Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 8 of 93
Found at i:4267118 original size:26 final size:27
Alignment explanation
Indices: 4267088--4267138 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
4267078 CTTAATGAAA
*
4267088 TTACACGTCATGGTT-AAAAA-AAATTG
1 TTACACATCAT-GTTGAAAAAGAAATTG
4267114 TTACACATCATGTTGAAAAAGAAAT
1 TTACACATCATGTTGAAAAAGAAAT
4267139 ATTGTTGTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 15 0.68
27 4 0.18
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (27 bp):
TTACACATCATGTTGAAAAAGAAATTG
Found at i:4267177 original size:24 final size:23
Alignment explanation
Indices: 4267145--4267194 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
4267135 AAATATTGTT
*
4267145 GTTACACGTTATA-TATAAAAACAA
1 GTTACACGTCATAGT-TAAAAA-AA
*
4267169 GTTATACGTCATAGTTAAAAAAA
1 GTTACACGTCATAGTTAAAAAAA
4267192 GTT
1 GTT
4267195 GTTACATGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 5 0.22
24 17 0.74
25 1 0.04
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.32
Consensus pattern (23 bp):
GTTACACGTCATAGTTAAAAAAA
Found at i:4267278 original size:82 final size:82
Alignment explanation
Indices: 4267088--4267279 Score: 233
Period size: 82 Copynumber: 2.3 Consensus size: 82
4267078 CTTAATGAAA
* * ** * * * * *
4267088 TTACACGTCATGGTTAAAAAAAATTGTTACACATCATGTTGAAAAAGAAATATTGTTGTTACACG
1 TTACACGTCATAGTTAAAAAAAGTTGTTACATGTTATATTGAAAAAAAAATATTATTGTTACACA
*
4267153 TTATATATAAAAACAAG
66 TCATATATAAAAACAAG
* *
4267170 TTATACGTCATAGTTAAAAAAAGTTGTTACATGTTATATTGAAAAAAAAATATTATTGTTATACA
1 TTACACGTCATAGTTAAAAAAAGTTGTTACATGTTATATTGAAAAAAAAATATTATTGTTACACA
*
4267235 TCATATATAAAAACATG
66 TCATATATAAAAACAAG
* *
4267252 TTACATGTCAT-GTTGAAAAAATGTTGTT
1 TTACACGTCATAGTT-AAAAAAAGTTGTT
4267280 GCTACACGTT
Statistics
Matches: 93, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
81 3 0.03
82 90 0.97
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.35
Consensus pattern (82 bp):
TTACACGTCATAGTTAAAAAAAGTTGTTACATGTTATATTGAAAAAAAAATATTATTGTTACACA
TCATATATAAAAACAAG
Found at i:4267300 original size:82 final size:80
Alignment explanation
Indices: 4267088--4267305 Score: 215
Period size: 82 Copynumber: 2.6 Consensus size: 80
4267078 CTTAATGAAA
* * * * * * *
4267088 TTACACGTCATGGTTAAAAAAAATTGTTACACATCATGTTGAAAAAGAAATATTGTTGTTACACG
1 TTACACGTCATAGTTAAAAAAAGTTGTTACACGTTATATTG-AAAA-AAATATTATTGTTACACA
*
4267153 TTATATATAAAAACAAG
64 TCATATATAAAAACAAG
* * *
4267170 TTATACGTCATAGTTAAAAAAAGTTGTTACATGTTATATTGAAAAAAAAATATTATTGTTATACA
1 TTACACGTCATAGTTAAAAAAAGTTGTTACACGTTATATTG--AAAAAAATATTATTGTTACACA
*
4267235 TCATATATAAAAACATG
64 TCATATATAAAAACAAG
* * *
4267252 TTACATGTCAT-GTTGAAAAAATGTTGTTGCTACACGTTATGTTG-AAAAAATATT
1 TTACACGTCATAGTT-AAAAAAAGTTG-T--TACACGTTATATTGAAAAAAATATT
4267306 GCTATTACAC
Statistics
Matches: 114, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
81 3 0.03
82 93 0.82
83 6 0.05
85 12 0.11
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (80 bp):
TTACACGTCATAGTTAAAAAAAGTTGTTACACGTTATATTGAAAAAAATATTATTGTTACACATC
ATATATAAAAACAAG
Found at i:4267314 original size:29 final size:29
Alignment explanation
Indices: 4267252--4267333 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 29
4267242 TAAAAACATG
* * * * *
4267252 TTACATGTCATGTTGAAAAAATGTTGTTG
1 TTACACGTTATGTTGAAAAAATATTGCTA
*
4267281 CTACACGTTATGTTGAAAAAATATTGCTA
1 TTACACGTTATGTTGAAAAAATATTGCTA
* * *
4267310 TTACACGCTATATT-TAAAAATATT
1 TTACACGTTATGTTGAAAAAATATT
4267334 TTGTTACAAT
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
28 9 0.21
29 34 0.79
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (29 bp):
TTACACGTTATGTTGAAAAAATATTGCTA
Found at i:4272076 original size:31 final size:31
Alignment explanation
Indices: 4272038--4272099 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4272028 AAGCATTATA
**
4272038 CCATTATTATTAATGATTATTTTAATTTGAT
1 CCATTATTATTAACAATTATTTTAATTTGAT
4272069 CCATTATTATTAACAATTATTTTAATTTGAT
1 CCATTATTATTAACAATTATTTTAATTTGAT
4272100 TATTTTTACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (31 bp):
CCATTATTATTAACAATTATTTTAATTTGAT
Found at i:4298611 original size:24 final size:23
Alignment explanation
Indices: 4298584--4298628 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
4298574 ATCTAGTTAG
4298584 ATTAGAATAACAATTCCTAATTCT
1 ATTAGAAT-ACAATTCCTAATTCT
* *
4298608 ATTAGGATACGATTCCTAATT
1 ATTAGAATACAATTCCTAATT
4298629 AAATTAGGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTAGAATACAATTCCTAATTCT
Found at i:4298623 original size:23 final size:23
Alignment explanation
Indices: 4298596--4298639 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4298586 TAGAATAACA
**
4298596 ATTCCTAATTCTATTAGGATACG
1 ATTCCTAATTAAATTAGGATACG
4298619 ATTCCTAATTAAATTAGGATA
1 ATTCCTAATTAAATTAGGATA
4298640 AGGTTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTAAATTAGGATACG
Found at i:4314288 original size:20 final size:20
Alignment explanation
Indices: 4314263--4314303 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
4314253 TTCAAATTTT
* *
4314263 TTGAATTTGTATTTTTAAAA
1 TTGAATTTGGATCTTTAAAA
4314283 TTGAATTTGGATCTTTAAAA
1 TTGAATTTGGATCTTTAAAA
4314303 T
1 T
4314304 AAATAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.51
Consensus pattern (20 bp):
TTGAATTTGGATCTTTAAAA
Found at i:4315119 original size:17 final size:16
Alignment explanation
Indices: 4315099--4315152 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
4315089 AGCTTATGAT
4315099 TTTTTTTATCGATTCTC
1 TTTTTTTAT-GATTCTC
* * *
4315116 TTTTTTTGTGCTTCTT
1 TTTTTTTATGATTCTC
4315132 TTTTTTTATTGATTCTTC
1 TTTTTTTA-TGATTC-TC
4315150 TTT
1 TTT
4315153 CAATATTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 12 0.41
17 13 0.45
18 4 0.14
ACGTcount: A:0.07, C:0.13, G:0.07, T:0.72
Consensus pattern (16 bp):
TTTTTTTATGATTCTC
Found at i:4317785 original size:57 final size:56
Alignment explanation
Indices: 4317693--4317802 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 56
4317683 CCAAACTTTG
*
4317693 ACTTTGATTGGCCAAACCAAAGATATAAAATCTCTTACTATTCTGAAAAGAGTCTC
1 ACTTTGATTGGCCAAACCAAAAATATAAAATCTCTTACTATTCTGAAAAGAGTCTC
* * * * *
4317749 ACTTTGGTTGGCTAAACTAAAAATACTAAAATCTCTTATTATTTTGAAAAGAGT
1 ACTTTGATTGGCCAAACCAAAAATA-TAAAATCTCTTACTATTCTGAAAAGAGT
4317803 ATAGAGAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 21 0.45
57 26 0.55
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (56 bp):
ACTTTGATTGGCCAAACCAAAAATATAAAATCTCTTACTATTCTGAAAAGAGTCTC
Found at i:4322072 original size:32 final size:34
Alignment explanation
Indices: 4321997--4322077 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 34
4321987 TAACTTTTAT
4321997 AATGCCTTTCAAGAATCAAGCACAACCTCTCAATAC
1 AATGCCTTTCAAGAATCAAGCACAACCTCTC-A-AC
* * *
4322033 AATGCCTTTTATGGATCAAGCACAACCT-TC-AC
1 AATGCCTTTCAAGAATCAAGCACAACCTCTCAAC
4322065 AATGCCTTCTCAA
1 AATGCCTT-TCAA
4322078 AGGTTAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 10 0.26
33 2 0.05
35 2 0.05
36 25 0.64
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.26
Consensus pattern (34 bp):
AATGCCTTTCAAGAATCAAGCACAACCTCTCAAC
Found at i:4322753 original size:21 final size:22
Alignment explanation
Indices: 4322702--4322753 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4322692 TTTAAACAAG
*
4322702 TTCAAAAATCATTAAAGCAATT
1 TTCAAAACTCATTAAAGCAATT
* *
4322724 TTCAAAACTCATTCAAGTAATT
1 TTCAAAACTCATTAAAGCAATT
4322746 TT-AAAACT
1 TTCAAAACT
4322754 TTTCACATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (22 bp):
TTCAAAACTCATTAAAGCAATT
Found at i:4322820 original size:21 final size:21
Alignment explanation
Indices: 4322796--4322861 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
4322786 TTATTTTAAA
**
4322796 AAGTTTAAAAGCTATTCAAAC
1 AAGTTTAAAAATTATTCAAAC
*
4322817 AAGTTCAAAAATTCATTCAAAC
1 AAGTTTAAAAATT-ATTCAAAC
*
4322839 AACTTTAAAAATTATTCAAAC
1 AAGTTTAAAAATTATTCAAAC
4322860 AA
1 AA
4322862 ATTCAAAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.29
Consensus pattern (21 bp):
AAGTTTAAAAATTATTCAAAC
Found at i:4322834 original size:22 final size:21
Alignment explanation
Indices: 4322808--4322868 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 21
4322798 GTTTAAAAGC
*
4322808 TATTCAAACAAGTTCAAAAAT
1 TATTCAAACAAATTCAAAAAT
* *
4322829 TCATTCAAACAACTTTAAAAAT
1 T-ATTCAAACAAATTCAAAAAT
4322851 TATTCAAACAAATTCAAA
1 TATTCAAACAAATTCAAA
4322869 GATCATTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 16 0.46
22 19 0.54
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (21 bp):
TATTCAAACAAATTCAAAAAT
Found at i:4326219 original size:25 final size:25
Alignment explanation
Indices: 4326191--4326265 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
4326181 CCCGTTTCTT
* *
4326191 TTTTTGCTTTCTCACCCAAAATCTC
1 TTTTTGCTCTCTCACCCAAGATCTC
4326216 TTTTTGCTCTCTCACCCAAGATCTC
1 TTTTTGCTCTCTCACCCAAGATCTC
*
4326241 ATTTTGCTCTCTCACCCAAGATCTC
1 TTTTTGCTCTCTCACCCAAGATCTC
4326266 CCTTTCTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.19, C:0.35, G:0.07, T:0.40
Consensus pattern (25 bp):
TTTTTGCTCTCTCACCCAAGATCTC
Found at i:4326279 original size:25 final size:25
Alignment explanation
Indices: 4326201--4326284 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
4326191 TTTTTGCTTT
* ** *
4326201 CTCACCCAAAATCTCTTTTTGCTCT
1 CTCACCCAAGATCTCACTTTGCTCA
* *
4326226 CTCACCCAAGATCTCATTTTGCTCT
1 CTCACCCAAGATCTCACTTTGCTCA
*
4326251 CTCACCCAAGATCTCCCTTT-CTTCA
1 CTCACCCAAGATCTCACTTTGC-TCA
4326276 CTCACCCAA
1 CTCACCCAA
4326285 ACCGGCGGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
24 1 0.02
25 52 0.98
ACGTcount: A:0.21, C:0.40, G:0.05, T:0.33
Consensus pattern (25 bp):
CTCACCCAAGATCTCACTTTGCTCA
Found at i:4327712 original size:17 final size:17
Alignment explanation
Indices: 4327685--4327726 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
4327675 ACAATGGCTC
4327685 CCTTTTT-TTTT-CTATT
1 CCTTTTTCTTTTGCT-TT
*
4327701 CTTTTTTCTTTTGCTTT
1 CCTTTTTCTTTTGCTTT
4327718 CCTTTTTCT
1 CCTTTTTCT
4327727 GCATTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 14 0.64
18 2 0.09
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.74
Consensus pattern (17 bp):
CCTTTTTCTTTTGCTTT
Found at i:4327760 original size:7 final size:7
Alignment explanation
Indices: 4327700--4327766 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
4327690 TTTTTTCTAT
*
4327700 TCTTTTT
1 TCTTTTC
4327707 TCTTTT-
1 TCTTTTC
* *
4327713 GCTTTCC
1 TCTTTTC
4327720 T-TTTTC
1 TCTTTTC
4327726 TGCATTTTC
1 T-C-TTTTC
*
4327735 TTTTTTC
1 TCTTTTC
4327742 T-TTTTC
1 TCTTTTC
4327748 TC-TTTC
1 TCTTTTC
4327754 TCTTTTC
1 TCTTTTC
4327761 TCTTTT
1 TCTTTT
4327767 TTCTCCATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
6 21 0.43
7 22 0.45
9 6 0.12
ACGTcount: A:0.01, C:0.22, G:0.03, T:0.73
Consensus pattern (7 bp):
TCTTTTC
Found at i:4328358 original size:7 final size:6
Alignment explanation
Indices: 4328293--4328358 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
4328283 TTTTTCCCCC
* *
4328293 TCTTTT T-TTTT TCTTTT TC--TT TCTTTT TCCCTTTT TC-CTC TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT T--CTTTT TCTTTT TCTTTT
*
4328339 TTTTTT TCTTTT TCTATTT T
1 TCTTTT TCTTTT TCT-TTT T
4328359 TCGTACTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.09
5 8 0.17
6 25 0.53
7 4 0.09
8 6 0.13
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:4336015 original size:69 final size:69
Alignment explanation
Indices: 4335892--4336030 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 69
4335882 ATAGATTTAT
* * * *
4335892 TGTATTTCAGTAATAAAGAAATTTTTTCAAAGTATGAACTTTACGATTTCTTAAATATAATATTA
1 TGTATTTCAGTAATAAAGAAATTTTTCCAAAGCATGAACTTTACGATTTCTTAAACATAAAATTA
4335957 ACAA
66 ACAA
* *
4335961 TGTACTTT-AGTAATAAAGAAATTTTTCCAAAGCATGAACTTTATGATTTTTTAAACATAAAATT
1 TGTA-TTTCAGTAATAAAGAAATTTTTCCAAAGCATGAACTTTACGATTTCTTAAACATAAAATT
4336025 AACAA
65 AACAA
4336030 T
1 T
4336031 AATAAATATG
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 60 0.95
70 3 0.05
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (69 bp):
TGTATTTCAGTAATAAAGAAATTTTTCCAAAGCATGAACTTTACGATTTCTTAAACATAAAATTA
ACAA
Found at i:4344026 original size:21 final size:21
Alignment explanation
Indices: 4344000--4344078 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
4343990 GTTTTGTGGT
*
4344000 TTTTGGGTATTACGTGACTGA
1 TTTTGGGTATTACGTAACTGA
* *
4344021 TTTTGGATATTGCGTAACTGA
1 TTTTGGGTATTACGTAACTGA
* * *
4344042 CTTTGGGTATTGCGTAACTAGT
1 TTTTGGGTATTACGTAACT-GA
**
4344064 TTTTAAGTATTACGT
1 TTTTGGGTATTACGT
4344079 GACTAGTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 35 0.74
22 12 0.26
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (21 bp):
TTTTGGGTATTACGTAACTGA
Found at i:4344110 original size:23 final size:22
Alignment explanation
Indices: 4344050--4344123 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
4344040 GACTTTGGGT
* *
4344050 ATTGCGTAACTAGTT-TTTAAGT
1 ATTGCGTAACTAGTTGATTAA-C
* *
4344072 ATTACGTGACTAGTTGATATAAC
1 ATTGCGTAACTAGTTGAT-TAAC
*
4344095 ATTGCGTAACTAGTTGATTGAC
1 ATTGCGTAACTAGTTGATTAAC
4344117 ATTGCGT
1 ATTGCGT
4344124 GACTTGTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 23 0.53
23 17 0.40
24 3 0.07
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.39
Consensus pattern (22 bp):
ATTGCGTAACTAGTTGATTAAC
Found at i:4344147 original size:23 final size:23
Alignment explanation
Indices: 4344116--4344174 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
4344106 AGTTGATTGA
*
4344116 CATTGCGTGACTTGTTAGTAAAG
1 CATTGCGTGACTTGTTAATAAAG
* * *
4344139 CATTACGTGACTAGTTAATAAGG
1 CATTGCGTGACTTGTTAATAAAG
*
4344162 CATTGTGTGACTT
1 CATTGCGTGACTT
4344175 AGGTATTACT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.36
Consensus pattern (23 bp):
CATTGCGTGACTTGTTAATAAAG
Found at i:4352667 original size:9 final size:9
Alignment explanation
Indices: 4352653--4352753 Score: 95
Period size: 9 Copynumber: 11.4 Consensus size: 9
4352643 CCATCCCGAT
*
4352653 TTTTTTTTA
1 TTTTATTTA
*
4352662 TTTTTTTTA
1 TTTTATTTA
*
4352671 TTTTTTTTA
1 TTTTATTTA
4352680 TTTTATTT-
1 TTTTATTTA
4352688 TTTTATTTA
1 TTTTATTTA
*
4352697 TTTAATTTA
1 TTTTATTTA
4352706 -TTTATTATTA
1 TTTTA-T-TTA
4352716 TTTTATTTA
1 TTTTATTTA
*
4352725 TTTAATTTA
1 TTTTATTTA
4352734 -TTTA-TTA
1 TTTTATTTA
4352741 TTATTA-TTA
1 TT-TTATTTA
4352750 TTTT
1 TTTT
4352754 TAATTTATGT
Statistics
Matches: 81, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
7 3 0.04
8 17 0.21
9 53 0.65
10 4 0.05
11 4 0.05
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:4352696 original size:4 final size:4
Alignment explanation
Indices: 4352676--4352739 Score: 69
Period size: 4 Copynumber: 15.5 Consensus size: 4
4352666 TTTTATTTTT
*
4352676 TTTA TTTTA TTTT TTTA TTTA TTTAA TTTA TTTA -TTA -TTA TTTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA -TTTA TTTA
4352725 TTTAA TTTA TTTA TT
1 TTT-A TTTA TTTA TT
4352740 ATTATTATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
3 6 0.11
4 32 0.60
5 15 0.28
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:4352714 original size:28 final size:28
Alignment explanation
Indices: 4352654--4352761 Score: 121
Period size: 28 Copynumber: 3.8 Consensus size: 28
4352644 CATCCCGATT
* * *
4352654 TTTTTTTATTTTTTTTATTTTTTTTATTTTA
1 TTTTTTTA-TTTATTTAATTTATTTA--TTA
4352685 TTTTTTTATTTATTTAATTTATTTATTA
1 TTTTTTTATTTATTTAATTTATTTATTA
*
4352713 TTATTTTATTTATTTAATTTATTTATTA
1 TTTTTTTATTTATTTAATTTATTTATTA
*
4352741 TTATTATTA-TT-TTTAATTTAT
1 TT-TTTTTATTTATTTAATTTAT
4352762 GTGTCTACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
27 10 0.14
28 34 0.49
29 4 0.06
30 14 0.20
31 8 0.11
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTTTTTATTTATTTAATTTATTTATTA
Found at i:4364089 original size:2 final size:2
Alignment explanation
Indices: 4364082--4364113 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4364072 AGATGCATAC
4364082 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4364114 TGATGTTCCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:4366889 original size:25 final size:24
Alignment explanation
Indices: 4366861--4366915 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
4366851 CCCCTTGCCC
**
4366861 TCTCTCCCTTCTTTCTCTATTCCCT
1 TCTCTCCCTTCGCTCTCT-TTCCCT
*
4366886 TCTCTTCCTTCGCTCTCTTTCCCT
1 TCTCTCCCTTCGCTCTCTTTCCCT
*
4366910 TTTCTC
1 TCTCTC
4366916 TTTACTTTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.02, C:0.44, G:0.02, T:0.53
Consensus pattern (24 bp):
TCTCTCCCTTCGCTCTCTTTCCCT
Found at i:4367539 original size:13 final size:13
Alignment explanation
Indices: 4367521--4367553 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
4367511 TTATCCCATG
4367521 TCTCTTT-ACTTCT
1 TCTCTTTCA-TTCT
4367534 TCTCTTTCATTCT
1 TCTCTTTCATTCT
4367547 TCTCTTT
1 TCTCTTT
4367554 GTTTTTGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 18 0.95
14 1 0.05
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (13 bp):
TCTCTTTCATTCT
Found at i:4369768 original size:7 final size:7
Alignment explanation
Indices: 4369721--4369887 Score: 60
Period size: 7 Copynumber: 23.4 Consensus size: 7
4369711 TATAATTAAA
4369721 ATAAAAT
1 ATAAAAT
*
4369728 ATATAAT
1 ATAAAAT
4369735 ATAAGAAT
1 ATAA-AAT
4369743 -TAGAAAT
1 ATA-AAAT
*
4369750 GAAAATAAT
1 -ATAA-AAT
4369759 ATAAAAT
1 ATAAAAT
*
4369766 ATAAAAC
1 ATAAAAT
4369773 ATTAAAATTT
1 A-TAAAA--T
*
4369783 ATATAAT
1 ATAAAAT
*
4369790 AT-AGAT
1 ATAAAAT
*
4369796 A-AAAGAA
1 ATAAA-AT
*
4369803 ATTAAA-
1 ATAAAAT
4369809 ATAAAAT
1 ATAAAAT
4369816 ATAAAAT
1 ATAAAAT
*
4369823 ATAAAAA
1 ATAAAAT
* *
4369830 ATTATATT
1 A-TAAAAT
*
4369838 AAAAAAT
1 ATAAAAT
*
4369845 ATATAAT
1 ATAAAAT
*
4369852 ATATAAT
1 ATAAAAT
**
4369859 ATTGTAAT
1 A-TAAAAT
4369867 A-AAAA-
1 ATAAAAT
4369872 ATAAAA-
1 ATAAAAT
4369878 ATAAAAT
1 ATAAAAT
4369885 ATA
1 ATA
4369888 TTTAAGAGAT
Statistics
Matches: 119, Mismatches: 25, Indels: 32
0.68 0.14 0.18
Matches are distributed among these distances:
5 1 0.01
6 21 0.18
7 63 0.53
8 25 0.21
9 8 0.07
10 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.31
Consensus pattern (7 bp):
ATAAAAT
Found at i:4369787 original size:50 final size:49
Alignment explanation
Indices: 4369733--4369841 Score: 112
Period size: 50 Copynumber: 2.2 Consensus size: 49
4369723 AAAATATATA
* * * *
4369733 ATATAAGAATTAG-AAATGAAAATAATATAAAATATAAAACATTAAAATTT
1 ATATAA-AA-TAGAAAAAGAAAATAAAATAAAATATAAAACATAAAAAATT
* * *
4369783 ATATAATATAGATAAAAGAAATTAAAATAAAATATAAAATATAAAAAATT
1 ATATAAAATAGA-AAAAGAAAATAAAATAAAATATAAAACATAAAAAATT
4369833 ATATTAAAA
1 ATA-TAAAA
4369842 AATATATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
48 3 0.06
49 1 0.02
50 40 0.83
51 4 0.08
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (49 bp):
ATATAAAATAGAAAAAGAAAATAAAATAAAATATAAAACATAAAAAATT
Found at i:4369792 original size:55 final size:56
Alignment explanation
Indices: 4369727--4369833 Score: 146
Period size: 55 Copynumber: 1.9 Consensus size: 56
4369717 TAAAATAAAA
** *
4369727 TATATAATATAAGA-ATTAGAAATGAAAAT-AATATAAAATATAAAACATTAAAATT
1 TATATAATAT-AGATAAAAGAAATGAAAATAAATATAAAATATAAAAAATTAAAATT
*
4369782 TATATAATATAGATAAAAGAAATTAAAATAAAATATAAAATATAAAAAATTA
1 TATATAATATAGATAAAAGAAATGAAAAT-AAATATAAAATATAAAAAATTA
4369834 TATTAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
54 3 0.07
55 22 0.49
57 20 0.44
ACGTcount: A:0.64, C:0.01, G:0.05, T:0.30
Consensus pattern (56 bp):
TATATAATATAGATAAAAGAAATGAAAATAAATATAAAATATAAAAAATTAAAATT
Found at i:4369843 original size:29 final size:29
Alignment explanation
Indices: 4369723--4369880 Score: 94
Period size: 29 Copynumber: 5.4 Consensus size: 29
4369713 TAATTAAAAT
* * *
4369723 AAAATATATAATAT-AAGAATTAGAAATGAA
1 AAAATATAAAATATAAAAAATTA-TAAT-AA
* * *
4369753 AATAATATAAAATATAAAACATTAAAATTTAT
1 AA-AATATAAAATATAAAAAATTATAA--TAA
* * *
4369785 ATAATAT-AGATA-AAAGAAATTA-AA-AT
1 AAAATATAAAATATAAA-AAATTATAATAA
*
4369811 AAAATATAAAATATAAAAAATTATATTAA
1 AAAATATAAAATATAAAAAATTATAATAA
* * * *
4369840 AAAATATATAATATATAATATTGTAATAA
1 AAAATATAAAATATAAAAAATTATAATAA
4369869 AAAATA-AAAATA
1 AAAATATAAAATA
4369881 AAATATATTT
Statistics
Matches: 102, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
26 8 0.08
27 10 0.10
28 9 0.09
29 36 0.35
30 11 0.11
31 19 0.19
32 8 0.08
33 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
AAAATATAAAATATAAAAAATTATAATAA
Found at i:4369846 original size:55 final size:55
Alignment explanation
Indices: 4369744--4369847 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
4369734 TATAAGAATT
* * *
4369744 AGAAATGAAAATAATATAAAATATAAAACATTAAAATTTATATAATATAGATAAA
1 AGAAATGAAAATAATATAAAATATAAAAAATTAAAATTTAAAAAATATAGATAAA
* *
4369799 AGAAATTAAAATAAAATATAAAATATAAAAAATT-ATA-TTAAAAAATATA
1 AGAAATGAAAAT--AATATAAAATATAAAAAATTAAAATTTAAAAAATATA
4369848 TAATATATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
55 21 0.50
56 2 0.05
57 19 0.45
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (55 bp):
AGAAATGAAAATAATATAAAATATAAAAAATTAAAATTTAAAAAATATAGATAAA
Found at i:4369883 original size:42 final size:41
Alignment explanation
Indices: 4369821--4369928 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
4369811 AAAATATAAA
* * * *
4369821 ATATAAAAAATTATATTAAAAAATATATAATATATAATATT
1 ATATAAAAAATAATAATAAAAAATATATAAGAGATAATATT
* * * * *
4369862 GTAATAAAAAATAAAAATAAAATATATTTAAGAGATGATATT
1 AT-ATAAAAAATAATAATAAAAAATATATAAGAGATAATATT
*
4369904 ATATAAAAATTAATAATAAAAAATA
1 ATATAAAAAATAATAATAAAAAATA
4369929 CAAGTATGTT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 21 0.40
42 32 0.60
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (41 bp):
ATATAAAAAATAATAATAAAAAATATATAAGAGATAATATT
Found at i:4369973 original size:100 final size:99
Alignment explanation
Indices: 4369867--4370066 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 99
4369857 ATATTGTAAT
4369867 AAAAAATAAAAATAAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATACAA
1 AAAAAATAAAAATAAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATACAA
4369932 GTATGTTAAACTTGTATTTTAATAAATATGAGTA
66 GTATGTTAAACTTGTATTTTAATAAATATGAGTA
4369966 ANAAAAATAAAAATAAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATACA
1 A-AAAAATAAAAATAAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATACA
4370031 AGTATGTTAAACTTGTATTTTAATAAATATGAGTA
65 AGTATGTTAAACTTGTATTTTAATAAATATGAGTA
4370066 A
1 A
4370067 TTTTGAAAAT
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 1 0.01
100 99 0.99
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.33
Consensus pattern (99 bp):
AAAAAATAAAAATAAAATATATTTAAGAGATGATATTATATAAAAATTAATAATAAAAAATACAA
GTATGTTAAACTTGTATTTTAATAAATATGAGTA
Found at i:4370208 original size:15 final size:15
Alignment explanation
Indices: 4370190--4370244 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
4370180 ATTTTTCTTG
* *
4370190 TAATTATATTGCTTA
1 TAATCATATTACTTA
** *
4370205 TAATCACGTTATTTA
1 TAATCATATTACTTA
*
4370220 TAATTATATTACTTA
1 TAATCATATTACTTA
4370235 TAATCATATT
1 TAATCATATT
4370245 GTATTGTAAA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (15 bp):
TAATCATATTACTTA
Found at i:4370856 original size:15 final size:16
Alignment explanation
Indices: 4370826--4370858 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4370816 CCCAAAAAAT
*
4370826 AATATTTATAATTTTA
1 AATATATATAATTTTA
4370842 AATATATAT-ATTTTA
1 AATATATATAATTTTA
4370857 AA
1 AA
4370859 ACATTATAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATATATAATTTTA
Found at i:4371172 original size:24 final size:24
Alignment explanation
Indices: 4371086--4371164 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 24
4371076 ACATACCATA
*
4371086 TACAAAAACATGTTACACGTTATG
1 TACAAAAACATGTTACACGTCATG
* *
4371110 TTGAAAAAAAATACTATTGTTACATGTCATG
1 -T---ACAAAA-AC-A-TGTTACACGTCATG
4371141 TACAAAAACATGTTACACGTCATG
1 TACAAAAACATGTTACACGTCATG
4371165 GTTAAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
24 13 0.30
25 2 0.05
26 2 0.05
27 5 0.12
28 5 0.12
29 2 0.05
30 2 0.05
31 12 0.28
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (24 bp):
TACAAAAACATGTTACACGTCATG
Found at i:4371172 original size:55 final size:55
Alignment explanation
Indices: 4371043--4371174 Score: 185
Period size: 55 Copynumber: 2.4 Consensus size: 55
4371033 TGTTTAGGTT
* *
4371043 TTACACGTCATATTGAAAAAAAATACTGTTATTACATACCATATACAAAAACATG
1 TTACACGTCATGTTGAAAAAAAATACTATTATTACATACCATATACAAAAACATG
* * ** *
4371098 TTACACGTTATGTTGAAAAAAAATACTATTGTTACATGTCATGTACAAAAACATG
1 TTACACGTCATGTTGAAAAAAAATACTATTATTACATACCATATACAAAAACATG
4371153 TTACACGTCATGGTT-AAAAAAA
1 TTACACGTCAT-GTTGAAAAAAA
4371175 GTTATTACAC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 65 0.96
56 3 0.04
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (55 bp):
TTACACGTCATGTTGAAAAAAAATACTATTATTACATACCATATACAAAAACATG
Found at i:4371243 original size:29 final size:29
Alignment explanation
Indices: 4371175--4371272 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
4371165 GTTAAAAAAA
*
4371175 GTTATTACACGCTATGTTGAAAAAAAATAATT
1 GTTATTACACGCCATGTTG--AAAAAAT-ATT
* * *
4371207 ATTGTTACAGGCCATGTTGAAAAAATATT
1 GTTATTACACGCCATGTTGAAAAAATATT
* * *
4371236 GTTATTACACGCCATATT-CAAAAACATT
1 GTTATTACACGCCATGTTGAAAAAATATT
4371264 -TTATTACAC
1 GTTATTACAC
4371273 TTTAATACCT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 9 0.16
28 8 0.14
29 17 0.30
30 7 0.12
32 15 0.27
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (29 bp):
GTTATTACACGCCATGTTGAAAAAATATT
Found at i:4385999 original size:3 final size:3
Alignment explanation
Indices: 4385983--4386063 Score: 58
Period size: 3 Copynumber: 25.0 Consensus size: 3
4385973 ATTTGTTCCA
*
4385983 ATT A-T ATT ATTT ATT ATTT ATTT ATT TTT CACTT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT A-TT A-TT ATT ATT -A-TT ATT ATT ATT ATT
*
4386029 ACT ATTT ATT ATTT ATT ATT -TT ATTT ATT ATT ATT
1 ATT A-TT ATT A-TT ATT ATT ATT A-TT ATT ATT ATT
4386064 TTTTAAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
2 4 0.06
3 40 0.62
4 19 0.29
5 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:4385999 original size:7 final size:7
Alignment explanation
Indices: 4385987--4386060 Score: 77
Period size: 7 Copynumber: 11.0 Consensus size: 7
4385977 GTTCCAATTA
4385987 TATTATT
1 TATTATT
4385994 TATTATT
1 TATTATT
4386001 TATTTATT
1 TA-TTATT
*
4386009 T-TTCACT
1 TATT-ATT
4386016 TATTA-T
1 TATTATT
4386022 TATTA-T
1 TATTATT
*
4386028 TACTATT
1 TATTATT
4386035 TATTATT
1 TATTATT
4386042 TATTA-T
1 TATTATT
4386048 T-TTATT
1 TATTATT
4386054 TATTATT
1 TATTATT
4386061 ATTTTTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
5 3 0.05
6 17 0.29
7 30 0.52
8 8 0.14
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (7 bp):
TATTATT
Found at i:4386037 original size:19 final size:18
Alignment explanation
Indices: 4386015--4386063 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
4386005 TATTTTTCAC
4386015 TTATTATTATTATTACTAT
1 TTATTATTATTATT-CTAT
*
4386034 TTATTATTTATTATTTTAT
1 TTATTA-TTATTATTCTAT
4386053 TTATTATTATT
1 TTATTATTATT
4386064 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.18
19 15 0.54
20 8 0.29
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTATTATTATTCTAT
Found at i:4389568 original size:3 final size:3
Alignment explanation
Indices: 4389560--4389584 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4389550 TCACAAATTA
4389560 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
4389585 ATTTGCAAAA
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:4390354 original size:25 final size:25
Alignment explanation
Indices: 4390326--4390375 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
4390316 TATTTTATTT
*
4390326 TTAAATATTAATAATTTATGATTAA
1 TTAAATATTAATAATTTATAATTAA
4390351 TTAAATATTAATAATTTATAATTAA
1 TTAAATATTAATAATTTATAATTAA
4390376 AATTTTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TTAAATATTAATAATTTATAATTAA
Found at i:4391555 original size:16 final size:16
Alignment explanation
Indices: 4391530--4391560 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4391520 ATTTATACTC
4391530 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
4391546 ATTAATAATTTAATA
1 ATTAAAAATTTAATA
4391561 AATAAAACAT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:4391613 original size:9 final size:8
Alignment explanation
Indices: 4391586--4391618 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
4391576 CCCTAAAATA
4391586 TTAATATT
1 TTAATATT
4391594 TTAATATT
1 TTAATATT
4391602 TTAATCATT
1 TTAAT-ATT
4391611 TTAATATT
1 TTAATATT
4391619 AATAATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TTAATATT
Found at i:4391613 original size:17 final size:16
Alignment explanation
Indices: 4391586--4391618 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
4391576 CCCTAAAATA
4391586 TTAATATTTTAATATT
1 TTAATATTTTAATATT
4391602 TTAATCATTTTAATATT
1 TTAAT-ATTTTAATATT
4391619 AATAATGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTAATATTTTAATATT
Found at i:4394607 original size:16 final size:15
Alignment explanation
Indices: 4394549--4394608 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
4394539 TTGATTCAAA
4394549 AATATTTAAAATATT
1 AATATTTAAAATATT
* *
4394564 -A-A-TT-AATTTTT
1 AATATTTAAAATATT
*
4394575 AAAATTTAAAATATT
1 AATATTTAAAATATT
4394590 AATATTTAAAACTATT
1 AATATTTAAAA-TATT
4394606 AAT
1 AAT
4394609 GTTCTATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
11 5 0.14
12 3 0.09
13 2 0.06
14 3 0.09
15 15 0.43
16 7 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTAAAATATT
Found at i:4394985 original size:17 final size:17
Alignment explanation
Indices: 4394974--4395032 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 17
4394964 TTTATAATTT
4394974 AAATATTATTATAAATA
1 AAATATTATTATAAATA
4394991 AAATATTA--A-AATATA
1 AAATATTATTATAA-ATA
* *
4395006 AAATTTTATTTTAAATTTA
1 AAATATTATTATAAA--TA
4395025 AAATATTA
1 AAATATTA
4395033 ATTTTGTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
17 9 0.27
18 2 0.06
19 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATATTATTATAAATA
Found at i:4394993 original size:42 final size:43
Alignment explanation
Indices: 4394911--4394997 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 43
4394901 TTATTTTTAT
**
4394911 TTTTATTTTCATTTAATAATTTAAACATTAATATTTTAAAATA
1 TTTTATTTTCATTTAATAATTTAAACATTAATATAATAAAATA
* *
4394954 TTTTATTTT-ATTT-ATAATTTAAATATTATTATAAATAAAATA
1 TTTTATTTTCATTTAATAATTTAAACATTAATAT-AATAAAATA
4394996 TT
1 TT
4394998 AAAATATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 17 0.44
42 13 0.33
43 9 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (43 bp):
TTTTATTTTCATTTAATAATTTAAACATTAATATAATAAAATA
Found at i:4395796 original size:139 final size:139
Alignment explanation
Indices: 4395546--4395818 Score: 370
Period size: 139 Copynumber: 2.0 Consensus size: 139
4395536 TTTGAGAACA
* * *
4395546 ATGTGATTTAGGCTCGAAAAGTTGCTAGGTCAGTACTTGGACTTGGGTCATTATATATGGTTTCA
1 ATGTGATTTAGGCTCGAAAAGTTACTAGGCCAGTACTTGGACTTGGGTCATTATAAATGGTTTCA
* *
4395611 GAACTTACGCCAATCCGATGTGAGCTTCCACATTGCTCTAGCGAGATCTTAG-TCCTATGGATGC
66 GAACTTACGCCAATCCGATATCAGCTTCCACATTGCTCTAGCGAGAT-TTAGATCCTATGGATGC
*
4395675 TTTAGATGCC
130 CTTAGATGCC
* * *
4395685 ATGTGATTTAGGCTCGAAAATTTACTAGGCCGGTGCTTGGACTTGGGTCATTATAAATGGTTTCA
1 ATGTGATTTAGGCTCGAAAAGTTACTAGGCCAGTACTTGGACTTGGGTCATTATAAATGGTTTCA
** * * * * *
4395750 GAGTTTACGCCAGTCCGATATCAGCTAT-CACATTGCTTTGGCGAGATTTTGATCCTGTGGATGC
66 GAACTTACGCCAATCCGATATCAGCT-TCCACATTGCTCTAGCGAGATTTAGATCCTATGGATGC
4395814 CTTAG
130 CTTAG
4395819 GCCCGTCGCA
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
138 3 0.03
139 112 0.97
140 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (139 bp):
ATGTGATTTAGGCTCGAAAAGTTACTAGGCCAGTACTTGGACTTGGGTCATTATAAATGGTTTCA
GAACTTACGCCAATCCGATATCAGCTTCCACATTGCTCTAGCGAGATTTAGATCCTATGGATGCC
TTAGATGCC
Found at i:4401102 original size:45 final size:44
Alignment explanation
Indices: 4400960--4401107 Score: 170
Period size: 45 Copynumber: 3.3 Consensus size: 44
4400950 TTTTTTCAAT
* * * *
4400960 ATGGCATGTAACAACCTAACCATAGTGTGTCACATGTTTTTGTAC
1 ATGGCGTGTAACAACCTAACCATGGCGTGTCACAT-TTTTTATAC
** * * *
4401005 ATGGCGTAAAATAACCTAGCCATGACGTGTCACATTGTTTTATAC
1 ATGGCGTGTAACAACCTAACCATGGCGTGTCACATT-TTTTATAC
*
4401050 ATGGCGTGTAACAACCTAACTATGGCGTGTCACATATTTTTATAC
1 ATGGCGTGTAACAACCTAACCATGGCGTGTCACAT-TTTTTATAC
*
4401095 ATAGCGTGTAACA
1 ATGGCGTGTAACA
4401108 TGTTTTTGTA
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
44 1 0.01
45 83 0.98
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (44 bp):
ATGGCGTGTAACAACCTAACCATGGCGTGTCACATTTTTTATAC
Found at i:4401148 original size:45 final size:45
Alignment explanation
Indices: 4401094--4401221 Score: 159
Period size: 45 Copynumber: 2.8 Consensus size: 45
4401084 TATTTTTATA
* * *
4401094 CATAGCGTGTAACATGTTTTTGTACATAACGTGTAACAA-CTTAAC
1 CATAACGTGTAACATGTTTTTGTATATGACGTGTAACAATC-TAAC
* *
4401139 TATAACGTGTCACATGTTTTTGTATATGACGTGTAACAATCTAAC
1 CATAACGTGTAACATGTTTTTGTATATGACGTGTAACAATCTAAC
* * * *
4401184 CATGACATGTAACATATTTTTATATATGACGTGTAACA
1 CATAACGTGTAACATGTTTTTGTATATGACGTGTAACA
4401222 TCATAACGTA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 70 0.99
46 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (45 bp):
CATAACGTGTAACATGTTTTTGTATATGACGTGTAACAATCTAAC
Found at i:4401218 original size:24 final size:24
Alignment explanation
Indices: 4401070--4401222 Score: 81
Period size: 24 Copynumber: 6.6 Consensus size: 24
4401060 ACAACCTAAC
* *
4401070 TATGGCGTGTCACATATTTTTATA
1 TATGACGTGTAACATATTTTTATA
* * *
4401094 CAT-AGCGTGTAACATGTTTTTGTA
1 TATGA-CGTGTAACATATTTTTATA
* * *
4401118 CATAACGTGTAACA-A--CTTA-A
1 TATGACGTGTAACATATTTTTATA
* * * *
4401138 CTATAACGTGTCACATGTTTTTGTA
1 -TATGACGTGTAACATATTTTTATA
*
4401163 TATGACGTGTAACA-A--TCTA-A
1 TATGACGTGTAACATATTTTTATA
* *
4401183 CCATGACATGTAACATATTTTTATA
1 -TATGACGTGTAACATATTTTTATA
4401208 TATGACGTGTAACAT
1 TATGACGTGTAACAT
4401223 CATAACGTAT
Statistics
Matches: 94, Mismatches: 23, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
20 2 0.02
21 28 0.30
22 1 0.01
24 60 0.64
25 3 0.03
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (24 bp):
TATGACGTGTAACATATTTTTATA
Found at i:4403307 original size:51 final size:51
Alignment explanation
Indices: 4403228--4403332 Score: 194
Period size: 51 Copynumber: 2.1 Consensus size: 51
4403218 GTCCTCAAAG
4403228 ATAACAATTGAAAAGACAACTTGATCAGGTGAATAATCACCGTTGGAAGTT
1 ATAACAATTGAAAAGACAACTTGATCAGGTGAATAATCACCGTTGGAAGTT
4403279 ATAACAATTGAAAAGACAACTT-AGTCAGGTGAATAATCACCGTTGGAAGTT
1 ATAACAATTGAAAAGACAACTTGA-TCAGGTGAATAATCACCGTTGGAAGTT
4403330 ATA
1 ATA
4403333 TATCTTTTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (51 bp):
ATAACAATTGAAAAGACAACTTGATCAGGTGAATAATCACCGTTGGAAGTT
Found at i:4406864 original size:29 final size:29
Alignment explanation
Indices: 4406832--4406919 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
4406822 CATGAAAAGA
*
4406832 TACAAGAGAAGAAACTGTATGTGAATAGG
1 TACAAAAGAAGAAACTGTATGTGAATAGG
** ***
4406861 TACAAAAGAAGAAGTTGTGCATGAATAGG
1 TACAAAAGAAGAAACTGTATGTGAATAGG
** *
4406890 TACAAAAGAAGAATGTGTATGTGAACAGG
1 TACAAAAGAAGAAACTGTATGTGAATAGG
4406919 T
1 T
4406920 GTACGAGAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (29 bp):
TACAAAAGAAGAAACTGTATGTGAATAGG
Found at i:4407170 original size:35 final size:33
Alignment explanation
Indices: 4407131--4407245 Score: 104
Period size: 35 Copynumber: 3.3 Consensus size: 33
4407121 TTGTTTCAAA
4407131 TGAAGTAGTGTTATACTTATTCTAATTGTTCTGCG
1 TGAAGTAGTGTT-TACTTATTCTAATTGTT-TGCG
* * *
4407166 TGAAGTAGTATTTCACTTGTTCTAATTGTTTTGCA
1 TGAAGTAGTGTTT-ACTTATTCTAATTG-TTTGCG
* * * * *
4407201 TGAAATAGTGCTTTACCTATTTTAGTTGTTTGGTG
1 TGAAGTAGTG-TTTACTTATTCTAATTGTTT-GCG
4407236 TGAAGTAGTG
1 TGAAGTAGTG
4407246 CTTCAATTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
34 4 0.06
35 55 0.86
36 5 0.08
ACGTcount: A:0.23, C:0.10, G:0.22, T:0.46
Consensus pattern (33 bp):
TGAAGTAGTGTTTACTTATTCTAATTGTTTGCG
Found at i:4407581 original size:24 final size:24
Alignment explanation
Indices: 4407545--4407601 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
4407535 TAGATTATTG
4407545 CACGTCATATATAAAAACATGTTA
1 CACGTCATATATAAAAACATGTTA
* * *
4407569 CACGTTATGTATAAAAATATGTTA
1 CACGTCATATATAAAAACATGTTA
*
4407593 CACGCCATA
1 CACGTCATA
4407602 GTTAGGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.30
Consensus pattern (24 bp):
CACGTCATATATAAAAACATGTTA
Found at i:4407613 original size:45 final size:45
Alignment explanation
Indices: 4407564--4407723 Score: 173
Period size: 45 Copynumber: 3.6 Consensus size: 45
4407554 TATAAAAACA
* * * *
4407564 TGTTACACGTTATGTATAAAAATATGTTACACGCCAT-AGTTAGGT
1 TGTTACACGTCATGTACAAAAACATGTGACACGCCATGA-TTAGGT
* *
4407609 TGTTATACGTCATGTACAAAAACATGTGGCACGCCATGATT-GGAT
1 TGTTACACGTCATGTACAAAAACATGTGACACGCCATGATTAGG-T
* * * *
4407654 TGTTACAC-ACTATATATAAAAACATGTGACATGCCATGATTAGGT
1 TGTTACACGTC-ATGTACAAAAACATGTGACACGCCATGATTAGGT
*
4407699 TGTTACATGTCATGTACAAAAACAT
1 TGTTACACGTCATGTACAAAAACAT
4407724 ATTACACATT
Statistics
Matches: 94, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
44 3 0.03
45 87 0.93
46 4 0.04
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (45 bp):
TGTTACACGTCATGTACAAAAACATGTGACACGCCATGATTAGGT
Found at i:4407621 original size:69 final size:70
Alignment explanation
Indices: 4407496--4407635 Score: 165
Period size: 69 Copynumber: 2.0 Consensus size: 70
4407486 TTTAATAAAA
* * * *
4407496 TTACACGTCATGTACAAAAACATCTGTACACGTCATGGTTAGATTATTGCACGTCATATATAAAA
1 TTACACGTCATGTACAAAAACATCTGTACACGCCATAGTTAGATTATTACACGTCATATACAAAA
4407561 ACATG
66 ACATG
* * * * * * * *
4407566 TTACACGTTATGTATAAAAATATGT-TACACGCCATAGTTAGGTTGTTATACGTCATGTACAAAA
1 TTACACGTCATGTACAAAAACATCTGTACACGCCATAGTTAGATTATTACACGTCATATACAAAA
4407630 ACATG
66 ACATG
4407635 T
1 T
4407636 GGCACGCCAT
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
69 37 0.64
70 21 0.36
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (70 bp):
TTACACGTCATGTACAAAAACATCTGTACACGCCATAGTTAGATTATTACACGTCATATACAAAA
ACATG
Found at i:4407802 original size:21 final size:21
Alignment explanation
Indices: 4407758--4407802 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4407748 GTGACACGAT
*
4407758 ATGATTAGGTTATTAGACGCC
1 ATGATTAGGTTATTACACGCC
* *
4407779 ATGATTAGGTTGTTACACGTC
1 ATGATTAGGTTATTACACGCC
4407800 ATG
1 ATG
4407803 TACAAAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (21 bp):
ATGATTAGGTTATTACACGCC
Found at i:4407843 original size:90 final size:90
Alignment explanation
Indices: 4407686--4407869 Score: 235
Period size: 90 Copynumber: 2.0 Consensus size: 90
4407676 CATGTGACAT
* ** * *
4407686 GCCATGATTAGGTTGTTACATGTCATGTACAAAAACATATTACACATTATGTACAAAAATATGTG
1 GCCATGATTAGGTTGTTACACGTCATGTACAAAAACATATTACACACCATATACAAAAATATATG
* *
4407751 ACACGATA-TGATTAGGTTATTAGAC
66 ACAAGATATTG-TTAGGTTATTACAC
* * **
4407776 GCCATGATTAGGTTGTTACACGTCATGTACAAAAACATGTTATATGCCATATACAAAAATATATG
1 GCCATGATTAGGTTGTTACACGTCATGTACAAAAACATATTACACACCATATACAAAAATATATG
* *
4407841 ACAAGTTATTGTTAGGTTGTTACAC
66 ACAAGATATTGTTAGGTTATTACAC
4407866 GCCA
1 GCCA
4407870 CATTGAAAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
90 78 0.98
91 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (90 bp):
GCCATGATTAGGTTGTTACACGTCATGTACAAAAACATATTACACACCATATACAAAAATATATG
ACAAGATATTGTTAGGTTATTACAC
Found at i:4411345 original size:3 final size:3
Alignment explanation
Indices: 4411337--4411361 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4411327 GTAAATGATG
4411337 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
4411362 TTCTTAGCCT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4416562 original size:21 final size:20
Alignment explanation
Indices: 4416526--4416567 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
4416516 TGATATGTTT
*
4416526 TAATGAATGATGATGTGACA
1 TAATGAATGATCATGTGACA
4416546 TAATGATATGATCATGTGACA
1 TAATGA-ATGATCATGTGACA
4416567 T
1 T
4416568 TTCACCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.33
Consensus pattern (20 bp):
TAATGAATGATCATGTGACA
Found at i:4424156 original size:21 final size:21
Alignment explanation
Indices: 4424116--4424157 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4424106 ACCTTAAATC
*
4424116 ACTAAAACCCTAAAATCGATT
1 ACTAAAACCCTAAAACCGATT
* *
4424137 ACTAAAACTCTCAAACCGATT
1 ACTAAAACCCTAAAACCGATT
4424158 CATCACACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (21 bp):
ACTAAAACCCTAAAACCGATT
Found at i:4424207 original size:22 final size:21
Alignment explanation
Indices: 4424182--4424259 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 21
4424172 ACTAGTTTAA
*
4424182 TAAAACTTAAAAATCAATTCAT
1 TAAAACCT-AAAATCAATTCAT
*
4424204 TAAAACCCTAAAACCAATTCAT
1 TAAAA-CCTAAAATCAATTCAT
* * *
4424226 CAAATCCT-AAATCAATTCGT
1 TAAAACCTAAAATCAATTCAT
4424246 TAAAACTCTAAAAT
1 TAAAAC-CTAAAAT
4424260 TGATTCACCA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 14 0.31
21 5 0.11
22 24 0.53
23 2 0.04
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.28
Consensus pattern (21 bp):
TAAAACCTAAAATCAATTCAT
Found at i:4424558 original size:17 final size:17
Alignment explanation
Indices: 4424533--4424567 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4424523 TGATTTAAGG
* *
4424533 TTTGGTTAATGAAATTA
1 TTTGCTTAAGGAAATTA
4424550 TTTGCTTAAGGAAATTA
1 TTTGCTTAAGGAAATTA
4424567 T
1 T
4424568 CTTCTGAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.46
Consensus pattern (17 bp):
TTTGCTTAAGGAAATTA
Found at i:4433142 original size:13 final size:15
Alignment explanation
Indices: 4433119--4433160 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
4433109 TATCAATAAA
4433119 AATCATAAAATT-TT
1 AATCATAAAATTGTT
4433133 AATC-TAAAATTGTT
1 AATCATAAAATTGTT
*
4433147 AATTATTAAAATTG
1 AATCA-TAAAATTG
4433161 AATGAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 7 0.29
14 9 0.38
16 8 0.33
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (15 bp):
AATCATAAAATTGTT
Found at i:4452333 original size:91 final size:91
Alignment explanation
Indices: 4452207--4452392 Score: 243
Period size: 91 Copynumber: 2.0 Consensus size: 91
4452197 ACACCATACC
* * *
4452207 TTTAGAATTTGAGCAAATACAATAAAAAATTATAAACTTATTGA-TTTTTAAAAAATACATTCAA
1 TTTAAAATTTGAGCAAATACAATAAAAAATTATAAACTTAGTGATTTTTTAAAAAATAAATT-AA
**
4452271 AAAGGAGTTAAAATAATCAATGTGGAATT
65 AAAAAAGTT-AAATAAT-AATGTGGAATT
* *
4452300 TTTAAAATTTGAGTAAATA-TA-AAAAAATTATAAACTTAGTGATTTTTTAAAAAATAAATTAAA
1 TTTAAAATTTGAGCAAATACAATAAAAAATTATAAACTTAGTGATTTTTTAAAAAATAAATTAAA
* *
4452363 AAAAAGTTAAATGATGATGTGGAATT
66 AAAAAGTTAAATAATAATGTGGAATT
4452389 TTTA
1 TTTA
4452393 TTCGGATTAA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
89 14 0.17
90 6 0.07
91 29 0.35
92 17 0.20
93 17 0.20
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.35
Consensus pattern (91 bp):
TTTAAAATTTGAGCAAATACAATAAAAAATTATAAACTTAGTGATTTTTTAAAAAATAAATTAAA
AAAAAGTTAAATAATAATGTGGAATT
Found at i:4462172 original size:20 final size:21
Alignment explanation
Indices: 4462143--4462190 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
4462133 TAAATTAAAA
* *
4462143 ATATATAAAAATTTAA-AATT
1 ATATAAAAAAAATTAATAATT
4462163 ATATAAAAAAAATTAATAATT
1 ATATAAAAAAAATTAATAATT
4462184 A-ATAAAA
1 ATATAAAA
4462191 TTATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATAAAAAAAATTAATAATT
Found at i:4462190 original size:18 final size:18
Alignment explanation
Indices: 4462134--4462190 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
4462124 TAATTTAATT
*
4462134 AAATTAAAAATATATAAA
1 AAATTAAAATTATATAAA
*
4462152 AATTTAAAATTATATAAAAA
1 AAATTAAAATTATAT--AAA
4462172 AAATTAATAATTA-ATAAA
1 AAATTAA-AATTATATAAA
4462190 A
1 A
4462191 TTATATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 17 0.52
20 11 0.33
21 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTAAAATTATATAAA
Found at i:4462307 original size:17 final size:17
Alignment explanation
Indices: 4462285--4462338 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
4462275 TTAATAAATT
4462285 TTAATTTTTATTATTTC
1 TTAATTTTTATTATTTC
*
4462302 TTAATTTTTAGAATATTT-
1 TTAATTTTT--ATTATTTC
*
4462320 TTAATTATTAATTATTTC
1 TTAATT-TTTATTATTTC
4462338 T
1 T
4462339 CTTATTTCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 15 0.50
18 7 0.23
19 8 0.27
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (17 bp):
TTAATTTTTATTATTTC
Found at i:4468456 original size:18 final size:18
Alignment explanation
Indices: 4468433--4468470 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4468423 ACGTCCGGTC
4468433 CTTCATGCGATTATACGA
1 CTTCATGCGATTATACGA
4468451 CTTCATGCGATTATACGA
1 CTTCATGCGATTATACGA
4468469 CT
1 CT
4468471 GCCATTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (18 bp):
CTTCATGCGATTATACGA
Found at i:4473883 original size:2 final size:2
Alignment explanation
Indices: 4473876--4473902 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4473866 TCTCTTAAGG
4473876 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 T
4473903 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4473983 original size:2 final size:2
Alignment explanation
Indices: 4473976--4474001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4473966 TCCTTCTTCN
4473976 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
4474002 TATTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4479159 original size:24 final size:27
Alignment explanation
Indices: 4479125--4479174 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
4479115 TTTTTGCACT
4479125 TTAAACTCG-AAAGAA-AAAAACAACC
1 TTAAACTCGAAAAGAAGAAAAACAACC
4479150 TTAAA-TCGAAAAGAAGAAAAACAAC
1 TTAAACTCGAAAAGAAGAAAAACAAC
4479175 ATCTTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 3 0.13
25 11 0.48
26 9 0.39
ACGTcount: A:0.62, C:0.16, G:0.10, T:0.12
Consensus pattern (27 bp):
TTAAACTCGAAAAGAAGAAAAACAACC
Found at i:4479846 original size:31 final size:31
Alignment explanation
Indices: 4479781--4479858 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
4479771 CATTTAAGAT
* *
4479781 GATGACGTGGC-ATGCTATATGGCACCAAGT
1 GATGACGTGGCAATGCTAGATGGCACCAAGC
* *
4479811 GATGACGTGGCAATGGTAGATGGCACTATA-C
1 GATGACGTGGCAATGCTAGATGGCACCA-AGC
* *
4479842 GATGACATGGCAGTGCT
1 GATGACGTGGCAATGCT
4479859 GGCGTGGCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 11 0.28
31 27 0.69
32 1 0.03
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.23
Consensus pattern (31 bp):
GATGACGTGGCAATGCTAGATGGCACCAAGC
Found at i:4480486 original size:108 final size:108
Alignment explanation
Indices: 4480297--4480506 Score: 375
Period size: 108 Copynumber: 1.9 Consensus size: 108
4480287 TAAAATAACT
* *
4480297 AAATATGTTGATTTAGTTACAACATTCACAATTTACAAATACACATTCTTTTGAAATTATTCAAC
1 AAATATCTTGATTTAGTTACAACATCCACAATTTACAAATACACATTCTTTTGAAATTATTCAAC
4480362 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
* *
4480405 AAATATCTTGATTTAGTTACAATATCCACAATTTACAAATACATATTCTTTTGAAATTATTCAAC
1 AAATATCTTGATTTAGTTACAACATCCACAATTTACAAATACACATTCTTTTGAAATTATTCAAC
*
4480470 TCTTACCTAATTTACCTTTTATTTAAATTTACTCAAA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
4480507 ATTTCTTATA
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 97 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.42
Consensus pattern (108 bp):
AAATATCTTGATTTAGTTACAACATCCACAATTTACAAATACACATTCTTTTGAAATTATTCAAC
TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGCA
Found at i:4513647 original size:15 final size:15
Alignment explanation
Indices: 4513627--4513659 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
4513617 CACAATGTGC
4513627 CAAAAATATTCAAGA
1 CAAAAATATTCAAGA
4513642 CAAAAATATTCAAGA
1 CAAAAATATTCAAGA
4513657 CAA
1 CAA
4513660 TGACAGTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (15 bp):
CAAAAATATTCAAGA
Found at i:4521182 original size:18 final size:19
Alignment explanation
Indices: 4521142--4521184 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
4521132 CCACTAAAAT
* *
4521142 TAAAATATATTTTTTAAGA
1 TAAAATATATTATTGAAGA
4521161 -AAAATATATTATTGAA-A
1 TAAAATATATTATTGAAGA
4521178 TAAAATA
1 TAAAATA
4521185 ATGTACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (19 bp):
TAAAATATATTATTGAAGA
Found at i:4530613 original size:6 final size:6
Alignment explanation
Indices: 4530602--4530631 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4530592 AGAATAATTT
4530602 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
4530632 AAAATAGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:4530640 original size:18 final size:18
Alignment explanation
Indices: 4530602--4530640 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4530592 AGAATAATTT
*
4530602 GAGAAAGAGAAAGAGAAA
1 GAGAAAGAGAAAGAAAAA
4530620 GAGAAAGAGAAA-AAAATA
1 GAGAAAGAGAAAGAAAA-A
4530638 GAG
1 GAG
4530641 GACCTTGACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
GAGAAAGAGAAAGAAAAA
Found at i:4546084 original size:2 final size:2
Alignment explanation
Indices: 4546077--4546107 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4546067 GTATATGCAT
4546077 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4546108 TCTNTACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4546152 original size:2 final size:2
Alignment explanation
Indices: 4546145--4546175 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4546135 GTATATGCAT
4546145 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4546176 CTGTTTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4546153 original size:68 final size:67
Alignment explanation
Indices: 4546044--4546175 Score: 255
Period size: 68 Copynumber: 2.0 Consensus size: 67
4546034 AGCCAAAGCG
4546044 TACATGTCATTGCAAGAAATGTTGTATATGCATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGT
1 TACATGTCATTGCAAGAAATGTTGTATATGCATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGT
4546109 CT
66 CT
4546111 NTACATGTCATTGCAAGAAATGTTGTATATGCATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
1 -TACATGTCATTGCAAGAAATGTTGTATATGCATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
4546176 CTGTTTGATA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.20
Consensus pattern (67 bp):
TACATGTCATTGCAAGAAATGTTGTATATGCATGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGT
CT
Found at i:4550437 original size:2 final size:2
Alignment explanation
Indices: 4550430--4550456 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4550420 ATGAGGTTAA
4550430 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 A
4550457 ACAGACAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4552938 original size:19 final size:20
Alignment explanation
Indices: 4552916--4552962 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
4552906 AAAATTATAA
*
4552916 ATTTTTTAAAT-AATTTTTT
1 ATTTTTTAAATCAAGTTTTT
*
4552935 ATTTTTTAGATCAAGTTTTT
1 ATTTTTTAAATCAAGTTTTT
*
4552955 ATATTTTA
1 ATTTTTTA
4552963 TTTTAAACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (20 bp):
ATTTTTTAAATCAAGTTTTT
Found at i:4553048 original size:10 final size:9
Alignment explanation
Indices: 4553039--4553078 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
4553029 TATTTTATAT
4553039 TATATAATA
1 TATATAATA
4553048 TAT-TAATA
1 TATATAATA
4553056 TATTATAATA
1 TA-TATAATA
4553066 TATGATAATA
1 TAT-ATAATA
4553076 TAT
1 TAT
4553079 TTTATGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.25
9 5 0.18
10 16 0.57
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATAATA
Found at i:4553059 original size:20 final size:20
Alignment explanation
Indices: 4553034--4553090 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
4553024 TTTATTATTT
4553034 TATATTATATAATATAT-TAA
1 TATATT-TATAATATATATAA
4553054 TATA-TTATAATATATGATAA
1 TATATTTATAATATAT-ATAA
*
4553074 TATATTTTATGATATAT
1 TATA-TTTATAATATAT
4553091 CTTAAAACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 10 0.31
19 1 0.03
20 11 0.34
22 10 0.31
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TATATTTATAATATATATAA
Found at i:4553077 original size:15 final size:15
Alignment explanation
Indices: 4553042--4553087 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
4553032 TTTATATTAT
4553042 ATAATATATTA-AT-
1 ATAATATATTATATG
* *
4553055 ATATTATAATATATG
1 ATAATATATTATATG
*
4553070 ATAATATATTTTATG
1 ATAATATATTATATG
4553085 ATA
1 ATA
4553088 TATCTTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 9 0.35
14 2 0.08
15 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
ATAATATATTATATG
Found at i:4561423 original size:46 final size:46
Alignment explanation
Indices: 4561370--4561475 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
4561360 AAAAAAAAAG
* *
4561370 GCTGCCCCTTTTCTTTGTTGATGAGGTTTTGGTTATTGATCATGAA
1 GCTGCCCCTTTTCTTTGCTGATGAGGTTTTGGTCATTGATCATGAA
4561416 GCTGCCCCTTTTCTTTGCTGATGAGGTTTTGGTCATTGATCATGAA
1 GCTGCCCCTTTTCTTTGCTGATGAGGTTTTGGTCATTGATCATGAA
4561462 GCTGCCCCTTTTCT
1 GCTGCCCCTTTTCT
4561476 CTACTTTATA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (46 bp):
GCTGCCCCTTTTCTTTGCTGATGAGGTTTTGGTCATTGATCATGAA
Found at i:4577515 original size:22 final size:22
Alignment explanation
Indices: 4577472--4577515 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4577462 AGATTAAAGG
* * **
4577472 TTGAAAATGAAATTAATGTGAA
1 TTGAAAAGGAAATAAAACTGAA
4577494 TTGAAAAGGAAATAAAACTGAA
1 TTGAAAAGGAAATAAAACTGAA
4577516 AACACTTATC
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:0.55, C:0.02, G:0.18, T:0.25
Consensus pattern (22 bp):
TTGAAAAGGAAATAAAACTGAA
Found at i:4579745 original size:17 final size:20
Alignment explanation
Indices: 4579716--4579756 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 20
4579706 GTTTTAGGTG
4579716 TTTT-ACATCTTAT-ATA-A
1 TTTTCACATCTTATAATAGA
4579733 TTTTCACAT-TTATAATAGA
1 TTTTCACATCTTATAATAGA
4579752 TTTTC
1 TTTTC
4579757 CTCTTTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTCACATCTTATAATAGA
Found at i:4587357 original size:231 final size:230
Alignment explanation
Indices: 4586938--4587437 Score: 528
Period size: 231 Copynumber: 2.2 Consensus size: 230
4586928 GCTCCTGATG
* * *
4586938 CAGAAAGAGCTTGAGAGGTATAAAGAAAAGCTTGAGGAAGCATCTAGGTGTCAAATACACTTGGA
1 CAGAAAGAGCTTGAGAGGTATAAGGAAAAGCTTGAGGAAACATCTAGGAGTCAAATACACTTGGA
** * *
4587003 AAAGCAAGCTTTGCAGATGGAAAGTGAATCCAGAGAGAAACTTCAGGAAGTTTGTGATGCTTTAG
66 AAAGCAAGCGGTGCAGATGAAAAATGAAT-CAGAGAGAAACTTCAGGAAGTTTGTGATGCTTTAG
* * * * *
4587068 AAGCAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAGCAGCTTCATTGATGAAGAGGGTTGAG
130 AAACAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAGCAGCTTCATTAAAGAAGAGGATTGAA
**
4587133 TCTTTGGATCAAATT-GAAGAGCAGT-GGCTCCAGACA
195 TCTTCAGATC-AATTAGAAGAGCAGTGGGC-CCAGACA
*** * *
4587169 CAGAAAGAGCTTGAGAGGTATAAGGATTTGCTTGAGGAAACATCTAGGAGTCAACGT-CAGTTGG
1 CAGAAAGAGCTTGAGAGGTATAAGGAAAAGCTTGAGGAAACATCTAGGAGTCAA-ATACACTTGG
* *
4587233 AAGAGCAAGCGGTGCATATGAAAAATGAAT-ATGAAGAGAAACTTC-GAGAAGTTTGTGATGCTT
65 AAAAGCAAGCGGTGCAGATGAAAAATGAATCA-G-AGAGAAACTTCAG-GAAGTTTGTGATGCTT
* * * ** * * *
4587296 TAGAAACTGCAAACTTTGAATTGGCTGAAGAACGTGAGAG-GACAGCTT-ATTTAAAGAAGAGGA
127 TAGAAACAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAG-CAGCTTCA-TTAAAGAAGAGGA
* * **
4587359 TTGAATCTTCAGATCACTTAGAAGAGCAGTGGGCCCTGAGG
190 TTGAATCTTCAGATCAATTAGAAGAGCAGTGGGCCCAGACA
* * * * *
4587400 CAGAAAGAACTTGACAGGTACAAGGAAATGTTTGAGGA
1 CAGAAAGAGCTTGAGAGGTATAAGGAAAAGCTTGAGGA
4587438 GTCATCTAAG
Statistics
Matches: 222, Mismatches: 39, Indels: 16
0.80 0.14 0.06
Matches are distributed among these distances:
229 1 0.00
230 7 0.03
231 210 0.95
232 4 0.02
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (230 bp):
CAGAAAGAGCTTGAGAGGTATAAGGAAAAGCTTGAGGAAACATCTAGGAGTCAAATACACTTGGA
AAAGCAAGCGGTGCAGATGAAAAATGAATCAGAGAGAAACTTCAGGAAGTTTGTGATGCTTTAGA
AACAGCAAAATCTGAATTAACAGAAGAACGAGAAAGAGCAGCTTCATTAAAGAAGAGGATTGAAT
CTTCAGATCAATTAGAAGAGCAGTGGGCCCAGACA
Found at i:4598844 original size:14 final size:14
Alignment explanation
Indices: 4598825--4598852 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4598815 ATTTTTGATG
4598825 ATTGTAGAATCAAT
1 ATTGTAGAATCAAT
4598839 ATTGTAGAATCAAT
1 ATTGTAGAATCAAT
4598853 CAATATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATTGTAGAATCAAT
Found at i:4609384 original size:14 final size:14
Alignment explanation
Indices: 4609365--4609391 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4609355 ATTTTTGATG
4609365 ATTGTAGAATCAAT
1 ATTGTAGAATCAAT
4609379 ATTGTAGAATCAA
1 ATTGTAGAATCAA
4609392 CCAATATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (14 bp):
ATTGTAGAATCAAT
Found at i:4620899 original size:26 final size:26
Alignment explanation
Indices: 4620870--4620922 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
4620860 GTCACGGTCC
4620870 TCGCATGGACATGAATCTCACATAAT
1 TCGCATGGACATGAATCTCACATAAT
4620896 TCGCATGGACATGAATCTCACATAAT
1 TCGCATGGACATGAATCTCACATAAT
4620922 T
1 T
4620923 GAGATAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (26 bp):
TCGCATGGACATGAATCTCACATAAT
Found at i:4621218 original size:104 final size:104
Alignment explanation
Indices: 4621034--4621241 Score: 344
Period size: 104 Copynumber: 2.0 Consensus size: 104
4621024 AAATCAGCGG
* * *
4621034 GTCAAAGCAGACAATATCTCACAGGAATTGGTGTAGACCGTGACACCCATGTTGTAGTGTAACAC
1 GTCAAAGCAGACAATATCTCACAAGAATTGATATAGACCGTGACACCCATGTTGTAGTGTAACAC
*
4621099 ATAGGCAATGCTTGAGAGTTTCAATAGCAAGCTACTAAT
66 ATAAGCAATGCTTGAGAGTTTCAATAGCAAGCTACTAAT
* * *
4621138 GTCAAAGCGGACAATATCTCACAAGAATTGATATATATCGTGACACCCATGTTGTAGTGTAACAC
1 GTCAAAGCAGACAATATCTCACAAGAATTGATATAGACCGTGACACCCATGTTGTAGTGTAACAC
*
4621203 ATAAGCAATGTTTGAGAGTTTCAATAGCAAGCTACTAAT
66 ATAAGCAATGCTTGAGAGTTTCAATAGCAAGCTACTAAT
4621242 ATAAACTCTC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (104 bp):
GTCAAAGCAGACAATATCTCACAAGAATTGATATAGACCGTGACACCCATGTTGTAGTGTAACAC
ATAAGCAATGCTTGAGAGTTTCAATAGCAAGCTACTAAT
Found at i:4622304 original size:7 final size:7
Alignment explanation
Indices: 4622289--4622337 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
4622279 TGAAAATAAG
*
4622289 TAAATTT
1 TAAAATT
4622296 TAAAATT
1 TAAAATT
4622303 TAAAATT
1 TAAAATT
4622310 CTAAAATT
1 -TAAAATT
*
4622318 TAATATT
1 TAAAATT
4622325 TATAAATT
1 TA-AAATT
4622333 TAAAA
1 TAAAA
4622338 ATACTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
7 24 0.65
8 13 0.35
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (7 bp):
TAAAATT
Found at i:4622314 original size:15 final size:14
Alignment explanation
Indices: 4622289--4622337 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
4622279 TGAAAATAAG
*
4622289 TAAATTTTAAAATT
1 TAAAATTTAAAATT
4622303 TAAAATTCTAAAATT
1 TAAAATT-TAAAATT
*
4622318 TAATATTTATAAATT
1 TAAAATTTA-AAATT
4622333 TAAAA
1 TAAAA
4622338 ATACTTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTTAAAATT
Found at i:4635067 original size:23 final size:22
Alignment explanation
Indices: 4635041--4635103 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
4635031 TGCCACCTCA
*
4635041 TTAAAATAAAAAATTATAAAGAC
1 TTAAAATAAAAAATTAAAAAG-C
* *
4635064 TTAAAATTAAATATTAAAAAGC
1 TTAAAATAAAAAATTAAAAAGC
* **
4635086 TTATAATAACTAATTAAA
1 TTAAAATAAAAAATTAAA
4635104 CAAAAAATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (22 bp):
TTAAAATAAAAAATTAAAAAGC
Found at i:4635880 original size:25 final size:25
Alignment explanation
Indices: 4635846--4635909 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
4635836 TGATAATGAG
*
4635846 TCTGTTTAAGACCATCATGCCTTTT
1 TCTGTTTAAGACCATCATGCCGTTT
* *
4635871 TCTGTTTAAGACCATCGTGTCGTTT
1 TCTGTTTAAGACCATCATGCCGTTT
4635896 TCTGTTTAA-ACCAT
1 TCTGTTTAAGACCAT
4635910 GGCTGGACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 5 0.14
25 31 0.86
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (25 bp):
TCTGTTTAAGACCATCATGCCGTTT
Found at i:4636643 original size:15 final size:15
Alignment explanation
Indices: 4636617--4636654 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4636607 TTGTGTTAAT
4636617 ATTATAAAAATTA-TA
1 ATTAT-AAAATTATTA
4636632 ACTTATAAAATTATTA
1 A-TTATAAAATTATTA
4636648 ATTATAA
1 ATTATAA
4636655 TAAATATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTATAAAATTATTA
Found at i:4639548 original size:20 final size:23
Alignment explanation
Indices: 4639520--4639564 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
4639510 ATTTTTATTT
4639520 AAACTTATAATAC-T-AAATATA
1 AAACTTATAATACATAAAATATA
4639541 AAAC-TATAATACATAAAATATA
1 AAACTTATAATACATAAAATATA
4639563 AA
1 AA
4639565 TAATTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (23 bp):
AAACTTATAATACATAAAATATA
Found at i:4647695 original size:2 final size:2
Alignment explanation
Indices: 4647690--4647718 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4647680 TCTCTCTCTC
4647690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4647719 TGTGTGTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4657152 original size:16 final size:15
Alignment explanation
Indices: 4657131--4657161 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
4657121 CTCAACCCCC
4657131 CCCCCCCCAAAAAAA
1 CCCCCCCCAAAAAAA
4657146 NCCCCCCCCAAAAAAA
1 -CCCCCCCCAAAAAAA
4657162 AAAAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.52, G:0.00, T:0.00
Consensus pattern (15 bp):
CCCCCCCCAAAAAAA
Found at i:4675158 original size:28 final size:28
Alignment explanation
Indices: 4675114--4675189 Score: 100
Period size: 28 Copynumber: 2.7 Consensus size: 28
4675104 TTTGAGAAAT
4675114 GATTT-GAGTTTAGGGTTTAAGATTTAAG
1 GATTTAGAGTTTA-GGTTTAAGATTTAAG
* * *
4675142 GATTTAGAGTTCAGGTTAAAGATTTAGG
1 GATTTAGAGTTTAGGTTTAAGATTTAAG
4675170 GATTTAGAGTTTAGAGTTTA
1 GATTTAGAGTTTAG-GTTTA
4675190 GGCAAAGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 31 0.76
29 10 0.24
ACGTcount: A:0.30, C:0.01, G:0.28, T:0.41
Consensus pattern (28 bp):
GATTTAGAGTTTAGGTTTAAGATTTAAG
Found at i:4686495 original size:25 final size:24
Alignment explanation
Indices: 4686449--4686517 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
4686439 ATTATATTTT
* *
4686449 AATTAATTAATAATTAATTATAAAA
1 AATTAATTAA-AATAAAATATAAAA
4686474 AATTAAATTAAAATAAAATATAAAA
1 AATT-AATTAAAATAAAATATAAAA
**
4686499 TTTTTAA-TAAAATAAAATA
1 -AATTAATTAAAATAAAATA
4686518 AAATAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
24 12 0.32
25 18 0.47
26 8 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AATTAATTAAAATAAAATATAAAA
Found at i:4686531 original size:27 final size:29
Alignment explanation
Indices: 4686477--4686535 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 29
4686467 TATAAAAAAT
*
4686477 TAAATTAAAATAAAATATAAAATTTTTAA
1 TAAAATAAAATAAAATATAAAATTTTTAA
*
4686506 TAAAATAAAAT-AAA-ATAATATTTTTAA
1 TAAAATAAAATAAAATATAAAATTTTTAA
4686533 TAA
1 TAA
4686536 TTTAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 15 0.54
28 3 0.11
29 10 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
TAAAATAAAATAAAATATAAAATTTTTAA
Found at i:4686534 original size:17 final size:18
Alignment explanation
Indices: 4686514--4686556 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
4686504 AATAAAATAA
4686514 AATAAAATAAT-ATTTTT
1 AATAAAATAATAATTTTT
**
4686531 AATAATTTAATAATTTTT
1 AATAAAATAATAATTTTT
4686549 AA-AAAATA
1 AATAAAATA
4686557 TTATGTTCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATAAAATAATAATTTTT
Found at i:4690840 original size:8 final size:8
Alignment explanation
Indices: 4690827--4690851 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4690817 TTCTTTGTCA
4690827 AAAAAAAG
1 AAAAAAAG
4690835 AAAAAAAG
1 AAAAAAAG
4690843 AAAAAAAG
1 AAAAAAAG
4690851 A
1 A
4690852 GTTTCTTCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:4693114 original size:25 final size:25
Alignment explanation
Indices: 4693067--4693121 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
4693057 ATATTTTAAA
4693067 TATTTTATATTTAAATAATAATA-T
1 TATTTTATATTTAAATAATAATATT
*
4693091 TATTTTCATATTTAAAATGA-AATATT
1 TATTTT-ATATTT-AAATAATAATATT
4693117 TATTT
1 TATTT
4693122 AAAAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 6 0.22
25 10 0.37
26 11 0.41
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TATTTTATATTTAAATAATAATATT
Found at i:4694900 original size:50 final size:50
Alignment explanation
Indices: 4694826--4694922 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
4694816 TGTCTCGTTA
4694826 TATTTATTTACATAACAGTTTTCAATATTCTTTTAAAATTTATATTTACT
1 TATTTATTTACATAACAGTTTTCAATATTCTTTTAAAATTTATATTTACT
* * *
4694876 TATTTATTTACTTAACAGTTTTCAATTTTCTTTTAAAGTTTATATTT
1 TATTTATTTACATAACAGTTTTCAATATTCTTTTAAAATTTATATTT
4694923 GTTCTTCCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (50 bp):
TATTTATTTACATAACAGTTTTCAATATTCTTTTAAAATTTATATTTACT
Found at i:4711088 original size:2 final size:2
Alignment explanation
Indices: 4711081--4711114 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4711071 GTACGCGTAC
4711081 AT AT AT AT A- AT AT AT AT A- 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
4711115 TAACAAATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4711095 original size:9 final size:9
Alignment explanation
Indices: 4711081--4711114 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
4711071 GTACGCGTAC
4711081 ATATATATA
1 ATATATATA
4711090 ATATATATA
1 ATATATATA
4711099 ATATATAT-
1 ATATATATA
4711107 ATATATAT
1 ATATATAT
4711115 TAACAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATATATATA
Found at i:4721500 original size:2 final size:2
Alignment explanation
Indices: 4721481--4721529 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
4721471 CATTTAAAAT
* * * *
4721481 GA GA GA GT GA GT GT GA GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
4721523 GA GA GA G
1 GA GA GA G
4721530 TGTGTGTGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.41, C:0.00, G:0.53, T:0.06
Consensus pattern (2 bp):
GA
Found at i:4730125 original size:277 final size:279
Alignment explanation
Indices: 4729596--4730157 Score: 806
Period size: 277 Copynumber: 2.0 Consensus size: 279
4729586 TTCAACTAGG
*
4729596 GCAAACTTGAACAACCCTATATGCCAATATGTGCCAAGGACGTGACATGCTAGAACACTTGAGCA
1 GCAAACTTGAACAACCCTATATG-CAATATGTGCCAAGGACGTGACATGCTAGAACACTTAAGCA
* * *
4729661 AAGACCTAGTTAACTGCACGCTTGCAATTGGTTGGCAACAGTGAACTTTAATGTAAAGATGACTG
65 AAGACCTAGTTAACTGCAAGCTTGCAATTGGTTGGCAACAGTAAACTCTAATGTAAAGATGACTG
* * * ** * *
4729726 TTTAAAATCAGACAAAGTGGTGAAAACAAAATTTAAGGATTCAATATTTCCAGATTGTTTGGTTT
130 TTTAAAATCAAACAAAGGGGTGAAAACAAAACTT-AGGATTCAATATTTCCAGACCGATTGGGTT
* * * ** *
4729791 CTAGTATTTAAGACTGCTTGACAGAATTTGTTTTATTGAAAGTGTTGGTTTCTAGTAGCTCAGCT
194 CAAGTATCTAAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGGTTTCTAGTAGCTCAGCT
*
4729856 CATTTAGCAGC-TGCCTCTAA
259 CATTTAGCAGCTTGCATCTAA
* * * *
4729876 GCAAACTTGAACAACCCTATATG-AATATGTGCCTAGGATGTGACATGCTAGGAGACTTAAGCAA
1 GCAAACTTGAACAACCCTATATGCAATATGTGCCAAGGACGTGACATGCTAGAACACTTAAGCAA
* * *
4729940 AGACCTAGTTAACTGCAAAGCTTGCAATTGGTTGGCAACAGTAAACTCTACTGTGAAGGTGACTG
66 AGACCTAGTTAACTGC-AAGCTTGCAATTGGTTGGCAACAGTAAACTCTAATGTAAAGATGACTG
* * * *
4730005 TTTAAAATCAAACAAAGGGGTGAAAATAAAACTT-GGGTTTAATTTTTCCAGACCGATTGGGTTC
130 TTTAAAATCAAACAAAGGGGTGAAAACAAAACTTAGGATTCAATATTTCCAGACCGATTGGGTTC
*
4730069 AAGTATCTGAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGGTTTCTAGTAGCTCAGCTC
195 AAGTATCTAAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGGTTTCTAGTAGCTCAGCTC
4730134 ATTTAGCAGCTTGCATCTAA
260 ATTTAGCAGCTTGCATCTAA
4730154 GCAA
1 GCAA
4730158 TACCAGTCAT
Statistics
Matches: 250, Mismatches: 30, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
277 91 0.36
278 64 0.26
279 72 0.29
280 23 0.09
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (279 bp):
GCAAACTTGAACAACCCTATATGCAATATGTGCCAAGGACGTGACATGCTAGAACACTTAAGCAA
AGACCTAGTTAACTGCAAGCTTGCAATTGGTTGGCAACAGTAAACTCTAATGTAAAGATGACTGT
TTAAAATCAAACAAAGGGGTGAAAACAAAACTTAGGATTCAATATTTCCAGACCGATTGGGTTCA
AGTATCTAAGACTGCCTGACAGAATTTACTTTATCGAAAGTGTTGGTTTCTAGTAGCTCAGCTCA
TTTAGCAGCTTGCATCTAA
Done.