGTCATATT-AAAAATTTAGTTATTACACATCAT
3971258 GAAAAAAAAG
Statistics
Matches: 102, Mismatches: 25, Indels: 1
0.80 0.20 0.01
Matches are distributed among these distances:
82 82 0.80
83 20 0.20
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.40
Consensus pattern (82 bp):
ATAATTGTTACACGTCATATTAAAAATTTAGTTATTACACATCATATTAAAAAGTTAATTATTAC
ATACTACATTAAAAAAT
Found at i:3971798 original size:2 final size:2
Alignment explanation
Indices: 3971791--3971833 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3971781 GTACAAACGA
3971791 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
3971833 A
1 A
3971834 AGGAAATAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3976908 original size:46 final size:46
Alignment explanation
Indices: 3976858--3976951 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
3976848 ATTTATTTTT
3976858 ACTCTATTCGTACATAATAATTAGTAAATTCATTTTACGTAAAATA
1 ACTCTATTCGTACATAATAATTAGTAAATTCATTTTACGTAAAATA
*
3976904 ACTCTATTCGTACATAATAATTAGTAAATTTATTTTACGTAAAATA
1 ACTCTATTCGTACATAATAATTAGTAAATTCATTTTACGTAAAATA
3976950 AC
1 AC
3976952 CATACATGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.13, G:0.06, T:0.39
Consensus pattern (46 bp):
ACTCTATTCGTACATAATAATTAGTAAATTCATTTTACGTAAAATA
Found at i:3979967 original size:15 final size:15
Alignment explanation
Indices: 3979947--3979980 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3979937 TTTTGTATTC
3979947 TAAATTATATTA-ATA
1 TAAATTA-ATTATATA
3979962 TAAATTAATTATATA
1 TAAATTAATTATATA
3979977 TAAA
1 TAAA
3979981 GTTTATCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATTAATTATATA
Found at i:3982301 original size:48 final size:47
Alignment explanation
Indices: 3982226--3982321 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 47
3982216 GTCCGGTGGC
*
3982226 ATAGTAATTCTAGCTAGTGATAGCAAAGTTCTATACAATTACAAAAAT
1 ATAGTAATTCTAGCTAGTGATA-CAAAGTTCCATACAATTACAAAAAT
3982274 ATAGTAATTCTAGCTAGTAGCAT-CAAAGTTCCATACAATTACAAAAAT
1 ATAGTAATTCTAGCTAGT-G-ATACAAAGTTCCATACAATTACAAAAAT
3982322 TTTCCCCTGC
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
48 42 0.93
49 1 0.02
50 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (47 bp):
ATAGTAATTCTAGCTAGTGATACAAAGTTCCATACAATTACAAAAAT
Found at i:3983414 original size:21 final size:21
Alignment explanation
Indices: 3983390--3983429 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3983380 GACGTAAACA
3983390 ACACCTACAATAAGACATTTT
1 ACACCTACAATAAGACATTTT
*
3983411 ACACCTACAATGAGACATT
1 ACACCTACAATAAGACATT
3983430 CATTATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.25
Consensus pattern (21 bp):
ACACCTACAATAAGACATTTT
Found at i:3996722 original size:26 final size:26
Alignment explanation
Indices: 3996691--3996759 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
3996681 AATTAGTATA
3996691 TATTAATA-AGTATACTATGAATAGTG
1 TATTAATATA-TATACTATGAATAGTG
* * * *
3996717 TGTTAAGATATGTACTATGTATAGTG
1 TATTAATATATATACTATGAATAGTG
3996743 TATTAATATAT-TACTAT
1 TATTAATATATATACTAT
3996760 ATATAGTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 6 0.17
26 29 0.81
27 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.43
Consensus pattern (26 bp):
TATTAATATATATACTATGAATAGTG
Found at i:3996769 original size:21 final size:19
Alignment explanation
Indices: 3996745--3996783 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
3996735 GTATAGTGTA
3996745 TTAATATATTACTATATATAG
1 TTAATATA-TACT-TATATAG
3996766 TTAATATATACTTATATA
1 TTAATATATACTTATATA
3996784 AAATATAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (19 bp):
TTAATATATACTTATATAG
Found at i:3996859 original size:21 final size:18
Alignment explanation
Indices: 3996807--3996858 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
3996797 CCAAGAAGTC
3996807 ATAATA-TATA-TATTAT
1 ATAATAGTATATTATTAT
3996823 ATAATAGTATATTATTAT
1 ATAATAGTATATTATTAT
*
3996841 ATAATAGTAAATTATTAT
1 ATAATAGTATATTATTAT
3996859 TGACTAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
16 6 0.18
17 4 0.12
18 23 0.70
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
ATAATAGTATATTATTAT
Found at i:4003598 original size:18 final size:18
Alignment explanation
Indices: 4003575--4003610 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4003565 TATATTTATT
4003575 ATTATTTATTAGTTTTTA
1 ATTATTTATTAGTTTTTA
*
4003593 ATTATTTATTATTTTTTA
1 ATTATTTATTAGTTTTTA
4003611 GAGCTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTATTTATTAGTTTTTA
Found at i:4009736 original size:2 final size:2
Alignment explanation
Indices: 4009729--4009761 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4009719 TGTCATCATT
4009729 TA 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 T
4009762 GTGGGTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4011091 original size:16 final size:16
Alignment explanation
Indices: 4011065--4011097 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4011055 ATCTGATACG
4011065 TTTTATTTTTGTATTTT
1 TTTTATTTTTG-ATTTT
4011082 TTTTA-TTTTGATTTT
1 TTTTATTTTTGATTTT
4011097 T
1 T
4011098 GTTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTATTTTTGATTTT
Found at i:4014355 original size:39 final size:40
Alignment explanation
Indices: 4014294--4014369 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 40
4014284 ACATTGTGAA
* * *
4014294 AACACTAATTATGATAAGGTTAG-AAACCCCATTAAAGTG
1 AACACCAATTATGACAAAGTTAGAAAACCCCATTAAAGTG
*
4014333 AACACCAATTTTGACAAAGTTAGAAAACCCCATTAAA
1 AACACCAATTATGACAAAGTTAGAAAACCCCATTAAA
4014370 ATGTATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.24
Consensus pattern (40 bp):
AACACCAATTATGACAAAGTTAGAAAACCCCATTAAAGTG
Found at i:4015298 original size:13 final size:13
Alignment explanation
Indices: 4015282--4015306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4015272 ATAAAGCTTC
4015282 GCAATAAGTTTCT
1 GCAATAAGTTTCT
4015295 GCAATAAGTTTC
1 GCAATAAGTTTC
4015307 CTAAACTTTT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GCAATAAGTTTCT
Found at i:4023615 original size:28 final size:28
Alignment explanation
Indices: 4023581--4023634 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
4023571 ATTTAAAATT
* *
4023581 TTATTTATATTTGATGTAATGTATTTAC
1 TTATTTATATTTAACGTAATGTATTTAC
*
4023609 TTATTTATATTTAACGTAATTTATTT
1 TTATTTATATTTAACGTAATGTATTT
4023635 GTTTGTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (28 bp):
TTATTTATATTTAACGTAATGTATTTAC
Found at i:4025852 original size:12 final size:12
Alignment explanation
Indices: 4025829--4025859 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
4025819 TTAAAAAAAA
4025829 AAATTATTTTTTT
1 AAATT-TTTTTTT
4025842 AAATTTTTTTTT
1 AAATTTTTTTTT
4025854 AAATTT
1 AAATTT
4025860 ATGTTTGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
AAATTTTTTTTT
Found at i:4029032 original size:2 final size:2
Alignment explanation
Indices: 4029025--4029049 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4029015 ATGGTCCTTG
4029025 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
4029050 ATCTTGCCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4034896 original size:20 final size:19
Alignment explanation
Indices: 4034855--4034898 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
4034845 TTCCTTTTCC
* *
4034855 TTTTTTTTTAATTTTGAAA
1 TTTTTTTCTAATTTTCAAA
*
4034874 TTTTTTTCTAATTTTTCATA
1 TTTTTTTCTAA-TTTTCAAA
4034894 TTTTT
1 TTTTT
4034899 CTCTCTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTTTCTAATTTTCAAA
Found at i:4039066 original size:54 final size:54
Alignment explanation
Indices: 4038988--4039098 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
4038978 GCTCAAGAAA
*
4038988 TTTTCACTAGTCGGTAAACAGGTAAGGTAATAGAAGTAAAGGGAATGACTAAAT
1 TTTTCACTAGTCGGTAAAAAGGTAAGGTAATAGAAGTAAAGGGAATGACTAAAT
4039042 TTTTCACTAGTCGGTAAAAAGGTAAGGTAATAGAAGTAAAGGGAATGACTAAAT
1 TTTTCACTAGTCGGTAAAAAGGTAAGGTAATAGAAGTAAAGGGAATGACTAAAT
4039096 TTT
1 TTT
4039099 GAATGACAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (54 bp):
TTTTCACTAGTCGGTAAAAAGGTAAGGTAATAGAAGTAAAGGGAATGACTAAAT
Found at i:4042025 original size:84 final size:84
Alignment explanation
Indices: 4041884--4042044 Score: 250
Period size: 84 Copynumber: 1.9 Consensus size: 84
4041874 CACCTCTTTT
* * *
4041884 AATCGATTTTGATGCTAATAGTATAATGGAGCTTATGCATATTCAAACCCTGTCTCCTATTCTTG
1 AATCGATTTTGATGATAATAGCATAATGGAGCTTATGCATATTCAAACCCTGTCTCCTATTCTTA
4041949 GATTATATTTCTTAATTAC
66 GATTATATTTCTTAATTAC
* * ** *
4041968 AATCGATTTTGATGATAATGGCATAATGGGGCTTATGCATATTCAAACTTTGTCTCCTGTTCTTA
1 AATCGATTTTGATGATAATAGCATAATGGAGCTTATGCATATTCAAACCCTGTCTCCTATTCTTA
4042033 GATTATATTTCT
66 GATTATATTTCT
4042045 AAATCGCAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
84 69 1.00
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (84 bp):
AATCGATTTTGATGATAATAGCATAATGGAGCTTATGCATATTCAAACCCTGTCTCCTATTCTTA
GATTATATTTCTTAATTAC
Found at i:4047313 original size:26 final size:25
Alignment explanation
Indices: 4047284--4047340 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
4047274 ATAAAAGAAT
***
4047284 ATAAATTTAATTGGATATAAATAAAA
1 ATAAATTTAATCAAATAT-AATAAAA
*
4047310 ATAATTTTTAATCAAATATAATAAAA
1 ATAA-ATTTAATCAAATATAATAAAA
4047336 ATAAA
1 ATAAA
4047341 AAAACAGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
ATAAATTTAATCAAATATAATAAAA
Found at i:4047523 original size:3 final size:3
Alignment explanation
Indices: 4047515--4047539 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4047505 TAGTAAATAC
4047515 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
4047540 TTGTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4048407 original size:20 final size:20
Alignment explanation
Indices: 4048370--4048411 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
4048360 TATAAACCAT
4048370 ATTAAAAAATCTCAATTATAA
1 ATTAAAAAATCTCAATTA-AA
* *
4048391 ATTAAAAATTTTC-ATTAAA
1 ATTAAAAAATCTCAATTAAA
4048410 AT
1 AT
4048412 ATGAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAAAAAATCTCAATTAAA
Found at i:4052386 original size:22 final size:22
Alignment explanation
Indices: 4052339--4052386 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
4052329 GCTAAACCTT
** * *
4052339 TTTAAAGTACATGTTTTTTTTT
1 TTTAAAGTACATGTTGATATTA
4052361 TTTAAAGTACATGTTGATATTA
1 TTTAAAGTACATGTTGATATTA
4052383 TTTA
1 TTTA
4052387 CAGATGGGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTAAAGTACATGTTGATATTA
Found at i:4052453 original size:2 final size:2
Alignment explanation
Indices: 4052441--4052471 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4052431 CATAATATTC
*
4052441 TA TA CA 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 T
4052472 GGGGAGGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4056228 original size:45 final size:45
Alignment explanation
Indices: 4056164--4056251 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
4056154 TATCATACCG
4056164 TCTCACACTCCCCCTCTAAAGGCAAGAGAAGAGAAGAGAAACTGT
1 TCTCACACTCCCCCTCTAAAGGCAAGAGAAGAGAAGAGAAACTGT
* * *
4056209 TCTCACTCTCTCCCTCTAAAGGCAAGAGAAGAGAAGAGCAACT
1 TCTCACACTCCCCCTCTAAAGGCAAGAGAAGAGAAGAGAAACT
4056252 ATGTTTCTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.17
Consensus pattern (45 bp):
TCTCACACTCCCCCTCTAAAGGCAAGAGAAGAGAAGAGAAACTGT
Found at i:4058772 original size:3 final size:3
Alignment explanation
Indices: 4058766--4058790 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4058756 AATAATAATA
4058766 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
4058791 AAATATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:4059186 original size:29 final size:29
Alignment explanation
Indices: 4059119--4059174 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
4059109 TTTGATTTAA
* *
4059119 AATAAAAATATAAATATTTAATTGAATGT
1 AATAAAAATATAAAAATTTAATTAAATGT
*
4059148 AATAAAAATATAAAAATTTATTTAAAT
1 AATAAAAATATAAAAATTTAATTAAAT
4059175 TTTTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (29 bp):
AATAAAAATATAAAAATTTAATTAAATGT
Found at i:4059218 original size:23 final size:23
Alignment explanation
Indices: 4059174--4059219 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4059164 TTTATTTAAA
*
4059174 TTTTTTAAAAATAATTTAATAAT
1 TTTTTTAAAAATAATGTAATAAT
*
4059197 TTTTTTAAAATATTATGT-ATAAT
1 TTTTTTAAAA-ATAATGTAATAAT
4059220 AATAATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTTTAAAAATAATGTAATAAT
Found at i:4059221 original size:3 final size:3
Alignment explanation
Indices: 4059215--4059242 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4059205 AATATTATGT
4059215 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4059243 GAATTGCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4059447 original size:161 final size:163
Alignment explanation
Indices: 4059273--4059597 Score: 636
Period size: 161 Copynumber: 2.0 Consensus size: 163
4059263 AAATTTGAAG
4059273 AAGAGAGATAGAAATAATGTTTTTAGCTATAAATAATGGAAACTCCAAACACGAAACTTCAATTT
1 AAGAGAGATAGAAATAATGTTTTTAGCTATAAATAATGGAAACTCCAAACACGAAACTTCAATTT
4059338 CTAATTGGGATCTTTCGGATTGTTATTA-TTTTTTGGCC-TTTTATGATTTTCCTAATAATAAAA
66 CTAATTGGGATCTTTCGGATTGTTATTATTTTTTTGGCCTTTTTATGATTTTCCTAATAATAAAA
4059401 TGAAGCCTTGCTGACTAGTGATTATTTATGGTA
131 TGAAGCCTTGCTGACTAGTGATTATTTATGGTA
4059434 AAGAGAGATAGAAATAATGTTTTTAGCTATAAATAATGGAAACTCCAAACACGAAACTTCAATTT
1 AAGAGAGATAGAAATAATGTTTTTAGCTATAAATAATGGAAACTCCAAACACGAAACTTCAATTT
4059499 CTAATTGGGATCTTTCGGATTGTTATTATTTTTTTGGCCTTTTTATGATTTTCCTAATAATAAAA
66 CTAATTGGGATCTTTCGGATTGTTATTATTTTTTTGGCCTTTTTATGATTTTCCTAATAATAAAA
4059564 TGAAGCCTTGCTGACTAGTGATTATTTATGGTA
131 TGAAGCCTTGCTGACTAGTGATTATTTATGGTA
4059597 A
1 A
4059598 CAATCTGATT
Statistics
Matches: 162, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 93 0.57
162 10 0.06
163 59 0.36
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (163 bp):
AAGAGAGATAGAAATAATGTTTTTAGCTATAAATAATGGAAACTCCAAACACGAAACTTCAATTT
CTAATTGGGATCTTTCGGATTGTTATTATTTTTTTGGCCTTTTTATGATTTTCCTAATAATAAAA
TGAAGCCTTGCTGACTAGTGATTATTTATGGTA
Found at i:4062101 original size:2 final size:2
Alignment explanation
Indices: 4062094--4062122 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4062084 ATGCATATGC
4062094 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
4062123 AATCTTAATG
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:4064661 original size:67 final size:66
Alignment explanation
Indices: 4064531--4064665 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 66
4064521 TGATCTATAA
* * * * * *
4064531 TTTAATCCTTTTGGAAGTAAGGTACTTGAATTGTTTTTTGAGGTACGCAGACCTTGATGTATAAT
1 TTTAATCCTTTTGGAAGCAAAGTACTTGAATTATATTTTGAGATACGCAGACCTTAATGTATAAT
4064596 T
66 T
* * * * *
4064597 TTTAATTCCTTTTGGAAGCAAAGTACTTGTATTATATTTTGAGATATGCATATCTTAATTTATAA
1 TTTAA-TCCTTTTGGAAGCAAAGTACTTGAATTATATTTTGAGATACGCAGACCTTAATGTATAA
4064662 TT
65 TT
4064664 TT
1 TT
4064666 CTTGTGGCAG
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
66 5 0.09
67 52 0.91
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (66 bp):
TTTAATCCTTTTGGAAGCAAAGTACTTGAATTATATTTTGAGATACGCAGACCTTAATGTATAAT
T
Found at i:4075001 original size:4 final size:5
Alignment explanation
Indices: 4074987--4075020 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
4074977 TATCTGTTGG
4074987 AAATA AAAT- AAAT- AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA A
4075021 TAAAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:4075010 original size:18 final size:18
Alignment explanation
Indices: 4074987--4075029 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
4074977 TATCTGTTGG
4074987 AAATAAAAT-AAATAAATA
1 AAATAAAATAAAAT-AATA
4075005 AAATAAAATAAAATAATA
1 AAATAAAATAAAATAATA
4075023 AAA-AAAA
1 AAATAAAA
4075030 GCCATGTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATAAAATAAAATAATA
Found at i:4075022 original size:13 final size:14
Alignment explanation
Indices: 4074987--4075025 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
4074977 TATCTGTTGG
4074987 AAATAAAAT-AAAT
1 AAATAAAATAAAAT
4075000 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
4075014 AAA-ATAATAAAA
1 AAATAAAATAAAA
4075026 AAAAGCCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 17 0.71
14 7 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:4078875 original size:4 final size:5
Alignment explanation
Indices: 4078860--4078891 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
4078850 ATGTCTGTTG
4078860 AAAAT AAAAT -AAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
4078892 ATAAGAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:4081676 original size:138 final size:138
Alignment explanation
Indices: 4081428--4081686 Score: 378
Period size: 138 Copynumber: 1.9 Consensus size: 138
4081418 TATAAGCTCG
* * *
4081428 TGACATTTAAATGTAAATATTTATTTTTTTATTTATTTGAAATATAAAATTATATAAAGCAAAAA
1 TGACATTTAAATGTAAATACTTATTTTTTAATTTATTTGAAATATAAAATTATATAAAACAAAAA
*
4081493 TGTTTCTAAAATGTAAAATTAATTGTTTTAAATAAAAGAAAATTATAAATAAAAAATTATAAATG
66 TGTTTCTAAAATGTAAAATTAATTGTTCTAAATAAAAGAAAATTATAAATAAAAAATTATAAATG
4081558 TGGGCCCA
131 TGGGCCCA
* *
4081566 TGACATTTACAA-GTAAATACTTA-TTTTTAATTTATTTTTAAATATAAAATTATATAAAATAAA
1 TGACATTTA-AATGTAAATACTTATTTTTTAATTTA-TTTGAAATATAAAATTATATAAAACAAA
* ** * * *
4081629 AATTTTTCTGCAATGTAAAATTAATTGTTCTAAGTAAAAGATAATTATAATTAAAAAA
64 AATGTTTCTAAAATGTAAAATTAATTGTTCTAAATAAAAGAAAATTATAAATAAAAAA
4081687 AATTATATTT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
137 10 0.09
138 95 0.89
139 2 0.02
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (138 bp):
TGACATTTAAATGTAAATACTTATTTTTTAATTTATTTGAAATATAAAATTATATAAAACAAAAA
TGTTTCTAAAATGTAAAATTAATTGTTCTAAATAAAAGAAAATTATAAATAAAAAATTATAAATG
TGGGCCCA
Found at i:4085233 original size:2 final size:2
Alignment explanation
Indices: 4085228--4085260 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4085218 TCTTGGTGTG
4085228 TA 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 T
4085261 TCGAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4086321 original size:16 final size:17
Alignment explanation
Indices: 4086300--4086337 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
4086290 TTTATGAAAA
4086300 AAAATAAATT-TAATGT
1 AAAATAAATTATAATGT
*
4086316 AAAATATATTATAATGT
1 AAAATAAATTATAATGT
*
4086333 CAAAT
1 AAAAT
4086338 GTTTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAATAAATTATAATGT
Found at i:4105359 original size:17 final size:17
Alignment explanation
Indices: 4105333--4105366 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4105323 TCCATTTCGA
4105333 CAAGCATTGCTTCTTGC
1 CAAGCATTGCTTCTTGC
* *
4105350 CAAGCTTTGCTTTTTGC
1 CAAGCATTGCTTCTTGC
4105367 TGCACCAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (17 bp):
CAAGCATTGCTTCTTGC
Found at i:4109410 original size:15 final size:16
Alignment explanation
Indices: 4109381--4109410 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4109371 TTCTCAGTCT
4109381 TTTAATTTCTTTCCCG
1 TTTAATTTCTTTCCCG
4109397 TTTAATTT-TTTCCC
1 TTTAATTTCTTTCCC
4109411 TTTTTTCTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.60
Consensus pattern (16 bp):
TTTAATTTCTTTCCCG
Found at i:4123984 original size:49 final size:49
Alignment explanation
Indices: 4123886--4124012 Score: 182
Period size: 49 Copynumber: 2.6 Consensus size: 49
4123876 ACAAACTTAA
* * *
4123886 ACTTAATCTTGATCACGAACTTGCTTGATCTTCATTTCAAGAGTCTTTATG
1 ACTTAATCTTGATCACGAAC--ACTTGATCTTCACTTCAAGAGTATTTATG
* *
4123937 ACTTAATCTTGATCACGAACACTTGATCTTTACTTCAAGGGTATTTATG
1 ACTTAATCTTGATCACGAACACTTGATCTTCACTTCAAGAGTATTTATG
*
4123986 ACTTAATTTTGATCACGAACACTTGAT
1 ACTTAATCTTGATCACGAACACTTGAT
4124013 ATCTTGATCA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
49 50 0.71
51 20 0.29
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (49 bp):
ACTTAATCTTGATCACGAACACTTGATCTTCACTTCAAGAGTATTTATG
Found at i:4124554 original size:81 final size:81
Alignment explanation
Indices: 4124386--4124683 Score: 458
Period size: 81 Copynumber: 3.7 Consensus size: 81
4124376 TTTGATTTTC
* * * *
4124386 ATCTCTAAATTAATAT-AATTA-TTAGAGATAAATTAGATGACCAATAATTAA-TTTTGATTGGT
1 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTAGATGACCAATAACTAATTTTTGATTGGT
* *
4124448 AAAAAATATTAATATT
66 CAAAAATATAAATATT
* *
4124464 ATCTTTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACTAATTTTTGATTGGT
1 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTAGATGACCAATAACTAATTTTTGATTGGT
4124529 CAAAAATATAAATATT
66 CAAAAATATAAATATT
* * *
4124545 ATCTCTAAATTATTTTAATTTATTTAGAGATAAATTAGATGACCAATAAGTAATTTGTGATTGGT
1 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTAGATGACCAATAACTAATTTTTGATTGGT
4124610 CAAAAATATAAATATT
66 CAAAAATATAAATATT
* *
4124626 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGATCAATAACTAATTTTT
1 ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTAGATGACCAATAACTAATTTTT
4124684 TTATTAGTCC
Statistics
Matches: 199, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
78 13 0.07
79 4 0.02
80 28 0.14
81 154 0.77
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (81 bp):
ATCTCTAAATTATTTTGATTTATTTAGAGATAAATTAGATGACCAATAACTAATTTTTGATTGGT
CAAAAATATAAATATT
Found at i:4124584 original size:161 final size:160
Alignment explanation
Indices: 4124386--4124683 Score: 508
Period size: 162 Copynumber: 1.9 Consensus size: 160
4124376 TTTGATTTTC
*
4124386 ATCTCTAAATTAATATAATTATTAGAGATAAATTAGATGACCAATAATTAATTT-TGATTGGTAA
1 ATCTCTAAATTAATATAATTATTAGAGATAAATTAGATGACCAATAAGTAATTTGTGATTGGTAA
* *
4124450 AAAATATTAATATTATCTTTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACT
66 AAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACT
4124515 AATTTTTGATTGGTCAAAAATATAAATATT
131 AATTTTTGATTGGTCAAAAATATAAATATT
* *
4124545 ATCTCTAAATTATTTTAATTTATTTAGAGATAAATTAGATGACCAATAAGTAATTTGTGATTGGT
1 ATCTCTAAATTAATATAA-TTA-TTAGAGATAAATTAGATGACCAATAAGTAATTTGTGATTGGT
* *
4124610 CAAAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGATCAATAA
64 AAAAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAA
4124675 CTAATTTTT
129 CTAATTTTT
4124684 TTATTAGTCC
Statistics
Matches: 129, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
159 16 0.12
160 3 0.02
161 32 0.25
162 78 0.60
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.42
Consensus pattern (160 bp):
ATCTCTAAATTAATATAATTATTAGAGATAAATTAGATGACCAATAAGTAATTTGTGATTGGTAA
AAAATATAAATATTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACT
AATTTTTGATTGGTCAAAAATATAAATATT
Found at i:4124659 original size:38 final size:38
Alignment explanation
Indices: 4124536--4124660 Score: 88
Period size: 38 Copynumber: 3.2 Consensus size: 38
4124526 GGTCAAAAAT
*
4124536 ATAAATATTATCTCTAAATTATTTTAATTTATTTAGAG
1 ATAAATATTATCTCTAAATTATTTTGATTTATTTAGAG
* * ** * * ** ** * *
4124574 ATAAATTAGATGACCAATAAGTAATTTGTGATTGGTCAAAAAT
1 ATAAA-T--ATTATCTCTAAATTATTT-TGATTTAT-TTAGAG
4124617 ATAAATATTATCTCTAAATTATTTTGATTTATTTAGAG
1 ATAAATATTATCTCTAAATTATTTTGATTTATTTAGAG
4124655 ATAAAT
1 ATAAAT
4124661 TGGATGATCA
Statistics
Matches: 57, Mismatches: 25, Indels: 10
0.62 0.27 0.11
Matches are distributed among these distances:
38 13 0.23
39 7 0.12
40 12 0.21
41 12 0.21
42 6 0.11
43 7 0.12
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.43
Consensus pattern (38 bp):
ATAAATATTATCTCTAAATTATTTTGATTTATTTAGAG
Found at i:4125498 original size:39 final size:39
Alignment explanation
Indices: 4125452--4125530 Score: 124
Period size: 39 Copynumber: 2.0 Consensus size: 39
4125442 TTCATGTTTG
* *
4125452 AAATCATGCAAGCCACCA-TTAGTTTCAATTGTCATGCTA
1 AAATCATGCAAGCCACCACTT-GTTTCAATTGCCACGCTA
4125491 AAATCATGCAAGCCACCACTTGTTTCAATTGCCACGCTA
1 AAATCATGCAAGCCACCACTTGTTTCAATTGCCACGCTA
4125530 A
1 A
4125531 GTCTCCTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.28
Consensus pattern (39 bp):
AAATCATGCAAGCCACCACTTGTTTCAATTGCCACGCTA
Found at i:4125970 original size:76 final size:75
Alignment explanation
Indices: 4125833--4126084 Score: 227
Period size: 76 Copynumber: 3.3 Consensus size: 75
4125823 ATTTAAAGTA
* * * * **
4125833 GTGCTTTTTACAATAGCATGCAATTTGTTATCCTCGGAGGGTGCTCTTTATAATAACACTTATTG
1 GTGC-TTTTAAAATAGCATACAATTTATTATCCTCGAAAAGTGCTCTTTATAATAACACTTATTG
4125898 ATCCTTAGGAG
65 ATCCTTAGGAG
**
4125909 GTGCATTTTAAAATAGCATACAATTTATTATCCTCGAAAAGTGCTCTTTATAATAGTACTTATTG
1 GTGC-TTTTAAAATAGCATACAATTTATTATCCTCGAAAAGTGCTCTTTATAATAACACTTATTG
*
4125974 ATCCTTGGGAG
65 ATCCTTAGGAG
* *** ** ** * * * * *
4125985 GTACTCTTCCTAATAGCATACAATTTATTAT-CTTTAGAGGGTGCTTTTTATCATAGCGCTTGTT
1 GTGCT-TTTAAAATAGCATACAATTTATTATCCTCGA-AAAGTGCTCTTTATAATAACACTTATT
*
4126049 GATCCTTGGGAG
64 GATCCTTAGGAG
* *
4126061 GTGCTCTTTATACTAGCATACAAT
1 GTGCT-TTTAAAATAGCATACAAT
4126085 GTAGAATCAC
Statistics
Matches: 147, Mismatches: 27, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
75 4 0.03
76 143 0.97
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.39
Consensus pattern (75 bp):
GTGCTTTTAAAATAGCATACAATTTATTATCCTCGAAAAGTGCTCTTTATAATAACACTTATTGA
TCCTTAGGAG
Found at i:4129673 original size:64 final size:64
Alignment explanation
Indices: 4129549--4129675 Score: 175
Period size: 64 Copynumber: 2.0 Consensus size: 64
4129539 AATATATATA
* * **
4129549 TTTTTACCTTAATTTTTACCTAAGTTGTCATTTTAAGGATTTTCAACTTAGCAGTTTTTTTTTT
1 TTTTTACCTTAATTTTTACCTAAGTTGTCATGTTAAGGATTTTCAACTTAACAGACTTTTTTTT
* * *
4129613 TTTTTGCCTTAACTTTTT-CCTAAGTTGTCCTGTTAAGGATTTTCAACTTAACTGACTTTTTTT
1 TTTTTACCTTAA-TTTTTACCTAAGTTGTCATGTTAAGGATTTTCAACTTAACAGACTTTTTTT
4129676 AGGTGCAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 50 0.91
65 5 0.09
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.54
Consensus pattern (64 bp):
TTTTTACCTTAATTTTTACCTAAGTTGTCATGTTAAGGATTTTCAACTTAACAGACTTTTTTTT
Found at i:4138031 original size:15 final size:15
Alignment explanation
Indices: 4138011--4138044 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
4138001 GAAATTGGTG
4138011 ATAAAATA-AAATGAA
1 ATAAAATAGAAAT-AA
4138026 ATAAAATAGAAATAA
1 ATAAAATAGAAATAA
4138041 ATAA
1 ATAA
4138045 TCATATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
ATAAAATAGAAATAA
Found at i:4138089 original size:20 final size:20
Alignment explanation
Indices: 4138064--4138102 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4138054 AGTTTTAGTT
4138064 ATAAATTA-ACAATATTTAAA
1 ATAAATTATA-AATATTTAAA
4138084 ATAAATTATAAATATTTAA
1 ATAAATTATAAATATTTAA
4138103 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATTATAAATATTTAAA
Found at i:4144979 original size:23 final size:23
Alignment explanation
Indices: 4144951--4144997 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4144941 TCATTTCTTC
4144951 TCTTTAATTATTCTTTTAAGTTA
1 TCTTTAATTATTCTTTTAAGTTA
* *
4144974 TCTTTATTTGTTCTTTTAAGTTA
1 TCTTTAATTATTCTTTTAAGTTA
4144997 T
1 T
4144998 ATTCATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (23 bp):
TCTTTAATTATTCTTTTAAGTTA
Found at i:4145614 original size:26 final size:26
Alignment explanation
Indices: 4145578--4145727 Score: 92
Period size: 26 Copynumber: 5.8 Consensus size: 26
4145568 TAATTTTAAA
4145578 GATAATTTTACCATCAAAAGTGGATG
1 GATAATTTTACCATCAAAAGTGGATG
** *
4145604 GATAATTTTACCATCAAAA-TCTAAG
1 GATAATTTTACCATCAAAAGTGGATG
* * * *
4145629 AATACTTTTACCA-CTAGAAGTAGATG
1 GATAATTTTACCATC-AAAAGTGGATG
* * * ** *
4145655 GATAATTATACCATTATAA-TCTAAG
1 GATAATTTTACCATCAAAAGTGGATG
* ***
4145680 AATAATTTTACCA-CTAGTGGTGGATG
1 GATAATTTTACCATC-AAAAGTGGATG
*
4145706 GATAATTTTACTATCAAAAGTG
1 GATAATTTTACCATCAAAAGTG
4145728 AATAGATGCC
Statistics
Matches: 87, Mismatches: 31, Indels: 12
0.67 0.24 0.09
Matches are distributed among these distances:
24 1 0.01
25 32 0.37
26 53 0.61
27 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (26 bp):
GATAATTTTACCATCAAAAGTGGATG
Found at i:4145659 original size:51 final size:51
Alignment explanation
Indices: 4145579--4145724 Score: 195
Period size: 51 Copynumber: 2.9 Consensus size: 51
4145569 AATTTTAAAG
*
4145579 ATAATTTTACCA-TCAAAAGTGGATGGATAATTTTACCATCAAAATCTAAGA
1 ATAATTTTACCACT-AGAAGTGGATGGATAATTTTACCATCAAAATCTAAGA
* * * * *
4145630 ATACTTTTACCACTAGAAGTAGATGGATAATTATACCATTATAATCTAAGA
1 ATAATTTTACCACTAGAAGTGGATGGATAATTTTACCATCAAAATCTAAGA
** *
4145681 ATAATTTTACCACTAGTGGTGGATGGATAATTTTACTATCAAAA
1 ATAATTTTACCACTAGAAGTGGATGGATAATTTTACCATCAAAA
4145725 GTGAATAGAT
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 79 0.99
52 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (51 bp):
ATAATTTTACCACTAGAAGTGGATGGATAATTTTACCATCAAAATCTAAGA
Found at i:4152224 original size:17 final size:18
Alignment explanation
Indices: 4152202--4152235 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4152192 TTCTCAAAAT
4152202 TTCTTTA-AGTTTTATTG
1 TTCTTTATAGTTTTATTG
*
4152219 TTCTTTATATTTTTATT
1 TTCTTTATAGTTTTATT
4152236 TAATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (18 bp):
TTCTTTATAGTTTTATTG
Found at i:4152857 original size:26 final size:27
Alignment explanation
Indices: 4152818--4152870 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
4152808 AGCAAACTTA
*
4152818 GAAAAAAATGTTATTACATATCATGTT
1 GAAAAAAATATTATTACATATCATGTT
*
4152845 GAAAAAAA-ATTATTACATGTCATGTT
1 GAAAAAAATATTATTACATATCATGTT
4152871 TAAAGTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 16 0.67
27 8 0.33
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.36
Consensus pattern (27 bp):
GAAAAAAATATTATTACATATCATGTT
Found at i:4152973 original size:27 final size:27
Alignment explanation
Indices: 4152942--4153004 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 27
4152932 ACCATGTTTA
4152942 AAAAATAATATTA-TCACATGTCATGTTC
1 AAAAA-AATATTACT-ACATGTCATGTTC
*
4152970 AAAAAAATATTACTACATGTCATGTTG
1 AAAAAAATATTACTACATGTCATGTTC
4152997 AAAAAAAT
1 AAAAAAAT
4153005 GTTGTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAAAAATATTACTACATGTCATGTTC
Found at i:4152977 original size:30 final size:29
Alignment explanation
Indices: 4152934--4153002 Score: 90
Period size: 27 Copynumber: 2.4 Consensus size: 29
4152924 AATTACACAC
*
4152934 CATGTTTAAAAAATAATATTA-TCACATGT
1 CATGTTCAAAAAATAATATTACT-ACATGT
4152963 CATGTTC-AAAAA-AATATTACTACATGT
1 CATGTTCAAAAAATAATATTACTACATGT
*
4152990 CATGTTGAAAAAA
1 CATGTTCAAAAAA
4153003 ATGTTGTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 19 0.53
28 11 0.31
29 6 0.17
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (29 bp):
CATGTTCAAAAAATAATATTACTACATGT
Found at i:4153325 original size:126 final size:128
Alignment explanation
Indices: 4153033--4153338 Score: 309
Period size: 125 Copynumber: 2.4 Consensus size: 128
4153023 TAAGATGTGT
* * * * * * * *
4153033 AACTCCAAAAGTTTATATCTTAGTGAAATATATAGATAGAGACCAAGTTAAACGTCACATTGAAA
1 AACTTCAAAAATTTATATCATAGTGAAATATAAAGATAAAGACTAAGTTACATGTCACATTGAAA
* * *
4153098 AAGAAGAGTTGTTACATGTTACATTGAAAAAAAAGTTATTACACGCTATATTTAAAGTGTTTA
66 AAGAAGAGTTATTACATGTTACATTGAAAAAAAAATTATTACACGCTATATTTAAAGTATTTA
* * * *
4153161 AACTTCAATAATTTATGTTATAGTGAAATATAAA-ATAAAGACTAAGTTACATGAT-ATATTGAA
1 AACTTCAAAAATTTATATCATAGTGAAATATAAAGATAAAGACTAAGTTACATG-TCACATTGAA
* * ** * *
4153224 AAA-AA-AGTTATTGCATTTTATGTTGAAAAAAGAAATTATTACATGCTATATTTAAGGTATTT-
65 AAAGAAGAGTTATTACATGTTACATTGAAAAAA-AAATTATTACACGCTATATTTAAAGTATTTA
* * * * *
4153286 AATTTTAAAAATTTATATCCTAGTGAAATACAAAGATAAAAGA-TAAATTACAT
1 AACTTCAAAAATTTATATCATAGTGAAATATAAAGAT-AAAGACTAAGTTACAT
4153339 ACCATATTTA
Statistics
Matches: 145, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
125 48 0.33
126 39 0.27
127 30 0.21
128 28 0.19
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.34
Consensus pattern (128 bp):
AACTTCAAAAATTTATATCATAGTGAAATATAAAGATAAAGACTAAGTTACATGTCACATTGAAA
AAGAAGAGTTATTACATGTTACATTGAAAAAAAAATTATTACACGCTATATTTAAAGTATTTA
Found at i:4153346 original size:126 final size:125
Alignment explanation
Indices: 4153121--4153346 Score: 278
Period size: 126 Copynumber: 1.8 Consensus size: 125
4153111 ACATGTTACA
* * * * *
4153121 TTGAAAAAAAAGTTATTACACGCTATATTTAAAGTGTTTAAACTTCAATAATTTATGTTATAGTG
1 TTGAAAAAAAAATTATTACACGCTATATTTAAAGTATTTAAACTTCAAAAATTTATATCATAGTG
* * *
4153186 AAATATAAAATAAAGACTAAGTTACATGATATATTGAAAAAAAAGTTATTGCATTTTATG
66 AAATACAAAATAAAGACTAAATTACATGACATATTGAAAAAAAAGTTATTGCATTTTATG
* * * * *
4153246 TTGAAAAAAGAAATTATTACATGCTATATTTAAGGTATTT-AATTTTAAAAATTTATATCCTAGT
1 TTGAAAAAA-AAATTATTACACGCTATATTTAAAGTATTTAAACTTCAAAAATTTATATCATAGT
4153310 GAAATACAAAGATAAAAGA-TAAATTACAT-ACCATATT
65 GAAATACAAA-AT-AAAGACTAAATTACATGA-CATATT
4153347 TAAATTATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
125 37 0.44
126 42 0.50
127 5 0.06
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (125 bp):
TTGAAAAAAAAATTATTACACGCTATATTTAAAGTATTTAAACTTCAAAAATTTATATCATAGTG
AAATACAAAATAAAGACTAAATTACATGACATATTGAAAAAAAAGTTATTGCATTTTATG
Found at i:4154962 original size:228 final size:227
Alignment explanation
Indices: 4154220--4155113 Score: 831
Period size: 228 Copynumber: 3.9 Consensus size: 227
4154210 CCTCGAACAA
* * * *
4154220 GATGCAGATCTTCGTGAAAACCTTAACCGGCAAAACCATCACCCTCGAGGTGGAGAGCTCAGACA
1 GATGCAGATCTTCGTCAAAACCTTAACCGG-AAAACCATCACTCTTGAGGTGGAGAGCTCTGACA
* * * * * * * *
4154285 CCATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGCATTCCTCCTGATCAACAGCGCTTG
65 CAATCGACAACGTCAAGGCAAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTG
* * * *
4154350 ATCTTCGCCGGCAAGCAACTT-GAAGACGGCCGAACCCTTGCGGATTACAATATCCAAAAGGAAT
130 ATCTTCGCCGGCAAGC-AGTTGGAGGACGGCCGCACCCTTGCGGATTACAATATCCAGAAGGAAT
* * * * * * * *
4154414 CGACTCTCCACCTGGTACTCCGTCTCCGTGGCGG
194 CAACCCTTCACCTTGTGCTCAGGCTCCGTGGAGG
* * * * * *
4154448 TATGCAGATCTTCGTCAAAACCCTAACCGGCAAGACCATCACTCTTGAAGTCGAAAGCTCTGACA
1 GATGCAGATCTTCGTCAAAACCTTAACCGG-AAAACCATCACTCTTGAGGTGGAGAGCTCTGACA
* * * * * * *
4154513 CGATCGACAACGTTAAGGCCAAGATCCAAGACAAGG-AGGGCATCCCTCCGGACCAACAGCGATT
65 CAATCGACAACGTCAAGGCAAAAATCCAAGACAAGGAAGGG-ATCCCTCCGGATCAACAGAGGTT
* * * * * *
4154577 GATCTTCGCTGGCAAGCAGCTCGAGGACGGCCGCACCCTGGCCGACTACAATATCCAGAAGGAAT
129 GATCTTCGCCGGCAAGCAGTTGGAGGACGGCCGCACCCTTGCGGATTACAATATCCAGAAGGAAT
* *
4154642 CAACCCTTCACCTTGTGCTCAGGCTGCGCGGAGG
194 CAACCCTTCACCTTGTGCTCAGGCTCCGTGGAGG
* * * * * * * * * *
4154676 CATGCAGATTTTCGTCAAAACCTTGACCGGGAAAACTATTACTCTGGAGGTAGAGAGTTCGGATA
1 GATGCAGATCTTCGTCAAAACCTTAACC-GGAAAACCATCACTCTTGAGGTGGAGAGCTCTGACA
* * * * *
4154741 CAATTGATAACGTCAAGGCAAAAATCCAGGATAAGGAAGGGATCCCTCCGGATCAGCAGAGGTTG
65 CAATCGACAACGTCAAGGCAAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTG
* * * * *
4154806 ATATTCGCCGGGAAGCAGTTGGAGGACGGCAGGACCCTTGCGGATTACAATATCCAGAAGGAGTC
130 ATCTTCGCCGGCAAGCAGTTGGAGGACGGCCGCACCCTTGCGGATTACAATATCCAGAAGGAATC
* * *
4154871 CACTCTTCACCTTGTGCTGAGGCTCCGTGGAGG
195 AACCCTTCACCTTGTGCTCAGGCTCCGTGGAGG
* * * * * * * *
4154904 GATGCAGATCTTCGTGAAGACGC-TGACCGGAAAGACGATTACGCTTGAGGTGGAGAGTTCTGAT
1 GATGCAGATCTTCGTCAAAAC-CTTAACCGGAAA-ACCATCACTCTTGAGGTGGAGAGCTCTGAC
* * * * * * * * * * * *
4154968 ACAATCGATAATGTGAAAGCAAAAATTCAAGATAAGGAGGGGATTCCACCTGATCAGCAGAGGCT
64 ACAATCGACAACGTCAAGGCAAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTT
* * * * * * * *
4155033 CATCTTCGCTGGGAAGCAGTTGGAGGACGGGCGCACTCTTGCAGATTACAACATCCAGAAGGAGT
129 GATCTTCGCCGGCAAGCAGTTGGAGGACGGCCGCACCCTTGCGGATTACAATATCCAGAAGGAAT
*
4155098 CTACCCTTCACCTTGT
194 CAACCCTTCACCTTGT
4155114 CCTTCGCCTT
Statistics
Matches: 551, Mismatches: 109, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
227 10 0.02
228 534 0.97
229 7 0.01
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.20
Consensus pattern (227 bp):
GATGCAGATCTTCGTCAAAACCTTAACCGGAAAACCATCACTCTTGAGGTGGAGAGCTCTGACAC
AATCGACAACGTCAAGGCAAAAATCCAAGACAAGGAAGGGATCCCTCCGGATCAACAGAGGTTGA
TCTTCGCCGGCAAGCAGTTGGAGGACGGCCGCACCCTTGCGGATTACAATATCCAGAAGGAATCA
ACCCTTCACCTTGTGCTCAGGCTCCGTGGAGG
Found at i:4156296 original size:14 final size:14
Alignment explanation
Indices: 4156274--4156430 Score: 54
Period size: 14 Copynumber: 11.1 Consensus size: 14
4156264 GTAATGTTAT
4156274 AATTAAAATAAAAA
1 AATTAAAATAAAAA
*
4156288 AATTCAAAT-AAAA
1 AATTAAAATAAAAA
* * * *
4156301 TA-TATAATATAAG
1 AATTAAAATAAAAA
*
4156314 AATCAAAAATTAAAATA
1 AAT-TAAAA-TAAAA-A
*
4156331 AAATAAAATATAAAA
1 AATTAAAATA-AAAA
* * *
4156346 AATTAAAATTTATAT
1 AATTAAAA-TAAAAA
*
4156361 AA-TATAAGTAAAAA
1 AATTA-AAATAAAAA
*
4156375 AATTAAAAT-AAGA
1 AATTAAAATAAAAA
* *
4156388 TA-TATAATATAAAA
1 AATTAAAATA-AAAA
* * *
4156402 AATTATATTAAAGA
1 AATTAAAATAAAAA
*
4156416 AATAAAAATAAAAA
1 AATTAAAATAAAAA
4156430 A
1 A
4156431 TAAAAAAATA
Statistics
Matches: 98, Mismatches: 33, Indels: 24
0.63 0.21 0.15
Matches are distributed among these distances:
12 9 0.09
13 12 0.12
14 36 0.37
15 27 0.28
16 12 0.12
17 2 0.02
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (14 bp):
AATTAAAATAAAAA
Found at i:4156364 original size:24 final size:25
Alignment explanation
Indices: 4156336--4156436 Score: 55
Period size: 27 Copynumber: 3.7 Consensus size: 25
4156326 AAATAAAATA
4156336 AAATATAAAAAATTAAAATTTATATAATA
1 AAATATAAAAAATTAAAA--TA-A-AATA
*
4156365 TAAGTA-AAAAAATTAAAATAAGATATA
1 -AAATATAAAAAATTAAAATAA-A-ATA
*
4156392 TAATATAAAAAATTATATTAA-AGAAATA
1 AAATATAAAAAATTA-A--AATA-AAATA
*
4156420 AAA-ATAAAAAATAAAAA
1 AAATATAAAAAATTAAAA
4156437 AATATATGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
24 2 0.03
26 6 0.10
27 24 0.41
28 6 0.10
29 14 0.24
30 7 0.12
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (25 bp):
AAATATAAAAAATTAAAATAAAATA
Found at i:4156374 original size:29 final size:28
Alignment explanation
Indices: 4156296--4156406 Score: 94
Period size: 27 Copynumber: 4.1 Consensus size: 28
4156286 AAAATTCAAA
4156296 TAAAA-TATATAATATAAG-AATCAAAAAT
1 TAAAATTATATAATATAAGTAA--AAAAAT
*
4156324 TAAAA-TA-A-AATA-AAATATAAAAAAT
1 TAAAATTATATAATATAAGTA-AAAAAAT
4156349 TAAAATTTATATAATATAAGTAAAAAAAT
1 TAAAA-TTATATAATATAAGTAAAAAAAT
* *
4156378 TAAAATAAGAT-ATATAA-TATAAAAAAT
1 TAAAATTATATAATATAAGTA-AAAAAAT
4156405 TA
1 TA
4156407 TATTAAAGAA
Statistics
Matches: 71, Mismatches: 4, Indels: 17
0.77 0.04 0.18
Matches are distributed among these distances:
25 13 0.18
26 7 0.10
27 19 0.27
28 12 0.17
29 16 0.23
30 4 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30
Consensus pattern (28 bp):
TAAAATTATATAATATAAGTAAAAAAAT
Found at i:4156422 original size:49 final size:48
Alignment explanation
Indices: 4156325--4156435 Score: 118
Period size: 49 Copynumber: 2.3 Consensus size: 48
4156315 ATCAAAAATT
* * * *
4156325 AAAATAAAATAAAATATAAAAAATTAAAATTTATATAATATAAGTAAA
1 AAAATAAAATAAAATATAAAAAATAAAAAATTATATAATAGAAATAAA
* * *
4156373 AAAATTAAAATAAGATATATAATATAAAAAATTATATTAA-AGAAATAAA
1 AAAA-TAAAATAAAATATAAAAAATAAAAAATTATA-TAATAGAAATAAA
4156422 AATAA-AAAATAAAA
1 AA-AATAAAATAAAA
4156436 AAATATATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
48 12 0.23
49 35 0.67
50 5 0.10
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (48 bp):
AAAATAAAATAAAATATAAAAAATAAAAAATTATATAATAGAAATAAA
Found at i:4156429 original size:54 final size:52
Alignment explanation
Indices: 4156309--4156463 Score: 138
Period size: 54 Copynumber: 2.9 Consensus size: 52
4156299 AATATATAAT
* * * * * *
4156309 ATAAGAATCAAAAATTAAAATAAA-ATAAAATATAAAAAATTAAAATTTATATA
1 ATAAAAATAAAAAATTAAAATAAATATATAATATAAAAAATT-ATA-TTAAAAA
* *
4156362 ATATAAGTAAAAAAATTAAAATAAGATATATAATATAAAAAATTATATTAAAGAA
1 ATAAAAAT-AAAAAATTAAAATAA-ATATATAATATAAAAAATTATATTAAA-AA
* *
4156417 ATAAAAATAAAAAA-TAAAA-AAATATATGATATTAAAAA-TATAATTAA
1 ATAAAAATAAAAAATTAAAATAAATATATAATATAAAAAATTAT-ATTAA
4156464 GGGATGATAT
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
50 3 0.04
51 20 0.24
52 2 0.02
53 10 0.12
54 24 0.28
55 10 0.12
56 16 0.19
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (52 bp):
ATAAAAATAAAAAATTAAAATAAATATATAATATAAAAAATTATATTAAAAA
Found at i:4156646 original size:31 final size:31
Alignment explanation
Indices: 4156597--4156657 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4156587 TATATTTTTT
* *
4156597 ACATTTTAATCATTATTTTTTTTATATATCAA
1 ACATTGTAATCATTATTTTATTTATA-ATCAA
4156629 ACATTGTAAT-ATTATTTTATTTATAATCA
1 ACATTGTAATCATTATTTTATTTATAATCA
4156658 CATTACATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 14 0.52
32 9 0.33
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (31 bp):
ACATTGTAATCATTATTTTATTTATAATCAA
Found at i:4184010 original size:1 final size:1
Alignment explanation
Indices: 4184004--4184033 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
4183994 TACCTAAACC
4184004 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4184034 GAGAAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4186717 original size:2 final size:2
Alignment explanation
Indices: 4186710--4186742 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4186700 AAATGTCCAT
*
4186710 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4186743 CCCTTGCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4187102 original size:14 final size:14
Alignment explanation
Indices: 4187061--4187094 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4187051 TTTCTCTCTA
4187061 AATTAAAA-TTATT
1 AATTAAAAGTTATT
*
4187074 AATTAAAAGTAATT
1 AATTAAAAGTTATT
4187088 AATTAAA
1 AATTAAA
4187095 TTTTATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
AATTAAAAGTTATT
Found at i:4189235 original size:27 final size:30
Alignment explanation
Indices: 4189173--4189227 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
4189163 GTTGATAGAA
4189173 ATACCTCCATTGAAAAGGTAGTTATGGGTT
1 ATACCTCCATTGAAAAGGTAGTTATGGGTT
*
4189203 ATACCTCTATT-AAAAGGTA-TTATGG
1 ATACCTCCATTGAAAAGGTAGTTATGG
4189228 TTGAACCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 6 0.25
29 8 0.33
30 10 0.42
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.35
Consensus pattern (30 bp):
ATACCTCCATTGAAAAGGTAGTTATGGGTT
Found at i:4191462 original size:2 final size:2
Alignment explanation
Indices: 4191455--4191479 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4191445 TATTCTTAAT
4191455 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4191480 TTTTATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4209191 original size:18 final size:19
Alignment explanation
Indices: 4209168--4209212 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
4209158 AATTCTTAGG
*
4209168 TTTTTTCTATTTT-TTTGT
1 TTTTTTCTATTTTCTTGGT
*
4209186 TTTTTTTTATTTTCTTGGT
1 TTTTTTCTATTTTCTTGGT
*
4209205 TTTGTTCT
1 TTTTTTCT
4209213 TAATGTTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.04, C:0.07, G:0.09, T:0.80
Consensus pattern (19 bp):
TTTTTTCTATTTTCTTGGT
Found at i:4212392 original size:33 final size:33
Alignment explanation
Indices: 4212354--4212416 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
4212344 CAAGGTTCAA
4212354 AACTCTTACAACAACCCTTAGAGTGTGCAAGGT
1 AACTCTTACAACAACCCTTAGAGTGTGCAAGGT
*
4212387 AACTCTTACAACAGCCCTTAGAGTGTGCAA
1 AACTCTTACAACAACCCTTAGAGTGTGCAA
4212417 CCTAAACCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (33 bp):
AACTCTTACAACAACCCTTAGAGTGTGCAAGGT
Found at i:4218467 original size:2 final size:2
Alignment explanation
Indices: 4218416--4218457 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4218406 ACTGAGGTTT
4218416 TA TA -A 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
4218457 T
1 T
4218458 GCTGTATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4223835 original size:19 final size:18
Alignment explanation
Indices: 4223813--4223860 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
4223803 AATCTTTATT
4223813 AATTAATTTAAATGAATCC
1 AATTAATTTAAATGAAT-C
* *
4223832 AATTCATATTAAATTAATC
1 AATTAAT-TTAAATGAATC
4223851 AATTCAATTT
1 AATT-AATTT
4223861 CATAGATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (18 bp):
AATTAATTTAAATGAATC
Found at i:4228991 original size:33 final size:33
Alignment explanation
Indices: 4228954--4229024 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
4228944 AGATCATGTT
* * * *
4228954 ATTATGCTAAATTAACATGTTACATTATCATCA
1 ATTATGATAAATCAACATGTCACATCATCATCA
** *
4228987 ATTATGATATGTCAATATGTCACATCATCATCA
1 ATTATGATAAATCAACATGTCACATCATCATCA
4229020 ATTAT
1 ATTAT
4229025 AATATGTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.39
Consensus pattern (33 bp):
ATTATGATAAATCAACATGTCACATCATCATCA
Found at i:4229043 original size:33 final size:33
Alignment explanation
Indices: 4228975--4229044 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
4228965 TTAACATGTT
* * * *
4228975 ACATTATCATCAATTATGATATGTCAATATGTC
1 ACATCATCATCAATTATAATATGTCAAGATATC
*
4229008 ACATCATCATCAATTATAATATGTTAAGATATC
1 ACATCATCATCAATTATAATATGTCAAGATATC
4229041 ACAT
1 ACAT
4229045 GATATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.40, C:0.16, G:0.07, T:0.37
Consensus pattern (33 bp):
ACATCATCATCAATTATAATATGTCAAGATATC
Found at i:4243065 original size:33 final size:31
Alignment explanation
Indices: 4243018--4243088 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
4243008 TAAATTATAT
* * *
4243018 AATATAGAAAATTATATTAAGAAATGAAAATAA
1 AATATATAAAATTATAATAAAAAAT-AAAA-AA
* *
4243051 AATATATAAGATTATAATAAAAAATTAAAAA
1 AATATATAAAATTATAATAAAAAATAAAAAA
4243082 AATATAT
1 AATATAT
4243089 GACATTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 9 0.27
32 3 0.09
33 21 0.64
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.30
Consensus pattern (31 bp):
AATATATAAAATTATAATAAAAAATAAAAAA
Found at i:4243340 original size:15 final size:15
Alignment explanation
Indices: 4243308--4243347 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4243298 CTTCTCTGTG
4243308 ATCACATTACTTACA
1 ATCACATTACTTACA
* **
4243323 ATCATATTACTTGTA
1 ATCACATTACTTACA
4243338 ATCACATTAC
1 ATCACATTAC
4243348 ATTATAACGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.38
Consensus pattern (15 bp):
ATCACATTACTTACA
Found at i:4246288 original size:20 final size:21
Alignment explanation
Indices: 4246260--4246332 Score: 86
Period size: 20 Copynumber: 3.8 Consensus size: 21
4246250 ATTGAACAAT
4246260 TTAAATATTAATA-TTTTAAG
1 TTAAATATTAATATTTTTAAG
* *
4246280 TTAACTATTAATATTTTTAAA
1 TTAAATATTAATATTTTTAAG
4246301 TT---T-TTAA-ATTTTTAAG
1 TTAAATATTAATATTTTTAAG
4246317 TTAAATATTAATATTT
1 TTAAATATTAATATTT
4246333 ATCAAAGTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.23
17 4 0.09
18 1 0.02
19 1 0.02
20 16 0.36
21 12 0.27
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (21 bp):
TTAAATATTAATATTTTTAAG
Found at i:4250899 original size:13 final size:13
Alignment explanation
Indices: 4250881--4250936 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
4250871 AACATTAAAT
4250881 ATATAATTAA-AAC
1 ATATAA-TAAGAAC
4250894 ATATAATAAGAAC
1 ATATAATAAGAAC
*
4250907 ATATCATTTAA-AA-
1 ATAT-A-ATAAGAAC
4250920 ATATAATAAGAAC
1 ATATAATAAGAAC
4250933 ATAT
1 ATAT
4250937 TAAAACATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
11 3 0.08
12 6 0.17
13 21 0.58
14 3 0.08
15 3 0.08
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (13 bp):
ATATAATAAGAAC
Found at i:4250910 original size:26 final size:26
Alignment explanation
Indices: 4250881--4250936 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
4250871 AACATTAAAT
4250881 ATAT-AATTAAAACATATAATAAGAAC
1 ATATCAATTAAAA-ATATAATAAGAAC
*
4250907 ATATCATTTAAAAATATAATAAGAAC
1 ATATCAATTAAAAATATAATAAGAAC
4250933 ATAT
1 ATAT
4250937 TAAAACATCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (26 bp):
ATATCAATTAAAAATATAATAAGAAC
Found at i:4251468 original size:18 final size:19
Alignment explanation
Indices: 4251447--4251482 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4251437 ATATGATGGG
4251447 TTATCCA-CTTTTAGTAGC
1 TTATCCATCTTTTAGTAGC
*
4251465 TTATCCATTTTTTAGTAG
1 TTATCCATCTTTTAGTAG
4251483 ATTACTGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (19 bp):
TTATCCATCTTTTAGTAGC
Found at i:4251522 original size:25 final size:26
Alignment explanation
Indices: 4251491--4251570 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
4251481 AGATTACTGC
* *
4251491 ATTTATCCACTTCTGGTGGT-AAATT
1 ATTTATCTACTTCTAGTGGTAAAATT
*
4251516 ATTTATCTACTTCTAATGGTAAAATT
1 ATTTATCTACTTCTAGTGGTAAAATT
* * *
4251542 ATCTATATACTTCTAGTGATAAAATT
1 ATTTATCTACTTCTAGTGGTAAAATT
4251568 ATT
1 ATT
4251571 CTTAGATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
25 17 0.37
26 29 0.63
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTTATCTACTTCTAGTGGTAAAATT
Found at i:4255578 original size:2 final size:2
Alignment explanation
Indices: 4255571--4255600 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4255561 ACCACCTTAA
4255571 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
4255601 CACAATAACT
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:4272815 original size:2 final size:2
Alignment explanation
Indices: 4272803--4272845 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
4272793 ATCCAAATCA
*
4272803 AT AT A- AT AT AT AT AT TT 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
4272844 AT
1 AT
4272846 CATTCTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4276597 original size:5 final size:6
Alignment explanation
Indices: 4276566--4276674 Score: 58
Period size: 6 Copynumber: 17.0 Consensus size: 6
4276556 CTTTTAAATA
* * * *
4276566 TATTTT TAATGTTA TATTTT TATTTT TATTTT TATTAT AATTTT GCATGTTT
1 TATTTT T-AT-TTT TATTTT TATTTT TATTTT TATTTT TATTTT -TAT-TTT
* * * * *
4276618 TATTTT TATTTCT TAATAT AATTTT CTATATTA TATATTT TATTTT AATTTT
1 TATTTT TATTT-T TATTTT TATTTT -TAT-TTT TAT-TTT TATTTT TATTTT
4276670 T-TTTT
1 TATTTT
4276675 CTTTTAAAAG
Statistics
Matches: 79, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
5 4 0.05
6 44 0.56
7 23 0.29
8 8 0.10
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (6 bp):
TATTTT
Found at i:4277339 original size:10 final size:10
Alignment explanation
Indices: 4277326--4277350 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
4277316 TTATATTATA
4277326 TATTTTATTT
1 TATTTTATTT
4277336 TATTTTATTT
1 TATTTTATTT
4277346 TATTT
1 TATTT
4277351 AAAAGATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTATTT
Found at i:4277351 original size:14 final size:15
Alignment explanation
Indices: 4277262--4277349 Score: 51
Period size: 13 Copynumber: 5.9 Consensus size: 15
4277252 TCATATGTTT
4277262 TATTTTCATTTCTATTA
1 TATTTT-ATTT-TATTA
* * *
4277279 TCTTATATTGT-TTA
1 TATTTTATTTTATTA
4277293 T-TTTTATTTT-TTA
1 TATTTTATTTTATTA
* *
4277306 -ATATAATTTT-TTA
1 TATTTTATTTTATTA
*
4277319 TATTATATATTTTATTT
1 TATT-T-TATTTTATTA
4277336 TATTTTATTTTATT
1 TATTTTATTTTATT
4277350 TAAAAGATAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
13 20 0.36
14 6 0.11
15 11 0.20
16 9 0.16
17 10 0.18
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (15 bp):
TATTTTATTTTATTA
Found at i:4294212 original size:79 final size:79
Alignment explanation
Indices: 4294076--4294230 Score: 258
Period size: 79 Copynumber: 2.0 Consensus size: 79
4294066 TATGATTGTA
*
4294076 AACCTGATGCCGGTGGGATGGCCGCCCTTTTTTCCCATGTATGGGTCCATCAGCCTGACAAGAAA
1 AACCTGATGCCGGTGGGATGGCCGCCCTTTTTTCCCATGTATGGGTCCATCACCCTGACAAGAAA
4294141 AGTCTTCATATATG
66 AGTCTTCATATATG
* * *
4294155 AACCTGGTGCTGGTGGGATGGCTTGCCC-TTTTTCCCATGTATGGGTCCATCACCCTGACAAGAA
1 AACCTGATGCCGGTGGGATGGC-CGCCCTTTTTTCCCATGTATGGGTCCATCACCCTGACAAGAA
4294219 AAGTCTTCATAT
65 AAGTCTTCATAT
4294231 GTGACATACT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
79 67 0.94
80 4 0.06
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (79 bp):
AACCTGATGCCGGTGGGATGGCCGCCCTTTTTTCCCATGTATGGGTCCATCACCCTGACAAGAAA
AGTCTTCATATATG
Found at i:4295480 original size:2 final size:2
Alignment explanation
Indices: 4295473--4295504 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4295463 CTGTTTCCTT
4295473 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
4295505 AAGAGAGAGA
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):
TA
Found at i:4300004 original size:11 final size:11
Alignment explanation
Indices: 4299964--4300004 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
4299954 AAAATCATGC
4299964 AAGAAAAAGAA
1 AAGAAAAAGAA
*
4299975 AAAAAAAAGAA
1 AAGAAAAAGAA
*
4299986 AAG-AAAAGAG
1 AAGAAAAAGAA
4299996 AAGAAAAAG
1 AAGAAAAAG
4300005 GTTTGTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAGAAAAAGAA
Found at i:4301735 original size:18 final size:18
Alignment explanation
Indices: 4301712--4301747 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
4301702 CATTTCAAGG
4301712 CAACTAGAATGCATTGGA
1 CAACTAGAATGCATTGGA
4301730 CAACTAGAATGCATTGGA
1 CAACTAGAATGCATTGGA
4301748 GACTCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (18 bp):
CAACTAGAATGCATTGGA
Found at i:4308566 original size:25 final size:25
Alignment explanation
Indices: 4308538--4308586 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
4308528 TATATATGCT
*
4308538 ATACCATGTCAATCAATAAA-AAAAC
1 ATACCATCTC-ATCAATAAATAAAAC
*
4308563 ATACCATCTCATTAATAAATAAAA
1 ATACCATCTCATCAATAAATAAAA
4308587 TTAAAGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.55, C:0.18, G:0.02, T:0.24
Consensus pattern (25 bp):
ATACCATCTCATCAATAAATAAAAC
Found at i:4309567 original size:28 final size:27
Alignment explanation
Indices: 4309520--4309572 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
4309510 GGTTGCTTGA
*
4309520 GAAATTTTAGATGGGAAAAAGTAAATT
1 GAAATTTTAGATGGGAAAAAATAAATT
*
4309547 GAAATGTTTA-ATTGGATAAAAATAAA
1 GAAAT-TTTAGATGGGA-AAAAATAAA
4309573 GATTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (27 bp):
GAAATTTTAGATGGGAAAAAATAAATT
Found at i:4309692 original size:17 final size:17
Alignment explanation
Indices: 4309670--4309708 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
4309660 TAAATATTGT
*
4309670 TAATTTTATTA-AAACAA
1 TAATTTT-TTAGAAAAAA
4309687 TAATTTTTTAGAAAAAA
1 TAATTTTTTAGAAAAAA
4309704 TAATT
1 TAATT
4309709 AAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TAATTTTTTAGAAAAAA
Found at i:4311315 original size:2 final size:2
Alignment explanation
Indices: 4311302--4311335 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4311292 AGGGTATAGA
*
4311302 AC AC AC AA AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4311336 CACTTCTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4316097 original size:13 final size:14
Alignment explanation
Indices: 4316067--4316098 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4316057 CTTTATCCTT
4316067 TTAATTCTTTTCCA
1 TTAATTCTTTTCCA
4316081 -TAATTCTTTT-CA
1 TTAATTCTTTTCCA
4316093 TTAATT
1 TTAATT
4316099 GGTTTCATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 15 0.88
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATTCTTTTCCA
Found at i:4319975 original size:29 final size:29
Alignment explanation
Indices: 4319933--4320017 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
4319923 AATAAAAACT
4319933 TTATTTATA-TTTGATATAATTAATTTAC
1 TTATTTATATTTTGATATAATTAATTTAC
* *
4319961 TTATTTATATTTTGATATAATTTATTTAT
1 TTATTTATATTTTGATATAATTAATTTAC
* *
4319990 TTATAATATATTTTTAT-TAATTAATTTA
1 TTAT-TTATATTTTGATATAATTAATTTA
4320018 TGAATTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
28 9 0.18
29 31 0.62
30 10 0.20
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.61
Consensus pattern (29 bp):
TTATTTATATTTTGATATAATTAATTTAC
Found at i:4325110 original size:5 final size:5
Alignment explanation
Indices: 4325100--4325129 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
4325090 GTGAACCATA
4325100 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
4325130 CCCCATTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:4332956 original size:3 final size:3
Alignment explanation
Indices: 4332948--4332988 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
4332938 ATAGGGTTGT
*
4332948 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4332989 TTGTAGTATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4333647 original size:2 final size:2
Alignment explanation
Indices: 4333640--4333667 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4333630 GAGAATCTCT
4333640 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
4333668 CATTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4337421 original size:19 final size:19
Alignment explanation
Indices: 4337397--4337437 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
4337387 AAACCAAAAA
*
4337397 AATTAAAATTCAAATCAAT
1 AATTAAAAATCAAATCAAT
*
4337416 AATTAAAAATCCAATCAAT
1 AATTAAAAATCAAATCAAT
4337435 AAT
1 AAT
4337438 ATTTTTGATC
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:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (19 bp):
AATTAAAAATCAAATCAAT
Found at i:4337628 original size:20 final size:20
Alignment explanation
Indices: 4337600--4337639 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
4337590 TAATTTAAAA
*
4337600 TAAAAATATAAAAATTTAAT
1 TAAAAATATAAAAATATAAT
*
4337620 TAAATATATAAAAATATAAT
1 TAAAAATATAAAAATATAAT
4337640 AATTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAAATATAAAAATATAAT
Found at i:4337634 original size:28 final size:26
Alignment explanation
Indices: 4337587--4337650 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 26
4337577 ATAATAATTT
*
4337587 ATTTAATTTAAAATAAAAATATAAAA
1 ATTTAATTAAAAATAAAAATATAAAA
*
4337613 ATTTAATTAAATATATAAAAATATAATA
1 ATTTAATTAAA-A-ATAAAAATATAAAA
4337641 ATTTAATTAA
1 ATTTAATTAA
4337651 CTTTTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 10 0.29
27 1 0.03
28 23 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTTAATTAAAAATAAAAATATAAAA
Found at i:4338870 original size:2 final size:2
Alignment explanation
Indices: 4338863--4338894 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4338853 ACAACCATAA
*
4338863 AT AT AT AT AT AT AT TT 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
4338895 GGATTGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4345650 original size:2 final size:2
Alignment explanation
Indices: 4345639--4345671 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4345629 GTTTCTCTTC
4345639 AT AT -T 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
4345672 GCATGCAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4346281 original size:2 final size:2
Alignment explanation
Indices: 4346274--4346319 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
4346264 CGTGATTTGC
* *
4346274 AG AG AG AG AG AT AG AG AG AA AG AG AG AG AG AG AG AG AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4346315 AG AG A
1 AG AG A
4346320 TCAATTGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.46, T:0.02
Consensus pattern (2 bp):
AG
Found at i:4348346 original size:17 final size:17
Alignment explanation
Indices: 4348322--4348378 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
4348312 CTATTGTTGG
4348322 TGTTTTCTCTTTATGTT
1 TGTTTTCTCTTTATGTT
* *
4348339 T-ATTT-TCTTTATATT
1 TGTTTTCTCTTTATGTT
4348354 TGTTTTCTCTTTATGTT
1 TGTTTTCTCTTTATGTT
4348371 TGTTTTCT
1 TGTTTTCT
4348379 TGTTTTGCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
15 10 0.29
16 6 0.18
17 18 0.53
ACGTcount: A:0.09, C:0.11, G:0.09, T:0.72
Consensus pattern (17 bp):
TGTTTTCTCTTTATGTT
Found at i:4348349 original size:15 final size:15
Alignment explanation
Indices: 4348329--4348379 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
4348319 TGGTGTTTTC
4348329 TCTTTATGTTTATTT
1 TCTTTATGTTTATTT
* *
4348344 TCTTTATATTTGTTTT
1 TCTTTATGTTT-ATTT
*
4348360 CTCTTTATGTTTGTTT
1 -TCTTTATGTTTATTT
4348376 TCTT
1 TCTT
4348380 GTTTTGCGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 14 0.47
16 6 0.20
17 10 0.33
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.73
Consensus pattern (15 bp):
TCTTTATGTTTATTT
Found at i:4351653 original size:3 final size:3
Alignment explanation
Indices: 4351645--4351677 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
4351635 GCTTATAACG
4351645 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4351678 AACAATGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:4354389 original size:30 final size:30
Alignment explanation
Indices: 4354333--4354389 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
4354323 ATGATTTTTT
**
4354333 AAAATTAAATGATCAAAACAAAAATTTTAA
1 AAAATTAAAAAATCAAAACAAAAATTTTAA
*
4354363 AAAATTAAAAAATTAAAA-AAATAATTT
1 AAAATTAAAAAATCAAAACAAA-AATTT
4354390 ACTCTAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 3 0.13
30 20 0.87
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (30 bp):
AAAATTAAAAAATCAAAACAAAAATTTTAA
Found at i:4356266 original size:13 final size:14
Alignment explanation
Indices: 4356244--4356281 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
4356234 TTGTTTCACC
*
4356244 TTTTAGTTATTT-A
1 TTTTATTTATTTAA
4356257 TTTTATTTATTTAA
1 TTTTATTTATTTAA
4356271 TTTTAATTTAT
1 TTTT-ATTTAT
4356282 GCATTAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.50
14 5 0.23
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (14 bp):
TTTTATTTATTTAA
Done.