Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 19 of 130
Found at i:5192466 original size:28 final size:28
Alignment explanation
Indices: 5192340--5192507 Score: 144
Period size: 28 Copynumber: 5.9 Consensus size: 28
5192330 CTTCACCTTC
* * *
5192340 CAAACTCTACAATCAAAACTCC-AAACCT
1 CAAACCCTAAAATCAAAAC-CCTAAATCT
* *
5192368 CAAAGCTCTAAAATCAAAACTCC-AAACCTT
1 CAAA-CCCTAAAATCAAAAC-CCTAAATC-T
* *
5192398 CAAACCCTAAAAT-TAAACCATAAATCCT
1 CAAACCCTAAAATCAAAACCCTAAAT-CT
* **
5192426 CTAAACCCTAAAACCAAAACTTTAAATCT
1 C-AAACCCTAAAATCAAAACCCTAAATCT
* *
5192455 CAAACCCTAAAATTAAAACCCCAAATCT
1 CAAACCCTAAAATCAAAACCCTAAATCT
*
5192483 CAAACCCTAAAATCAAAAACCTAAA
1 CAAACCCTAAAATCAAAACCCTAAA
5192508 CCCCAAAATC
Statistics
Matches: 117, Mismatches: 17, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
27 1 0.01
28 57 0.49
29 45 0.38
30 14 0.12
ACGTcount: A:0.50, C:0.30, G:0.01, T:0.19
Consensus pattern (28 bp):
CAAACCCTAAAATCAAAACCCTAAATCT
Found at i:5192502 original size:15 final size:15
Alignment explanation
Indices: 5192399--5192507 Score: 63
Period size: 14 Copynumber: 7.7 Consensus size: 15
5192389 CCAAACCTTC
5192399 AAACCCTAAAAT-T-
1 AAACCCTAAAATCTA
* *
5192412 AAACCAT-AAATCCTCT
1 AAACCCTAAAAT-CT-A
*
5192428 AAACCCTAAAA-CCA
1 AAACCCTAAAATCTA
* * *
5192442 AAA-CTTTAAATCTC
1 AAACCCTAAAATCTA
5192456 AAACCCTAAAAT-TA
1 AAACCCTAAAATCTA
* *
5192470 AAACCC-CAAATCTC
1 AAACCCTAAAATCTA
5192484 AAACCCTAAAATC-A
1 AAACCCTAAAATCTA
*
5192498 AAAACCTAAA
1 AAACCCTAAA
5192508 CCCCAAAATC
Statistics
Matches: 71, Mismatches: 16, Indels: 17
0.68 0.15 0.16
Matches are distributed among these distances:
12 4 0.06
13 15 0.21
14 31 0.44
15 12 0.17
16 6 0.08
17 3 0.04
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCCTAAAATCTA
Found at i:5192514 original size:28 final size:27
Alignment explanation
Indices: 5192267--5192514 Score: 156
Period size: 29 Copynumber: 8.6 Consensus size: 27
5192257 ATTAAACCTT
* * *
5192267 AAACCTTAAACCTCCTAACCTTAAAAATGA
1 AAACC-TAAACCT-CAAACCCT-AAAATCA
* *
5192297 AATCCTAAACCTTCTAAACCCTAAAATTA
1 AAACCTAAACC-TC-AAACCCTAAAATCA
** * *
5192326 AAACCTTCACCTTCCAAACTCTACAATCA
1 AAACCTAAACC-T-CAAACCCTAAAATCA
* *
5192355 AAACTCCAAACCTCAAAGCTCTAAAATCA
1 AAAC-CTAAACCTCAAA-CCCTAAAATCA
* *
5192384 AAACTCCAAACCTTCAAACCCTAAAAT-T
1 AAAC-CTAAACC-TCAAACCCTAAAATCA
*
5192412 AAACCATAAATCCTCTAAACCCTAAAACCA
1 AAACC-TAAA-CCTC-AAACCCTAAAATCA
* * *
5192442 AAACTTTAAATCTCAAACCCTAAAATTA
1 AAAC-CTAAACCTCAAACCCTAAAATCA
* *
5192470 AAACCCCAAATCTCAAACCCTAAAATCAA
1 AAA-CCTAAACCTCAAACCCTAAAATC-A
*
5192499 AAACCTAAACCCCAAA
1 AAACCTAAACCTCAAA
5192515 ATCTGAAACT
Statistics
Matches: 176, Mismatches: 29, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.01
28 57 0.32
29 90 0.51
30 28 0.16
ACGTcount: A:0.48, C:0.31, G:0.01, T:0.21
Consensus pattern (27 bp):
AAACCTAAACCTCAAACCCTAAAATCA
Found at i:5192553 original size:21 final size:22
Alignment explanation
Indices: 5192527--5192573 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
5192517 CTGAAACTTG
5192527 AAATCCT-AACCCTAAAATCCA
1 AAATCCTAAACCCTAAAATCCA
* *
5192548 AAATCCTAAACCTTAAAATTCA
1 AAATCCTAAACCCTAAAATCCA
5192570 AAAT
1 AAAT
5192574 TTTGAAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATCCTAAACCCTAAAATCCA
Found at i:5193975 original size:14 final size:12
Alignment explanation
Indices: 5193942--5193982 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
5193932 ATATTGATTT
5193942 AAATTTTTAATA
1 AAATTTTTAATA
*
5193954 AAATTTTTATTA
1 AAATTTTTAATA
5193966 AATTATTTTTAATA
1 AA--ATTTTTAATA
5193980 AAA
1 AAA
5193983 AATTTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 14 0.56
14 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
AAATTTTTAATA
Found at i:5193976 original size:26 final size:26
Alignment explanation
Indices: 5193944--5193995 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
5193934 ATTGATTTAA
*
5193944 ATTTTTAAT-AAAATTTTTATTAAATT
1 ATTTTTAATAAAAAATTTTA-TAAATT
5193970 ATTTTTAATAAAAAATTTTATAAATT
1 ATTTTTAATAAAAAATTTTATAAATT
5193996 TCACTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTTTAATAAAAAATTTTATAAATT
Found at i:5193987 original size:14 final size:14
Alignment explanation
Indices: 5193942--5193988 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
5193932 ATATTGATTT
5193942 AAATTTTTAAT--A
1 AAATTTTTAATAAA
*
5193954 AAATTTTTATTAAA
1 AAATTTTTAATAAA
**
5193968 TTATTTTTAATAAA
1 AAATTTTTAATAAA
5193982 AAATTTT
1 AAATTTT
5193989 ATAAATTTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
12 10 0.37
14 17 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AAATTTTTAATAAA
Found at i:5197141 original size:4 final size:5
Alignment explanation
Indices: 5197114--5197142 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5197104 AGTATTTATA
5197114 AATTT AATTT AATTT AATTT AA-TT AATTT
1 AATTT AATTT AATTT AATTT AATTT AATTT
5197143 TGATAAGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
AATTT
Found at i:5203900 original size:3 final size:3
Alignment explanation
Indices: 5203887--5203922 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
5203877 CCTCTACTTC
5203887 ATT AGTT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5203923 ATATATCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5209590 original size:14 final size:14
Alignment explanation
Indices: 5209571--5209601 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5209561 TCATGAATTC
*
5209571 AATATAGAAAACCT
1 AATATAGAAAACAT
5209585 AATATAGAAAACAT
1 AATATAGAAAACAT
5209599 AAT
1 AAT
5209602 TCTAGATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.23
Consensus pattern (14 bp):
AATATAGAAAACAT
Found at i:5212630 original size:32 final size:32
Alignment explanation
Indices: 5212543--5212632 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 32
5212533 TCATATTATC
*
5212543 CAAAAATCATCATCTAAATCTTT-AAAAATCTT
1 CAAAAATCATAATCTAAAT-TTTAAAAAATCTT
* *
5212575 CAAAAATCATAACCTAAGTTTTTAAAAAATCTT
1 CAAAAATCATAATCTAA-ATTTTAAAAAATCTT
* *
5212608 -TAAAATCATAATATAAACTTTTAAA
1 CAAAAATCATAATCTAAA-TTTTAAA
5212633 CATCTCACAT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
32 38 0.79
33 10 0.21
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.34
Consensus pattern (32 bp):
CAAAAATCATAATCTAAATTTTAAAAAATCTT
Found at i:5220152 original size:7 final size:7
Alignment explanation
Indices: 5220126--5220163 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
5220116 AAAGTCTAAA
5220126 TTTTT-T
1 TTTTTAT
*
5220132 TTTTTGT
1 TTTTTAT
*
5220139 TTCTTAT
1 TTTTTAT
5220146 TTTTTAT
1 TTTTTAT
5220153 TTTTTAT
1 TTTTTAT
5220160 TTTT
1 TTTT
5220164 ATTAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.87
Consensus pattern (7 bp):
TTTTTAT
Found at i:5220165 original size:20 final size:20
Alignment explanation
Indices: 5220126--5220166 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
5220116 AAAGTCTAAA
*
5220126 TTTTTTTTTTTGTTTCTTAT
1 TTTTTTTTTTTATTTCTTAT
5220146 TTTTTATTTTTTATTT-TTAT
1 TTTTT-TTTTTTATTTCTTAT
5220166 T
1 T
5220167 AATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTTTATTTCTTAT
Found at i:5221973 original size:19 final size:19
Alignment explanation
Indices: 5221935--5221973 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
5221925 TATTTAATAT
*
5221935 TAAAATTTAAAATTTTTTA
1 TAAAATTTAAAATTTATTA
5221954 TAAAA-TTAAAATTTCATTA
1 TAAAATTTAAAATTT-ATTA
5221973 T
1 T
5221974 TTTTAATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAAATTTAAAATTTATTA
Found at i:5225152 original size:15 final size:15
Alignment explanation
Indices: 5225132--5225160 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5225122 TTTTGAAAAG
5225132 AATAATCCTGGTAAA
1 AATAATCCTGGTAAA
5225147 AATAATCCTGGTAA
1 AATAATCCTGGTAA
5225161 GTTGGACGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (15 bp):
AATAATCCTGGTAAA
Found at i:5228786 original size:35 final size:35
Alignment explanation
Indices: 5228675--5228789 Score: 122
Period size: 35 Copynumber: 3.3 Consensus size: 35
5228665 TTTTACTTTA
* * * *
5228675 GATTCAATCTCAGTCATTGTTATTCTTTAACTCGT
1 GATTCAATCCCAGTCGTTGTTATTCTATGACTCGT
* * * * *
5228710 GATTTAATCCCAGTTGTTTTTATTTTATGACTCAT
1 GATTCAATCCCAGTCGTTGTTATTCTATGACTCGT
* *
5228745 GATTCAATCCCAGTCGTTGTTATTCTCTGATTCGT
1 GATTCAATCCCAGTCGTTGTTATTCTATGACTCGT
*
5228780 GGTTCAATCC
1 GATTCAATCC
5228790 TAATCATTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (35 bp):
GATTCAATCCCAGTCGTTGTTATTCTATGACTCGT
Found at i:5229235 original size:34 final size:35
Alignment explanation
Indices: 5229187--5229260 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
5229177 TTGATCGTCT
* * *
5229187 TTATTTTCTAACTCATAGTTTAATCTCAGTT-TCA
1 TTATTCTCTAACTCACAGTTTAATCCCAGTTGTCA
* * *
5229221 TTATTCTCTGACTCACGGTTTAATCCCGGTTGTCA
1 TTATTCTCTAACTCACAGTTTAATCCCAGTTGTCA
5229256 TTATT
1 TTATT
5229261 TTTTGACTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (35 bp):
TTATTCTCTAACTCACAGTTTAATCCCAGTTGTCA
Found at i:5229330 original size:35 final size:35
Alignment explanation
Indices: 5228905--5229350 Score: 152
Period size: 35 Copynumber: 12.7 Consensus size: 35
5228895 CTGATCATTG
*
5228905 TTATTTTTTGACTTGTGGTTTAATCTT-GATTGTCAT
1 TTATTTTTTGACTCGTGGTTTAATCTTAG-TTGTC-T
* ** *
5228941 TT-TTTTTTTACTCGTGGTTTAATCTTAGTCATTT
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
* * **** * *
5228975 TTATATTCTGA-TCAACAATTTAATCTTAGTCGTTT
1 TTATTTTTTGACTC-GTGGTTTAATCTTAGTTGTCT
* * * *
5229010 TTATTTTTTGACTTGTGATTTAATCTCAGTTGTTT
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
* * *** ** *
5229045 TTATTTTTTTTAACTAGCAATTTAATC-CCGATTGTCA
1 TTA--TTTTTTGACTCGTGGTTTAATCTTAG-TTGTCT
* * * *
5229082 TTATTCTCTGACTCATGGTTTAAT-TTCGGTTGTCAT
1 TTATTTTTTGACTCGTGGTTTAATCTT-AGTTGTC-T
** * * * * * ** *
5229118 TT-TCCTCTAACTTGTTGTTTAATCCTAGTCATTT
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
* *
5229152 TTATTTTTTGACTCGTAGTTTAATCTT-GATCGTCT
1 TTATTTTTTGACTCGTGGTTTAATCTTAG-TTGTCT
* * * * * *
5229187 TTATTTTCTAACTCATAGTTTAATCTCAGTT-TCA
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
* * ** *** *
5229221 TTATTCTCTGACTCACGGTTTAATCCCGGTTGTCA
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
* * ** * * ** *
5229256 TTATTTTTTGACTTGCGACTCAATCTCAGTCATCG
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
*
5229291 TTATTTTTTGACTTGTGGTTTAATCTTAGTTGTCT
1 TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
* *
5229326 TTATTTTTTGACTCGTAGTTCAATC
1 TTATTTTTTGACTCGTGGTTTAATC
5229351 CTGATCTTTT
Statistics
Matches: 302, Mismatches: 93, Indels: 31
0.71 0.22 0.07
Matches are distributed among these distances:
34 36 0.12
35 230 0.76
36 11 0.04
37 25 0.08
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (35 bp):
TTATTTTTTGACTCGTGGTTTAATCTTAGTTGTCT
Found at i:5229349 original size:70 final size:68
Alignment explanation
Indices: 5229152--5229350 Score: 177
Period size: 70 Copynumber: 2.9 Consensus size: 68
5229142 CTAGTCATTT
* * * * * *
5229152 TTATTTTTTGACTCGTAGTTTAATCTTGATCGTCTTTATTTTCTAACTCATAGTTTAATCTCAGT
1 TTATTTTTTGACTCGTGGTTTAATCTTG-TTGTCTTTATTTTTTGACTCGTAGTTCAATCTCAGT
*
5229217 TTCA
65 ATCA
* * ** ** * *
5229221 TTATTCTCTGACTCACGGTTTAATCCCGGTTGTCATTATTTTTTGACTTGCG-A-CTCAATCTCA
1 TTATTTTTTGACTCGTGGTTTAAT-CTTGTTGTCTTTATTTTTTGAC-T-CGTAGTTCAATCTCA
*
5229284 GTCATCG
63 GT-ATCA
*
5229291 TTATTTTTTGACTTGTGGTTTAATCTTAGTTGTCTTTATTTTTTGACTCGTAGTTCAATC
1 TTATTTTTTGACTCGTGGTTTAATCTT-GTTGTCTTTATTTTTTGACTCGTAGTTCAATC
5229351 CTGATCTTTT
Statistics
Matches: 98, Mismatches: 25, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
68 2 0.02
69 46 0.47
70 49 0.50
71 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.14, T:0.50
Consensus pattern (68 bp):
TTATTTTTTGACTCGTGGTTTAATCTTGTTGTCTTTATTTTTTGACTCGTAGTTCAATCTCAGTA
TCA
Found at i:5229364 original size:139 final size:139
Alignment explanation
Indices: 5229010--5229375 Score: 357
Period size: 139 Copynumber: 2.6 Consensus size: 139
5229000 TTAGTCGTTT
* * * * * * *
5229010 TTATTTTTTGACTTGTGATTTAATCTCAGTTGTTTTTATTTTTTTTAACTAGCAATTTAATCCCG
1 TTATTTTTTGACTTGTGGTTTAATCTTAGTTGTCTTTA--TTTTTTAACTCGTAGTTTAATCCTG
* ** * * *
5229075 ATTGTCATTATTCTCTGACTCATGGTTTAATTTCGGTTGTCATTTTCCTCTAACTTGTTGTTTAA
64 ATT-TCATTATTCTCTGACTCACGGTTTAATCCCGGTTGTCATTTTCCTCTAACTTGTCGCTCAA
**
5229140 TCCTAGTCATTT
128 TCCTAGTCATCG
* * * * * *
5229152 TTATTTTTTGACTCGTAGTTTAATCTT-GATCGTCTTTATTTTCTAACTCATAGTTTAAT-CTCA
1 TTATTTTTTGACTTGTGGTTTAATCTTAG-TTGTCTTTATTTTTTAACTCGTAGTTTAATCCTGA
* * *
5229215 GTTTCATTATTCTCTGACTCACGGTTTAATCCCGGTTGTCATTATT-TTTTGACTTG-CGACTCA
65 -TTTCATTATTCTCTGACTCACGGTTTAATCCCGGTTGTCATT-TTCCTCTAACTTGTCG-CTCA
5229278 AT-CTCAGTCATCG
127 ATCCT-AGTCATCG
* *
5229291 TTATTTTTTGACTTGTGGTTTAATCTTAGTTGTCTTTATTTTTTGACTCGTAGTTCAATCCTGAT
1 TTATTTTTTGACTTGTGGTTTAATCTTAGTTGTCTTTATTTTTTAACTCGTAGTTTAATCCTGAT
* *
5229356 CTT-TTTATTTTCTGACTCAC
66 -TTCATTATTCTCTGACTCAC
5229376 AGTTCAATTT
Statistics
Matches: 182, Mismatches: 34, Indels: 19
0.77 0.14 0.08
Matches are distributed among these distances:
138 3 0.02
139 122 0.67
140 26 0.14
141 1 0.01
142 30 0.16
ACGTcount: A:0.19, C:0.17, G:0.13, T:0.51
Consensus pattern (139 bp):
TTATTTTTTGACTTGTGGTTTAATCTTAGTTGTCTTTATTTTTTAACTCGTAGTTTAATCCTGAT
TTCATTATTCTCTGACTCACGGTTTAATCCCGGTTGTCATTTTCCTCTAACTTGTCGCTCAATCC
TAGTCATCG
Found at i:5229470 original size:35 final size:34
Alignment explanation
Indices: 5229421--5229487 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
5229411 CATCTCGATC
*
5229421 TCTTTATTTCCTGACTTACGATTCAATGCCAGTCG
1 TCTTTATTTCCTGACTCACGATTCAAT-CCAGTCG
*
5229456 TCTTTA-TTCTCTGACTCACGATTTAATCCAGT
1 TCTTTATTTC-CTGACTCACGATTCAATCCAGT
5229488 TCATTTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (34 bp):
TCTTTATTTCCTGACTCACGATTCAATCCAGTCG
Found at i:5229497 original size:35 final size:35
Alignment explanation
Indices: 5229421--5229499 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
5229411 CATCTCGATC
* *
5229421 TCTTTATTTCCTGACTTACGATTCAATGCCAGTCG
1 TCTTTATTTCCTGACTCACGATTCAATGCCAGTCA
*
5229456 TCTTTA-TTCTCTGACTCACGATTTAAT-CCAGTTCA
1 TCTTTATTTC-CTGACTCACGATTCAATGCCAG-TCA
*
5229491 TTTTTATTT
1 TCTTTATTT
5229500 TTTGAATCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 7 0.19
35 28 0.76
36 2 0.05
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (35 bp):
TCTTTATTTCCTGACTCACGATTCAATGCCAGTCA
Found at i:5231031 original size:3 final size:3
Alignment explanation
Indices: 5230980--5231017 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5230970 TTGTTACTTT
*
5230980 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5231018 GATGGTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5231443 original size:14 final size:14
Alignment explanation
Indices: 5231424--5231462 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5231414 TAAACCTTTC
5231424 AAACTCTAAAACTA
1 AAACTCTAAAACTA
* *
5231438 AAACTCTAAATCTC
1 AAACTCTAAAACTA
*
5231452 AAACCCTAAAA
1 AAACTCTAAAA
5231463 TCGAACCCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.21
Consensus pattern (14 bp):
AAACTCTAAAACTA
Found at i:5231521 original size:30 final size:31
Alignment explanation
Indices: 5231450--5231536 Score: 85
Period size: 30 Copynumber: 2.9 Consensus size: 31
5231440 ACTCTAAATC
* *
5231450 TCAAACCCTAAAATC-GAACCCTACAA--CCT
1 TCAAACCCTAAAATCAAAACCTTA-AACCCCT
*
5231479 TCAAACCTTAAAA-CTAAAACCTTAAACCCCT
1 TCAAACCCTAAAATC-AAAACCTTAAACCCCT
*
5231510 T-AAACCCTAAAATCAAAATCTTAAACC
1 TCAAACCCTAAAATCAAAACCTTAAACC
5231537 TTTCAAATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 14 0.29
30 28 0.58
31 5 0.10
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (31 bp):
TCAAACCCTAAAATCAAAACCTTAAACCCCT
Found at i:5231556 original size:22 final size:22
Alignment explanation
Indices: 5231522--5231573 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
5231512 AACCCTAAAA
*
5231522 TCAAAATCTTAAACCTTTCAAA-T
1 TCAAAA-C-TAAACCCTTCAAACT
5231545 TCTAAAACTAAACCCTTCAAACT
1 TC-AAAACTAAACCCTTCAAACT
5231568 TCAAAA
1 TCAAAA
5231574 TTAGAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 16 0.62
23 6 0.23
24 4 0.15
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (22 bp):
TCAAAACTAAACCCTTCAAACT
Found at i:5231619 original size:71 final size:70
Alignment explanation
Indices: 5231524--5231658 Score: 179
Period size: 71 Copynumber: 1.9 Consensus size: 70
5231514 CCCTAAAATC
*
5231524 AAAATCTTAAACCTTTCAAATTCTAAA-ACTAAACCCTTCAAA-CTTCAAAATTAGAAACCTTAA
1 AAAATCTTAAACCTTTCAAATTCTAAACACTAAACCCTTCAAACCCT-AAAATT-GAAACCTTAA
5231587 AATCTTT
64 AATCTTT
*
5231594 AAAACTCTTAAACC-TT-AAGATTTCTAAACTCTAAACCCTTCAAACCCTAAAATTGAAACCTTA
1 AAAA-TCTTAAACCTTTCAA-A-TTCTAAACACTAAACCCTTCAAACCCTAAAATTGAAACCTTA
5231657 AA
63 AA
5231659 CCCTAAAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
69 2 0.03
70 7 0.12
71 27 0.47
72 20 0.34
73 2 0.03
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (70 bp):
AAAATCTTAAACCTTTCAAATTCTAAACACTAAACCCTTCAAACCCTAAAATTGAAACCTTAAAA
TCTTT
Found at i:5231621 original size:25 final size:23
Alignment explanation
Indices: 5231578--5231630 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
5231568 TCAAAATTAG
5231578 AAACCTTAAAATCTTTAAAACTCTT
1 AAACCTTAAAATCTTT-AAACTC-T
*
5231603 AAACCTTAAGAT-TTCTAAACTCT
1 AAACCTTAAAATCTT-TAAACTCT
5231626 AAACC
1 AAACC
5231631 CTTCAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 8 0.31
25 12 0.46
ACGTcount: A:0.43, C:0.23, G:0.02, T:0.32
Consensus pattern (23 bp):
AAACCTTAAAATCTTTAAACTCT
Found at i:5231661 original size:21 final size:21
Alignment explanation
Indices: 5231630--5231683 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
5231620 AACTCTAAAC
**
5231630 CCTTCAAACCCTAAAATTGAAA
1 CCTT-AAACCCTAAAATCAAAA
5231652 CCTTAAACCCTAAAATCAAAA
1 CCTTAAACCCTAAAATCAAAA
*
5231673 CTTTAAACCCT
1 CCTTAAACCCT
5231684 CCAAACCCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (21 bp):
CCTTAAACCCTAAAATCAAAA
Found at i:5245138 original size:19 final size:18
Alignment explanation
Indices: 5245104--5245139 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
5245094 AAAGAATACT
5245104 TTTAAAAAATTAATTAAA
1 TTTAAAAAATTAATTAAA
*
5245122 TTTAAATAAATTTATTAA
1 TTTAAA-AAATTAATTAA
5245140 TAGTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAAAATTAATTAAA
Found at i:5248209 original size:9 final size:9
Alignment explanation
Indices: 5248192--5248229 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
5248182 ATTGTCATGT
*
5248192 AATTATAAA
1 AATTTTAAA
5248201 AATTTT-AA
1 AATTTTAAA
5248209 AATTTTAAA
1 AATTTTAAA
*
5248218 ACTTTTAAA
1 AATTTTAAA
5248227 AAT
1 AAT
5248230 AAATATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTTTAAA
Found at i:5248241 original size:9 final size:8
Alignment explanation
Indices: 5248199--5248245 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
5248189 TGTAATTATA
5248199 AAAATTTT
1 AAAATTTT
5248207 AAAATTTT
1 AAAATTTT
5248215 AAAACTTTT
1 AAAA-TTTT
*
5248224 AAAA--AT
1 AAAATTTT
5248230 AAATATTTT
1 AAA-ATTTT
5248239 AAAATTT
1 AAAATTT
5248246 AAATATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
6 4 0.12
7 1 0.03
8 16 0.48
9 12 0.36
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
AAAATTTT
Found at i:5248255 original size:15 final size:16
Alignment explanation
Indices: 5248192--5248253 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
5248182 ATTGTCATGT
*
5248192 AATTATAAAAATTTTAA
1 AATT-TAAATATTTTAA
5248209 AATTTTAAA-ACTTTTAA
1 AA-TTTAAATA-TTTTAA
*
5248226 AA-ATAAATATTTTAA
1 AATTTAAATATTTTAA
5248241 AATTTAAATATTT
1 AATTTAAATATTT
5248254 AATTATATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 12 0.31
16 11 0.28
17 14 0.36
18 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTAAATATTTTAA
Found at i:5251172 original size:12 final size:13
Alignment explanation
Indices: 5251155--5251183 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5251145 AAAATTTTAT
5251155 TTTCTTTCTT-TC
1 TTTCTTTCTTCTC
5251167 TTTCTTTCTTCTC
1 TTTCTTTCTTCTC
5251180 TTTC
1 TTTC
5251184 AGTCTTTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCTTCTC
Found at i:5251521 original size:104 final size:104
Alignment explanation
Indices: 5251341--5251692 Score: 605
Period size: 104 Copynumber: 3.4 Consensus size: 104
5251331 CTTGAACAGA
* **
5251341 ACCCATTCGACGTTTGCAGCAGCTTCAACATAACTTGATCTTGAACAGAACCCGATCCCTCAACG
1 ACCCATTCGACGTTTGCAGCAGCTTCAACAGAACCCGATCTTGAACAGAACCCGATCCCTCAACG
5251406 AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
66 AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
* *
5251445 ACCCATTCGACGTTTGCAGCAGCTTCAACAGAACCCGATCTTGAACAAAACCCGATCCTTCAACG
1 ACCCATTCGACGTTTGCAGCAGCTTCAACAGAACCCGATCTTGAACAGAACCCGATCCCTCAACG
*
5251510 AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAATAGC
66 AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
** *
5251549 ACCCATTCGACGTTTGCAATAGCTTCAACAGAACCCGATCTTGAACAGAACCTGATCCCTCAACG
1 ACCCATTCGACGTTTGCAGCAGCTTCAACAGAACCCGATCTTGAACAGAACCCGATCCCTCAACG
5251614 AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
66 AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
* *
5251653 ACCCATTCGACGTTTGTAGCAGCTTTAACAGAACCCGATC
1 ACCCATTCGACGTTTGCAGCAGCTTCAACAGAACCCGATC
5251693 CCTCAACAAA
Statistics
Matches: 232, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
104 232 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (104 bp):
ACCCATTCGACGTTTGCAGCAGCTTCAACAGAACCCGATCTTGAACAGAACCCGATCCCTCAACG
AAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
Found at i:5251555 original size:23 final size:23
Alignment explanation
Indices: 5251525--5251571 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5251515 CTGCTCGTTC
5251525 CACCCATTCGACGTTTGCAATAG
1 CACCCATTCGACGTTTGCAATAG
5251548 CACCCATTCGACGTTTGCAATAG
1 CACCCATTCGACGTTTGCAATAG
5251571 C
1 C
5251572 TTCAACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (23 bp):
CACCCATTCGACGTTTGCAATAG
Found at i:5251673 original size:20 final size:21
Alignment explanation
Indices: 5251629--5251673 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
5251619 CTGCTCGTTC
5251629 CACCCATTCGACGTTTGCAGTAG
1 CACCCATTCGACGTTT--AGTAG
5251652 CACCCATTCGACGTTT-GTAG
1 CACCCATTCGACGTTTAGTAG
5251672 CA
1 CA
5251674 GCTTTAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
23 16 0.73
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (21 bp):
CACCCATTCGACGTTTAGTAG
Found at i:5251698 original size:87 final size:87
Alignment explanation
Indices: 5251588--5251779 Score: 339
Period size: 87 Copynumber: 2.2 Consensus size: 87
5251578 AGAACCCGAT
* *
5251588 CTTGAACAGAACCTGATCCCTCAACGAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
1 CTTGAACAGAACCCGATCCCTCAACAAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
*
5251653 ACCCATTCGACGTTTGTAGCAG
66 ACCCATTCGACGTTTGCAGCAG
*
5251675 CTTTAACAGAACCCGATCCCTCAACAAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
1 CTTGAACAGAACCCGATCCCTCAACAAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
*
5251740 ACCCATTCGACGTTTGCAGTAG
66 ACCCATTCGACGTTTGCAGCAG
5251762 CTTGAACAGAACCCGATC
1 CTTGAACAGAACCCGATC
5251780 TTGAACAGAA
Statistics
Matches: 99, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 99 1.00
ACGTcount: A:0.24, C:0.34, G:0.18, T:0.23
Consensus pattern (87 bp):
CTTGAACAGAACCCGATCCCTCAACAAAGCCCTGCTCGTTCCACCCATTCGACGTTTGCAGTAGC
ACCCATTCGACGTTTGCAGCAG
Found at i:5251746 original size:23 final size:23
Alignment explanation
Indices: 5251716--5251762 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5251706 CTGCTCGTTC
5251716 CACCCATTCGACGTTTGCAGTAG
1 CACCCATTCGACGTTTGCAGTAG
5251739 CACCCATTCGACGTTTGCAGTAG
1 CACCCATTCGACGTTTGCAGTAG
5251762 C
1 C
5251763 TTGAACAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (23 bp):
CACCCATTCGACGTTTGCAGTAG
Found at i:5251784 original size:17 final size:17
Alignment explanation
Indices: 5251762--5251796 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5251752 TTTGCAGTAG
5251762 CTTGAACAGAACCCGAT
1 CTTGAACAGAACCCGAT
5251779 CTTGAACAGAACCCGAT
1 CTTGAACAGAACCCGAT
5251796 C
1 C
5251797 CCTCAACGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.31, G:0.17, T:0.17
Consensus pattern (17 bp):
CTTGAACAGAACCCGAT
Found at i:5251929 original size:25 final size:25
Alignment explanation
Indices: 5251901--5251954 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
5251891 GTCTAAATAA
* *
5251901 GAATGCCTTAATTAAATACCTTTAT
1 GAATGCCTAAATTAAATACCCTTAT
5251926 GAATGCCTAAATTAAATACCCTTAT
1 GAATGCCTAAATTAAATACCCTTAT
5251951 GAAT
1 GAAT
5251955 ATTGTGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (25 bp):
GAATGCCTAAATTAAATACCCTTAT
Found at i:5262570 original size:213 final size:213
Alignment explanation
Indices: 5262201--5262592 Score: 739
Period size: 213 Copynumber: 1.8 Consensus size: 213
5262191 GGACCCCCGA
5262201 ATTTTTAGTATCCTACTTTCACGCAATTCACAGGGTTCAACAAGCAATCGATATTTCACGATCAG
1 ATTTTTAGTATCCTACTTTCACGCAATTCACAGGGTTCAACAAGCAATCGATATTTCACGATCAG
5262266 GGGTGTAGTACTATTTGTTGTAGTAGCGGTCCTTATATATCGTATTAACAATCGAAATATGGTCA
66 GGGTGTAGTACTATTTGTTGTAGTAGCGGTCCTTATATATCGTATTAACAATCGAAATATGGTCA
*
5262331 AAAGAAAAAATATCTACTTAACAGGGCTTGACGTGGATTGAACGGTTTATGATAGGTTCTGATAC
131 AAAGAAAAAATATCTACTTAACAGGGCTTGACGTGGATCGAACGGTTTATGATAGGTTCTGATAC
5262396 CACTTGTCATGAGTCGAG
196 CACTTGTCATGAGTCGAG
5262414 ATTTTTAGTATCCTACTTTCACGCAATTCACAGGGTTCAACAAGCAATCGATATTTCACGATCAG
1 ATTTTTAGTATCCTACTTTCACGCAATTCACAGGGTTCAACAAGCAATCGATATTTCACGATCAG
*
5262479 GGGTGTAGTACTATTTGTTGTAGTAGCGGTCCTTATATATCGTATTAACAATCGAAATATGGTCG
66 GGGTGTAGTACTATTTGTTGTAGTAGCGGTCCTTATATATCGTATTAACAATCGAAATATGGTCA
* * *
5262544 AAAGAAAAAATCTCTACTTGACAGGGCTTGACGTTGATCGAACGGTTTA
131 AAAGAAAAAATATCTACTTAACAGGGCTTGACGTGGATCGAACGGTTTA
5262593 GGGCTGACTC
Statistics
Matches: 174, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
213 174 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (213 bp):
ATTTTTAGTATCCTACTTTCACGCAATTCACAGGGTTCAACAAGCAATCGATATTTCACGATCAG
GGGTGTAGTACTATTTGTTGTAGTAGCGGTCCTTATATATCGTATTAACAATCGAAATATGGTCA
AAAGAAAAAATATCTACTTAACAGGGCTTGACGTGGATCGAACGGTTTATGATAGGTTCTGATAC
CACTTGTCATGAGTCGAG
Found at i:5268224 original size:18 final size:17
Alignment explanation
Indices: 5268203--5268260 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
5268193 ATTTATTATA
5268203 AAAATAATTTAATATTTT
1 AAAAT-ATTTAATATTTT
*
5268221 AAAATATTTATTAATTTT
1 AAAATATTTAAT-ATTTT
* *
5268239 ATAAATATTAAATAATTT
1 A-AAATATTTAATATTTT
5268257 AAAA
1 AAAA
5268261 CTTTTATTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 9 0.26
18 16 0.47
19 9 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATATTTAATATTTT
Found at i:5268224 original size:37 final size:36
Alignment explanation
Indices: 5268183--5268269 Score: 88
Period size: 36 Copynumber: 2.4 Consensus size: 36
5268173 TTTTCTAACA
* * *
5268183 TAAAATTATTATTTATTATAAAAATAATTTAATATTT
1 TAAAATTATTATTAATTATAAAAAT-ATTAAATAATT
* *
5268220 TAAAA-TATTTATTAATTTTATAAATATTAAATAATT
1 TAAAATTA-TTATTAATTATAAAAATATTAAATAATT
5268256 TAAAACTT-TTATTA
1 TAAAA-TTATTATTA
5268270 CATATACATT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
36 22 0.52
37 19 0.45
38 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (36 bp):
TAAAATTATTATTAATTATAAAAATATTAAATAATT
Found at i:5268421 original size:21 final size:22
Alignment explanation
Indices: 5268371--5268423 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
5268361 ATTTTAATTT
5268371 TATCATTATAATAATTCATTTAA
1 TATCATTATAATAATT-ATTTAA
* *
5268394 TAT--TTATTATAATT-TTTAG
1 TATCATTATAATAATTATTTAA
5268413 TATCATTATAA
1 TATCATTATAA
5268424 CCAATCTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
19 7 0.28
21 15 0.60
23 3 0.12
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.53
Consensus pattern (22 bp):
TATCATTATAATAATTATTTAA
Found at i:5270122 original size:24 final size:24
Alignment explanation
Indices: 5270095--5270142 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5270085 TTTTATTTTT
5270095 AAAAA-ATTAAATTATTTTATAATA
1 AAAAAGATT-AATTATTTTATAATA
*
5270119 AAAAAGATTAATTTTTTTATAATA
1 AAAAAGATTAATTATTTTATAATA
5270143 TTATTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AAAAAGATTAATTATTTTATAATA
Found at i:5272289 original size:16 final size:17
Alignment explanation
Indices: 5272270--5272303 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5272260 AATTGAATAA
5272270 TAAAATATATT-TAAAT
1 TAAAATATATTGTAAAT
*
5272286 TAAATTATATTGTAAAT
1 TAAAATATATTGTAAAT
5272303 T
1 T
5272304 TGTAATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAAATATATTGTAAAT
Found at i:5272979 original size:21 final size:18
Alignment explanation
Indices: 5272952--5272998 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 18
5272942 AGAATTTGTC
5272952 TATGATGGTAAGAGAGAAGA
1 TATGATGG-AAGAG-GAAGA
5272972 TGATGAT-GAAGAGGAAGA
1 T-ATGATGGAAGAGGAAGA
5272990 TATAGATGG
1 TAT-GATGG
5272999 GGTAATAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.08
18 9 0.38
19 6 0.25
20 2 0.08
21 5 0.21
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (18 bp):
TATGATGGAAGAGGAAGA
Found at i:5273629 original size:16 final size:15
Alignment explanation
Indices: 5273594--5273631 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
5273584 AAAGGTTGAT
*
5273594 CTTTCTTTTCTTTTC
1 CTTTTTTTTCTTTTC
*
5273609 CTTTTTTTTCTTTTT
1 CTTTTTTTTCTTTTC
5273624 CTTTTTTT
1 CTTTTTTT
5273632 GGATAAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
CTTTTTTTTCTTTTC
Found at i:5276596 original size:13 final size:14
Alignment explanation
Indices: 5276578--5276617 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
5276568 ATTAAAAATT
5276578 ATTTATTATTAA-A
1 ATTTATTATTAATA
5276591 ATTTATTGA--AATA
1 ATTTATT-ATTAATA
5276604 ATTTATTATTAATA
1 ATTTATTATTAATA
5276618 TTATTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.13
13 15 0.65
14 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTATTATTAATA
Found at i:5276603 original size:58 final size:58
Alignment explanation
Indices: 5276530--5276641 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 58
5276520 AAAAATTTTG
* *
5276530 AAAATTTTTTAAAATAATATTAATA-TAATTATTA-AAATATTAAAAATTATTTATTATT
1 AAAATTTATTAAAATAAT-TTAATATTAA-TATTATAAATATTAAAAAATATTTATTATT
* * **
5276588 AAAATTTATTGAAATAATTTATTATTAATATTATTGATATTAAAAAATATTTAT
1 AAAATTTATTAAAATAATTTAATATTAATATTATAAATATTAAAAAATATTTAT
5276642 ATTTTAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
57 10 0.22
58 36 0.78
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (58 bp):
AAAATTTATTAAAATAATTTAATATTAATATTATAAATATTAAAAAATATTTATTATT
Found at i:5276609 original size:26 final size:25
Alignment explanation
Indices: 5276557--5276624 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
5276547 TATTAATATA
* *
5276557 ATTATTAAAA-TATTAAAAATTATTT
1 ATTATTAAAATTATT-GAAATAATTT
5276582 ATTATTAAAATTTATTGAAATAATTT
1 ATTATTAAAA-TTATTGAAATAATTT
*
5276608 ATTATTAATATTATTGA
1 ATTATTAAAATTATTGA
5276625 TATTAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 17 0.45
26 17 0.45
27 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
ATTATTAAAATTATTGAAATAATTT
Found at i:5276641 original size:29 final size:28
Alignment explanation
Indices: 5276566--5276641 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 28
5276556 AATTATTAAA
* *
5276566 ATATTAAAAATTATTTATTATTAAAATT
1 ATATTAAAAAATATTTATTAATAAAATT
* * **
5276594 -TATTGAAATAATTTATTATTAATATTATT
1 ATATT-AAAAAATAT-TTATTAATAAAATT
5276623 GATATTAAAAAATATTTAT
1 -ATATTAAAAAATATTTAT
5276642 ATTTTAATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
27 4 0.11
28 6 0.17
29 15 0.42
30 7 0.19
31 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
ATATTAAAAAATATTTATTAATAAAATT
Found at i:5276743 original size:18 final size:18
Alignment explanation
Indices: 5276720--5276796 Score: 91
Period size: 18 Copynumber: 4.2 Consensus size: 18
5276710 ATTATTCTTT
*
5276720 ATATTAAATATTAATATA
1 ATATTAATTATTAATATA
*
5276738 ATATTATTTATTAATATA
1 ATATTAATTATTAATATA
*
5276756 TTAATTAATTATTAATATA
1 AT-ATTAATTATTAATATA
* * *
5276775 ATATTATTTATAAATAAA
1 ATATTAATTATTAATATA
5276793 ATAT
1 ATAT
5276797 ACTAAAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
18 34 0.68
19 16 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTAATTATTAATATA
Found at i:5276743 original size:30 final size:34
Alignment explanation
Indices: 5276709--5276782 Score: 84
Period size: 37 Copynumber: 2.2 Consensus size: 34
5276699 TAAAACAATT
*
5276709 TATTATTCTT-TATATT-A-AA-TATTAATATAA
1 TATTATTATTATATATTAATAATTATTAATATAA
5276739 TATTATTTATTAATATATTAATTAATTATTAATATAA
1 TATTA-TTATT-ATATATTAA-TAATTATTAATATAA
5276776 TATTATT
1 TATTATT
5276783 TATAAATAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
30 5 0.14
31 4 0.11
33 6 0.17
34 1 0.03
36 4 0.11
37 16 0.44
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (34 bp):
TATTATTATTATATATTAATAATTATTAATATAA
Found at i:5276768 original size:26 final size:25
Alignment explanation
Indices: 5276721--5276769 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 25
5276711 TTATTCTTTA
5276721 TATTAAATATTAATATAATATTATT
1 TATTAAATATTAATATAATATTATT
5276746 TATTAATATATTAAT-TAATTATTA
1 TATTAA-ATATTAATATAA-TATTA
5276770 ATATAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTAAATATTAATATAATATTATT
Found at i:5285050 original size:24 final size:24
Alignment explanation
Indices: 5285023--5285074 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
5285013 TAGACAACGA
*
5285023 AACTCACTTTTTTGCTACTTTTTC
1 AACTCACCTTTTTGCTACTTTTTC
* *
5285047 AACTTACCTTTTTGCTATTTTTTC
1 AACTCACCTTTTTGCTACTTTTTC
5285071 AACT
1 AACT
5285075 ATGTTTACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.23, G:0.04, T:0.54
Consensus pattern (24 bp):
AACTCACCTTTTTGCTACTTTTTC
Found at i:5286997 original size:24 final size:24
Alignment explanation
Indices: 5286965--5287014 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
5286955 GACAATGAAG
*
5286965 CTCACTTTTTTGCTATTTTTTCAA
1 CTCACTTTTTTGCTATCTTTTCAA
5286989 CTCACTTTTTTGCTATCTTTTCAA
1 CTCACTTTTTTGCTATCTTTTCAA
5287013 CT
1 CT
5287015 ATGTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (24 bp):
CTCACTTTTTTGCTATCTTTTCAA
Found at i:5302894 original size:14 final size:13
Alignment explanation
Indices: 5302876--5302900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5302866 TTCCTTTAAA
5302876 AAAAAAAGAAAAC
1 AAAAAAAGAAAAC
5302889 AAAAAAAGAAAA
1 AAAAAAAGAAAA
5302901 TTTTAAGTTT
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:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAC
Found at i:5306552 original size:14 final size:13
Alignment explanation
Indices: 5306529--5306576 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
5306519 AAAAACAAAA
*
5306529 AAAAAAAAAAGAG
1 AAAAAGAAAAGAG
*
5306542 AAAGAAGAAAAAAG
1 AAA-AAGAAAAGAG
5306556 AAAAA-AGAAAGAG
1 AAAAAGA-AAAGAG
5306569 AAAAAGAA
1 AAAAAGAA
5306577 GTTTTCTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 1 0.03
13 16 0.55
14 12 0.41
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAG
Found at i:5306552 original size:29 final size:27
Alignment explanation
Indices: 5306520--5306576 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5306510 TGAATTTACA
5306520 AAAACAAAAAAAAAAAAAAGAGAAAGAAG
1 AAAA-AAAAAAAAAAAAAAGAGAAA-AAG
* *
5306549 -AAAAAAGAAAAAAGAAAGAGAAAAAG
1 AAAAAAAAAAAAAAAAAAGAGAAAAAG
5306575 AA
1 AA
5306577 GTTTTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 3 0.12
27 19 0.76
28 3 0.12
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAAAAAAAAAAGAGAAAAAG
Found at i:5306554 original size:17 final size:15
Alignment explanation
Indices: 5306519--5306565 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
5306509 GTGAATTTAC
* *
5306519 AAAAACAAAAAAAAA
1 AAAAAGAAAAAAAGA
*
5306534 AAAAAGAGAAAGAAGA
1 AAAAAGA-AAAAAAGA
5306550 AAAAAG-AAAAAAGA
1 AAAAAGAAAAAAAGA
5306564 AA
1 AA
5306566 GAGAAAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:5306554 original size:21 final size:20
Alignment explanation
Indices: 5306527--5306573 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
5306517 ACAAAAACAA
*
5306527 AAAAAAAAAAAAGAGAAAGAAG
1 AAAAAAGAAAAA-AGAAAG-AG
5306549 AAAAAAGAAAAAAGAAAGAG
1 AAAAAAGAAAAAAGAAAGAG
5306569 AAAAA
1 AAAAA
5306574 GAAGTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 7 0.29
21 6 0.25
22 11 0.46
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAAAAGAAAGAG
Found at i:5306562 original size:7 final size:7
Alignment explanation
Indices: 5306526--5306565 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
5306516 TACAAAAACA
*
5306526 AAAAAAA
1 AAAAAAG
5306533 AAAAAAG
1 AAAAAAG
5306540 AGAAAGAAG
1 A-AAA-AAG
5306549 AAAAAAG
1 AAAAAAG
5306556 AAAAAAG
1 AAAAAAG
5306563 AAA
1 AAA
5306566 GAGAAAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 20 0.67
8 6 0.20
9 4 0.13
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:5306577 original size:29 final size:25
Alignment explanation
Indices: 5306525--5306576 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 25
5306515 TTACAAAAAC
5306525 AAAAAAAAAAAAAAGAGAAAGAAGA
1 AAAAAAAAAAAAAAGAGAAAGAAGA
5306550 AAAAAGAAAAAAGAAAGAGAAA-AAGA
1 AAAAA-AAAAAA-AAAGAGAAAGAAGA
5306576 A
1 A
5306577 GTTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 5 0.20
26 11 0.44
27 9 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAAAAGAGAAAGAAGA
Found at i:5307650 original size:18 final size:18
Alignment explanation
Indices: 5307629--5307664 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5307619 AAAATAAAAC
5307629 AAGAAAAAA-AAGAGCAAA
1 AAGAAAAAACAA-AGCAAA
5307647 AAGAAAAAACAAAGCAAA
1 AAGAAAAAACAAAGCAAA
5307665 CTAAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (18 bp):
AAGAAAAAACAAAGCAAA
Found at i:5308868 original size:26 final size:26
Alignment explanation
Indices: 5308837--5308893 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5308827 TATCATATGT
* *
5308837 ATCATAACTAAAG-CATTTGCATTTGC
1 ATCATAA-AAAAGACATTTACATTTGC
5308863 ATCATAAAAAAGACATTTACATTTGC
1 ATCATAAAAAAGACATTTACATTTGC
5308889 ATCAT
1 ATCAT
5308894 GACATCTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (26 bp):
ATCATAAAAAAGACATTTACATTTGC
Found at i:5309456 original size:32 final size:32
Alignment explanation
Indices: 5309295--5309457 Score: 139
Period size: 32 Copynumber: 5.1 Consensus size: 32
5309285 ATTTAAGCTA
* *
5309295 AGTCAAGCTGGCACCCAAATTAAAC-AAAGCT
1 AGTCAAGCTGGCACCCAAATCAAACTAAACCT
* * *
5309326 CAGTCAAGCTGGCATCCAGATCAAACTAAACTT
1 -AGTCAAGCTGGCACCCAAATCAAACTAAACCT
* * * * * *
5309359 AGTCTAGCTAGCACCCAGATCAAATTAATCCC
1 AGTCAAGCTGGCACCCAAATCAAACTAAACCT
* * * * * *
5309391 AATCAAGTTGGCACTCAAATTAAATTAAGCCT
1 AGTCAAGCTGGCACCCAAATCAAACTAAACCT
* *
5309423 AGTCAAACTGGCACCCAAATCAAACCAAACCT
1 AGTCAAGCTGGCACCCAAATCAAACTAAACCT
5309455 AGT
1 AGT
5309458 TAAGTTAGCA
Statistics
Matches: 101, Mismatches: 29, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
32 97 0.96
33 4 0.04
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.20
Consensus pattern (32 bp):
AGTCAAGCTGGCACCCAAATCAAACTAAACCT
Found at i:5309467 original size:96 final size:96
Alignment explanation
Indices: 5309297--5309501 Score: 227
Period size: 96 Copynumber: 2.1 Consensus size: 96
5309287 TTAAGCTAAG
* * * * *
5309297 TCAAGCTGGCACCCAAATTAAACAAAGCTCAGTCAAGCTGGCATCCAGATCAAACTAAACTTAGT
1 TCAAGCTGGCACCCAAATTAAACAAAGCTCAGTCAAACTGGCACCCAAATCAAACCAAACCTAGT
5309362 CTAGCTAGCACCCAGATCAAATTAATCCCAA
66 CTAGCTAGCACCCAGATCAAATTAATCCCAA
* * **
5309393 TCAAGTTGGCACTCAAATTAAATTAAGC-CTAGTCAAACTGGCACCCAAATCAAACCAAACCTAG
1 TCAAGCTGGCACCCAAATTAAACAAAGCTC-AGTCAAACTGGCACCCAAATCAAACCAAACCTAG
* * * * *
5309457 T-TAAGTTAGCACCTAGATTAAACTAAGCCCAGA
65 TCT-AGCTAGCACCCAGATCAAATTAATCCCA-A
*
5309490 T-TAGCTGGCACC
1 TCAAGCTGGCACC
5309502 TAAACTAATC
Statistics
Matches: 89, Mismatches: 17, Indels: 6
0.79 0.15 0.05
Matches are distributed among these distances:
95 2 0.02
96 85 0.96
97 2 0.02
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (96 bp):
TCAAGCTGGCACCCAAATTAAACAAAGCTCAGTCAAACTGGCACCCAAATCAAACCAAACCTAGT
CTAGCTAGCACCCAGATCAAATTAATCCCAA
Found at i:5309532 original size:22 final size:22
Alignment explanation
Indices: 5309507--5309554 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5309497 GCACCTAAAC
* * *
5309507 TAATCTCTAAGACCTCTATGCA
1 TAATCACTAAGACCTCCAGGCA
*
5309529 TAATCACTAAGATCTCCAGGCA
1 TAATCACTAAGACCTCCAGGCA
5309551 TAAT
1 TAAT
5309555 TTTCAAGAAC
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:0.35, C:0.25, G:0.10, T:0.29
Consensus pattern (22 bp):
TAATCACTAAGACCTCCAGGCA
Found at i:5310146 original size:13 final size:13
Alignment explanation
Indices: 5310128--5310152 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5310118 TTTAATTTTA
5310128 TTATTATTATTAT
1 TTATTATTATTAT
5310141 TTATTATTATTA
1 TTATTATTATTA
5310153 ATCAAAATAA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:5314246 original size:12 final size:13
Alignment explanation
Indices: 5314229--5314260 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5314219 AAAATATTTA
5314229 ATTTTTAAAA-AT
1 ATTTTTAAAACAT
5314241 ATTTTTAAAACAT
1 ATTTTTAAAACAT
5314254 -TTTTTAA
1 ATTTTTAA
5314261 TATGGGAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.89
13 2 0.11
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTTTAAAACAT
Found at i:5315684 original size:21 final size:22
Alignment explanation
Indices: 5315643--5315685 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5315633 AAATTTTTTA
5315643 TTTTAAAATATTTAATGAATATT
1 TTTTAAAATATTTAA-GAATATT
5315666 TTTTAAAA-ATTATAA-AATAT
1 TTTTAAAATATT-TAAGAATAT
5315686 ATTTAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTAAAATATTTAAGAATATT
Found at i:5316347 original size:11 final size:11
Alignment explanation
Indices: 5316331--5316355 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5316321 AATATTTTCA
5316331 TTAGATAAATT
1 TTAGATAAATT
5316342 TTAGATAAATT
1 TTAGATAAATT
5316353 TTA
1 TTA
5316356 TTCATATACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
TTAGATAAATT
Found at i:5316564 original size:18 final size:18
Alignment explanation
Indices: 5316541--5316581 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5316531 ATACCAATCT
** *
5316541 TTTTTTTTTCTCTTTTTC
1 TTTTTTTTTAACTTTTCC
5316559 TTTTTTTTTAACTTTTCC
1 TTTTTTTTTAACTTTTCC
5316577 TTTTT
1 TTTTT
5316582 CCTTCTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTTTAACTTTTCC
Found at i:5316671 original size:8 final size:9
Alignment explanation
Indices: 5316657--5316681 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5316647 TGCAAAGTAT
5316657 TTTTTTTAC
1 TTTTTTTAC
5316666 TTTTTTTAC
1 TTTTTTTAC
5316675 TTTTTTT
1 TTTTTTT
5316682 TATATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTAC
Found at i:5323413 original size:2 final size:2
Alignment explanation
Indices: 5323406--5323449 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5323396 TCTGAACACA
5323406 AT AT AT AT AT AT AT -T 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
5323447 AT A
1 AT A
5323450 GATTGAATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5331282 original size:1 final size:1
Alignment explanation
Indices: 5331276--5331301 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5331266 GAAAGATGGG
5331276 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5331302 GTGCTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5334079 original size:21 final size:22
Alignment explanation
Indices: 5334039--5334081 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5334029 TATATAATAA
**
5334039 AATTTTAAAATTAATTTAATTT
1 AATTTTAAAATTAAGATAATTT
5334061 AATTTT-AAATTAAGATAATTT
1 AATTTTAAAATTAAGATAATTT
5334082 TAGATGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTTTAAAATTAAGATAATTT
Found at i:5334627 original size:23 final size:23
Alignment explanation
Indices: 5334601--5334661 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
5334591 TAGATATCTC
*
5334601 AAAATTATATTTTTTTA-ACATTT
1 AAAATTATAATTTTTTATA-ATTT
* * *
5334624 AAAACTTTTACTTTTTTATATTTT
1 AAAA-TTATAATTTTTTATAATTT
5334648 AAAATTATAATTTT
1 AAAATTATAATTTT
5334662 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 12 0.39
24 18 0.58
25 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
AAAATTATAATTTTTTATAATTT
Found at i:5334670 original size:23 final size:24
Alignment explanation
Indices: 5334621--5334671 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
5334611 TTTTTTAACA
* * *
5334621 TTTAAAACTTTTACTTTTTTATAT
1 TTTAAAACTTATAATTTTATATAT
*
5334645 TTTAAAA-TTATAATTTTATATTT
1 TTTAAAACTTATAATTTTATATAT
5334668 TTTA
1 TTTA
5334672 TTTTTTAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTAAAACTTATAATTTTATATAT
Found at i:5335073 original size:55 final size:58
Alignment explanation
Indices: 5334983--5335094 Score: 140
Period size: 55 Copynumber: 2.0 Consensus size: 58
5334973 TATATCCATT
* * *
5334983 TTCACTTATATCCAAAAAAAGAAGGTTTATTGTGTCT-T-AAATTTATGAATAAAATA
1 TTCACTTATATCCAAAAAAAGAAAGTTTATTGTGTCTATGAAATTTACGAAAAAAATA
* * * *
5335039 TTCATTTATATTC-AAAAATGAAAGTTTTTTGTGTCTATGAAATTTACGAAAAAAAT
1 TTCACTTATATCCAAAAAAAGAAAGTTTATTGTGTCTATGAAATTTACGAAAAAAAT
5335095 TAATTAATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
55 20 0.43
56 12 0.26
57 15 0.32
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (58 bp):
TTCACTTATATCCAAAAAAAGAAAGTTTATTGTGTCTATGAAATTTACGAAAAAAATA
Found at i:5335109 original size:55 final size:55
Alignment explanation
Indices: 5334997--5335110 Score: 126
Period size: 55 Copynumber: 2.1 Consensus size: 55
5334987 CTTATATCCA
* * * *
5334997 AAAAAAGAAGGTTTATTGTGTCTTAAATTTATGAATAAAATATTCATTTATATTC
1 AAAAAAGAAAGTTTATTGTGTCTTAAATTTACGAATAAAATATTAATTAATATTC
* *
5335052 AAAAATGAAAGTTTTTTGTGTCTATGAAATTTACGAA-AAAA-ATTAATTAATGA-TC
1 AAAAAAGAAAGTTTATTGTGTCT-T-AAATTTACGAATAAAATATTAATTAAT-ATTC
5335107 AAAA
1 AAAA
5335111 TTTAATTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
55 34 0.68
56 6 0.12
57 10 0.20
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (55 bp):
AAAAAAGAAAGTTTATTGTGTCTTAAATTTACGAATAAAATATTAATTAATATTC
Found at i:5342834 original size:120 final size:120
Alignment explanation
Indices: 5342619--5342852 Score: 378
Period size: 120 Copynumber: 1.9 Consensus size: 120
5342609 TACTTAGGGA
* * * ** *
5342619 TTTTCCTGAGCTTATATATTCACAATTTCTAGCAGCATTGACTGTACTATTGAGATTTAGAGACA
1 TTTTCCTGAGCTTATATATTCACAAATCCTAGCACCATCAACTGTACTATTGAGATTTAGACACA
5342684 ATATCTCTGCATTTCTTTTATTGATATTTCTGTTTTATGCAGGTTGGAATTTGGG
66 ATATCTCTGCATTTCTTTTATTGATATTTCTGTTTTATGCAGGTTGGAATTTGGG
*
5342739 TTTTCCTGAGCTTATATATTCACAAATCCTAGCACCATCAACTGTACTGTTGAGATTTAGACACA
1 TTTTCCTGAGCTTATATATTCACAAATCCTAGCACCATCAACTGTACTATTGAGATTTAGACACA
* * *
5342804 ATGTTTCTGCATTTCTTTTATTGATGTTTCTGTTTTATGCAGGTTGGAA
66 ATATCTCTGCATTTCTTTTATTGATATTTCTGTTTTATGCAGGTTGGAA
5342853 CATATTGATG
Statistics
Matches: 104, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 104 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (120 bp):
TTTTCCTGAGCTTATATATTCACAAATCCTAGCACCATCAACTGTACTATTGAGATTTAGACACA
ATATCTCTGCATTTCTTTTATTGATATTTCTGTTTTATGCAGGTTGGAATTTGGG
Found at i:5345319 original size:24 final size:24
Alignment explanation
Indices: 5345288--5345338 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5345278 GATCAAATTA
5345288 AAAAAAAAAGATTAAATTTTAGAT
1 AAAAAAAAAGATTAAATTTTAGAT
5345312 AAAAAAAAAGATTAAATTTTAGAT
1 AAAAAAAAAGATTAAATTTTAGAT
5345336 AAA
1 AAA
5345339 TTTATTGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (24 bp):
AAAAAAAAAGATTAAATTTTAGAT
Found at i:5345477 original size:59 final size:59
Alignment explanation
Indices: 5345372--5345486 Score: 137
Period size: 59 Copynumber: 1.9 Consensus size: 59
5345362 ATATATTTTA
* **
5345372 TTAATTTAAGTTTATATTTATATATAAAAATTATATTGATAAAATTATTATATAATATT
1 TTAATTTAAGTTTATATTTATATATAAAAATTATATTAATAAAATTAAGATATAATATT
* *
5345431 TTAATTTAAGATATTA-ATTTA-ATA-AAATATTATATTAAATATAATTAAGATATAAT
1 TTAATTTAAG-T-TTATATTTATATATAAAAATTATATT-AATAAAATTAAGATATAAT
5345487 TTATATAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
58 11 0.23
59 28 0.58
60 6 0.12
61 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (59 bp):
TTAATTTAAGTTTATATTTATATATAAAAATTATATTAATAAAATTAAGATATAATATT
Found at i:5348180 original size:2 final size:2
Alignment explanation
Indices: 5348173--5348201 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5348163 TCCATTTCTT
5348173 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
5348202 TCATTATGTT
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:5349749 original size:31 final size:33
Alignment explanation
Indices: 5349714--5349784 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 33
5349704 TCTTGCGTCG
* *
5349714 TAATTGTGTAATTGTGTTTTAT-GAT-TAGATT
1 TAATTGTGTAATTATGTTTTATAGATAAAGATT
*
5349745 TAATTGTGTAATTATGTTTTATAGATAAAGTTT
1 TAATTGTGTAATTATGTTTTATAGATAAAGATT
5349778 TAATTGT
1 TAATTGT
5349785 AAAACAACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 21 0.60
32 3 0.09
33 11 0.31
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.54
Consensus pattern (33 bp):
TAATTGTGTAATTATGTTTTATAGATAAAGATT
Found at i:5365943 original size:15 final size:15
Alignment explanation
Indices: 5365923--5365953 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5365913 CTTATGAGTT
5365923 ACTTAGGCATTTGTC
1 ACTTAGGCATTTGTC
5365938 ACTTAGGCATTTGTC
1 ACTTAGGCATTTGTC
5365953 A
1 A
5365954 ATTAACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (15 bp):
ACTTAGGCATTTGTC
Found at i:5368124 original size:15 final size:15
Alignment explanation
Indices: 5368082--5368129 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
5368072 TTTATTTTAA
*
5368082 AATTTATTTATT-TA
1 AATTTATTTATTATT
*
5368096 AATTTGTTTGATTATT
1 AATTTATTT-ATTATT
*
5368112 ATTTTATTTATTATT
1 AATTTATTTATTATT
5368127 AAT
1 AAT
5368130 AAATATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 8 0.30
15 11 0.41
16 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (15 bp):
AATTTATTTATTATT
Found at i:5376348 original size:171 final size:168
Alignment explanation
Indices: 5376004--5376420 Score: 414
Period size: 169 Copynumber: 2.4 Consensus size: 168
5375994 ATAACTCGAT
* * * * * * *
5376004 CAAAAAGCTCGAATTCAGCTCGGTCAAAAGAGCTGGGATCTATGAAATG-CTTTCATAAAGGCCC
1 CAAAGAGCTCGGACTCAGCTTGATCAAAAGAG-TTGGATCTATGAAATGCCTTT-ATAAAGGCTC
* * * * * *
5376068 AATTCGATAAAATAGTTTGCTAAAGAGTTCAGATTCAGTTCGGCCAAAAGAGCTATGATCTATGA
64 AATTCGATAAAATAGTTGGCTAAAAAGCTCAGACTCAGCTCGGCCAAAAGAGCTATGATCTATCA
* *
5376133 AATGTACTCATAAAGGTCCAATTCGAGAAAACATCTCAGC
129 AATATACTCATAAAGGTCCAATTCGACAAAACATCTCAGC
* *
5376173 CAAAGAGCTCGGACTCAGCTTGATCAAAAGAGTTCGGATCTATGAAATGCCTTTACAAATGCTCA
1 CAAAGAGCTCGGACTCAGCTTGATCAAAAGAGTT-GGATCTATGAAATGCCTTTATAAAGGCTCA
* * *
5376238 ATTCGGTAAAATAGTTCGGCTAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCA-GATCTA-
65 ATTCGATAAAATAGTT-GGCT-AAAAAGCTCAGACTCAGCTCGGCCAAAAGAGCT-ATGATCTAT
**
5376301 CAAA-ATACTTTCATAAAGG-CTCAATTCGACAAAACATCTTGGC
127 CAAATATAC--TCATAAAGGTC-CAATTCGACAAAACATCTCAGC
* * * * * *
5376344 CAAAGAAACTCGGTCTTAGCTCTGCT-AAAAGAGCTTGGATCTACGAAATGCATTTATAAAGGCT
1 CAAAG-AGCTCGGACTCAGCT-TGATCAAAAGAG-TTGGATCTATGAAATGCCTTTATAAAGGCT
* *
5376408 CAACTCAATAAAA
63 CAATTCGATAAAA
5376421 GAGCTCGTCC
Statistics
Matches: 204, Mismatches: 33, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
168 1 0.00
169 67 0.33
170 11 0.05
171 66 0.32
172 54 0.26
173 5 0.02
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (168 bp):
CAAAGAGCTCGGACTCAGCTTGATCAAAAGAGTTGGATCTATGAAATGCCTTTATAAAGGCTCAA
TTCGATAAAATAGTTGGCTAAAAAGCTCAGACTCAGCTCGGCCAAAAGAGCTATGATCTATCAAA
TATACTCATAAAGGTCCAATTCGACAAAACATCTCAGC
Found at i:5376433 original size:86 final size:85
Alignment explanation
Indices: 5375917--5376443 Score: 300
Period size: 86 Copynumber: 6.2 Consensus size: 85
5375907 GAAACGGTAT
* * * * ** * * * *
5375917 GGCCAAAAGAGCTCGAACTTAGTTCGATCAAAAGAGCTCGAATCTACCAAATGCCTTCATAAAGG
1 GGCCAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCGGATCTACGAAATG-CTTTATAAAGG
* * * *
5375982 CCCAATT--ACAAAATAACTC
65 CTCAATTCGATAAAACAGCTC
** * * * * * *
5376001 GATC-AAAAAGCTCGAATTCAGCTCGGTCAAAAGAGCTGGGATCTATGAAATGCTTTCATAAAGG
1 GGCCAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCGGATCTACGAAATGCTTT-ATAAAGG
* * *
5376065 CCCAATTCGATAAAATAG-TT
65 CTCAATTCGATAAAACAGCTC
* * * * * * * * ** * *
5376085 TG-CTAAAGAGTTCAGATTCAGTTCGGCCAAAAGAGCTATGATCTATGAAATG-TACTCATAAAG
1 GGCCAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCGGATCTACGAAATGCT--TTATAAAG
* *
5376148 G-TCCAATTCGAGAAAACATCTC
64 GCT-CAATTCGATAAAACAGCTC
* * * ** * * *
5376170 AGCC-AAAGAGCTCGGACTCAGCTTGATCAAAAGAGTTCGGATCTATGAAATGCCTTTACAAATG
1 GGCCAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCGGATCTACGAAATG-CTTTATAAAGG
* * *
5376234 CTCAATTCGGTAAAATAGTTC
65 CTCAATTCGATAAAACAGCTC
* * * *
5376255 GGCTAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCAGATCTACAAAATACTTTCATAAAGG
1 GGCCAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCGGATCTACGAAATGCTTT-ATAAAGG
* * *
5376320 CTCAATTCGACAAAACATCTT
65 CTCAATTCGATAAAACAGCTC
* * * *
5376341 GGCCAAAGAAA-CTCGGTCTTAGCTCTGCTAAAAGAGCTT-GGATCTACGAAATGCATTTATAAA
1 GGCCAAA-AAAGCTCGGACTCAGCTCGGCCAAAAGAG-TTCGGATCTACGAAATGC-TTTATAAA
* * *
5376404 GGCTCAACTCAATAAAAGAGCTC
63 GGCTCAATTCGATAAAACAGCTC
* *
5376427 GTCCAAAAGAGCTCGGA
1 GGCCAAAAAAGCTCGGA
5376444 TCTACGAAAT
Statistics
Matches: 340, Mismatches: 85, Indels: 34
0.74 0.19 0.07
Matches are distributed among these distances:
82 3 0.01
83 55 0.16
84 63 0.19
85 76 0.22
86 134 0.39
87 9 0.03
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (85 bp):
GGCCAAAAAAGCTCGGACTCAGCTCGGCCAAAAGAGTTCGGATCTACGAAATGCTTTATAAAGGC
TCAATTCGATAAAACAGCTC
Found at i:5376487 original size:61 final size:61
Alignment explanation
Indices: 5376361--5376495 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
5376351 ACTCGGTCTT
* * * * *
5376361 AGCTCTGCTAAAAGAGCTTGGATCTACGAAATGCATTTATAAAGGCTCAACTCAATAAAAG
1 AGCTCAGCCAAAAGAGCTCGGATCTACGAAATGCATTTATAAAGGCTCAACTCAACAAAAC
* * * **
5376422 AGCTC-GTCCAAAAGAGCTCGGATCTACGAAATG-TTTTCATAAAGGTTTAACTTGACAAAAC
1 AGCTCAG-CCAAAAGAGCTCGGATCTACGAAATGCATTT-ATAAAGGCTCAACTCAACAAAAC
5376483 AGCTCAGCCAAAA
1 AGCTCAGCCAAAA
5376496 AGTTCGAACT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
60 4 0.06
61 57 0.92
62 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (61 bp):
AGCTCAGCCAAAAGAGCTCGGATCTACGAAATGCATTTATAAAGGCTCAACTCAACAAAAC
Found at i:5376835 original size:19 final size:19
Alignment explanation
Indices: 5376799--5376857 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
5376789 TTAGTTTAGC
5376799 CAAAAGAGCTCAGCTCGG-
1 CAAAAGAGCTCAGCTCGGT
5376817 CTAAAAGAGCTCA-CTTCGGT
1 C-AAAAGAGCTCAGC-TCGGT
* *
5376837 CAAAAGAACTCATCTCGGT
1 CAAAAGAGCTCAGCTCGGT
5376856 CA
1 CA
5376858 TCTCGATCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 2 0.06
19 32 0.89
20 2 0.06
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (19 bp):
CAAAAGAGCTCAGCTCGGT
Found at i:5377037 original size:121 final size:121
Alignment explanation
Indices: 5376817--5377085 Score: 355
Period size: 121 Copynumber: 2.2 Consensus size: 121
5376807 CTCAGCTCGG
* * *
5376817 CTAAAAGAGCTCACTTCGGTCAAAAGAACTCATCTCGGTCATCTCGATCAAAGAGCTTATCTTGA
1 CTAAAAGAGCTCACTTCGATCAAAAGAACTCATCTCGGTAATCTCGATCAAAGAGCTCATCTTGA
* * * * *
5376882 TAAATTATCTACATAAAGGCTTGGCTGGATCACCTTGGCCAATGTGATTAACTAGA
66 TAAATTACCTACATAAAGGCTTGGCTGGACCACCTCGACCAAAGTGATTAACTAGA
* * *
5376938 CTAAAAGAGCTCACCTT-GATCAAAAGAATTCATCTCGGTAATCTTGGTCAAAGAGCTCAT-TTC
1 CTAAAAGAGCTCA-CTTCGATCAAAAGAACTCATCTCGGTAATCTCGATCAAAGAGCTCATCTT-
* *
5377001 GATAAATTGCCTACATGAAGGCTTGGCTAGG-CCACCTCGACCAAAGTGATTAACTAGA
64 GATAAATTACCTACATAAAGGCTTGGCT-GGACCACCTCGACCAAAGTGATTAACTAGA
* *
5377059 CTAAAAGAGCTCATTTCGGTCAAAAGA
1 CTAAAAGAGCTCACTTCGATCAAAAGA
5377086 GTTAATCTTG
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
120 4 0.03
121 120 0.93
122 5 0.04
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (121 bp):
CTAAAAGAGCTCACTTCGATCAAAAGAACTCATCTCGGTAATCTCGATCAAAGAGCTCATCTTGA
TAAATTACCTACATAAAGGCTTGGCTGGACCACCTCGACCAAAGTGATTAACTAGA
Found at i:5384890 original size:24 final size:23
Alignment explanation
Indices: 5384863--5384921 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
5384853 TTATTTCTAA
*
5384863 AATTTTTTTAAAGTTTCATTTTAT
1 AATTTTTTTAAAGTTTCATCTT-T
* *
5384887 AATTTTTAT-AATTTTCATCTTT
1 AATTTTTTTAAAGTTTCATCTTT
5384909 AATTTTTTCTAAA
1 AATTTTTT-TAAA
5384922 ATTTAATCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 8 0.28
23 11 0.38
24 10 0.34
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.61
Consensus pattern (23 bp):
AATTTTTTTAAAGTTTCATCTTT
Found at i:5384911 original size:22 final size:22
Alignment explanation
Indices: 5384867--5384915 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5384857 TTCTAAAATT
*
5384867 TTTTTAAAGTTTCATTTTATAA
1 TTTTTAAAGTTTCATCTTATAA
*
5384889 TTTTTATAATTTTCATCTT-TAA
1 TTTTTA-AAGTTTCATCTTATAA
5384911 TTTTT
1 TTTTT
5384916 TCTAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTTAAAGTTTCATCTTATAA
Found at i:5384977 original size:21 final size:22
Alignment explanation
Indices: 5384953--5385006 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
5384943 TTAAAACAAA
*
5384953 ATAAATAAAGAAAAT-AATAAC
1 ATAAATAAAAAAAATAAATAAC
*
5384974 ATAAA-ACAAAAAAATAAATACC
1 ATAAATA-AAAAAAATAAATAAC
5384996 A-AAATAAAAAA
1 ATAAATAAAAAA
5385007 CCTGTTCGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 20 0.71
22 7 0.25
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (22 bp):
ATAAATAAAAAAAATAAATAAC
Found at i:5384990 original size:13 final size:14
Alignment explanation
Indices: 5384944--5385003 Score: 59
Period size: 16 Copynumber: 4.0 Consensus size: 14
5384934 ATAATATTTT
5384944 TAAAACAAAATAAA
1 TAAAACAAAATAAA
*
5384958 TAAAGAAAATAATAACA
1 TAAA-ACAA-AATAA-A
5384975 TAAAACAAAA-AAA
1 TAAAACAAAATAAA
5384988 TAAATACCAAAATAAA
1 TAAA-A-CAAAATAAA
5385004 AAACCTGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.13
14 7 0.18
15 10 0.26
16 11 0.29
17 5 0.13
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (14 bp):
TAAAACAAAATAAA
Found at i:5386424 original size:33 final size:32
Alignment explanation
Indices: 5386390--5386452 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
5386380 TCGTAAAAAT
* *
5386390 TTTTAAATTTGCAAGGATTTGATTCGCAAGAA
1 TTTTAAATTTACAAGAATTTGATTCGCAAGAA
** *
5386422 TTTTAGGTTTACAAGAATTTGATTCTCAAGA
1 TTTTAAATTTACAAGAATTTGATTCGCAAGA
5386453 GTTCAGGTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (32 bp):
TTTTAAATTTACAAGAATTTGATTCGCAAGAA
Found at i:5387168 original size:17 final size:18
Alignment explanation
Indices: 5387127--5387168 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
5387117 GAAATATATA
* *
5387127 TATATATATGTTGTATTT
1 TATATATATGTTGAAATT
5387145 TACTATATATG-TGAAATT
1 TA-TATATATGTTGAAATT
5387163 TATATA
1 TATATA
5387169 AGATAGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 9 0.43
19 8 0.38
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (18 bp):
TATATATATGTTGAAATT
Found at i:5400158 original size:18 final size:17
Alignment explanation
Indices: 5400136--5400319 Score: 103
Period size: 18 Copynumber: 10.5 Consensus size: 17
5400126 ATTTTACCTT
5400136 TAAATAATATTATATTAA
1 TAAATAATATTA-ATTAA
* *
5400154 CAAATCATATATTAATAAA
1 TAAAT-A-ATATTAATTAA
* *
5400173 TAATATACTATTAATAAA
1 TAA-ATAATATTAATTAA
* * *
5400191 CAATATTATAATATATTAA
1 TAA-ATAATATTA-ATTAA
*
5400210 TAAATAATATATTATTAA
1 TAAATAATAT-TAATTAA
*
5400228 TAAAGAATA-TAA-TAA
1 TAAATAATATTAATTAA
5400243 TAAATAATATTAATTTAA
1 TAAATAATATTAA-TTAA
5400261 CT-AATAAATATT-A-TAA
1 -TAAAT-AATATTAATTAA
*
5400277 T-AAT-ATATTAATAAA
1 TAAATAATATTAATTAA
* *
5400292 TAATATTATAATATATTAA
1 TAA-ATAATATTA-ATTAA
5400311 TAAATAATA
1 TAAATAATA
5400320 AAATAATTTT
Statistics
Matches: 130, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
13 5 0.04
14 1 0.01
15 18 0.14
16 9 0.07
17 2 0.02
18 58 0.45
19 29 0.22
20 8 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATAATATTAATTAA
Found at i:5400173 original size:33 final size:34
Alignment explanation
Indices: 5400136--5400319 Score: 130
Period size: 33 Copynumber: 5.3 Consensus size: 34
5400126 ATTTTACCTT
*
5400136 TAAATAATATTA-TATTAACAAATCATATATTAA
1 TAAATAATATTATTATTAACAAATAATATATTAA
*
5400169 TAAATAATATACTATTAATAAACAATATTATAATATATTAA
1 TAAATAATAT--TATT-ATTAAC-A-A--ATAATATATTAA
* * *
5400210 TAAATAATA-TATTATTAATAAAGAATATAATAA
1 TAAATAATATTATTATTAACAAATAATATATTAA
* *
5400243 TAAATAATATTAAT-TTAACTAATAA-ATATT-A
1 TAAATAATATTATTATTAACAAATAATATATTAA
* *
5400274 T-AATAATA-TATTAATAAATAATATTATAATATATTAA
1 TAAATAATATTATT-AT---TAACA-AATAATATATTAA
5400311 TAAATAATA
1 TAAATAATA
5400320 AAATAATTTT
Statistics
Matches: 118, Mismatches: 15, Indels: 31
0.72 0.09 0.19
Matches are distributed among these distances:
29 3 0.03
30 7 0.06
31 3 0.03
32 4 0.03
33 37 0.31
34 6 0.05
35 7 0.06
36 7 0.06
37 11 0.09
38 12 0.10
39 1 0.01
41 20 0.17
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (34 bp):
TAAATAATATTATTATTAACAAATAATATATTAA
Found at i:5400205 original size:41 final size:40
Alignment explanation
Indices: 5400160--5400304 Score: 165
Period size: 41 Copynumber: 3.7 Consensus size: 40
5400150 TTAACAAATC
*
5400160 ATATATTAATAAATAATATACTATTAATAAACAATATTATA
1 ATATATTAATAAATAATATA-TATTAATAAACAATATAATA
*
5400201 ATATATTAATAAATAATATATTATTAATAAAGAATATAATA
1 ATATATTAATAAATAATATA-TATTAATAAACAATATAATA
* * * * * *
5400242 ATA-AATAAT-ATTAATTTA-ACTAATAAATATTATAATA
1 ATATATTAATAAATAATATATATTAATAAACAATATAATA
5400279 ATATATTAATAAATAATAT-TA-TAATA
1 ATATATTAATAAATAATATATATTAATA
5400305 TATTAATAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
37 19 0.21
38 10 0.11
39 14 0.16
40 5 0.06
41 41 0.46
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (40 bp):
ATATATTAATAAATAATATATATTAATAAACAATATAATA
Found at i:5400216 original size:15 final size:15
Alignment explanation
Indices: 5400141--5400297 Score: 105
Period size: 15 Copynumber: 10.5 Consensus size: 15
5400131 ACCTTTAAAT
* *
5400141 AATATTATATTAACA
1 AATAATATATTAATA
*
5400156 AATCATATATTAATA
1 AATAATATATTAATA
* *
5400171 AATAATATACT-ATT
1 AATAATATATTAATA
* *
5400185 AATAA-ACAAT-AT-
1 AATAATATATTAATA
*
5400197 TATAATATATTAATA
1 AATAATATATTAATA
5400212 AATAATATATTATTAATA
1 AAT-A-ATA-TATTAATA
* *
5400230 AAGAATATAATAATA
1 AATAATATATTAATA
5400245 AATAATATTAATTTAACT-
1 AATAATA-T-A-TTAA-TA
5400263 AATAA-ATATT-AT-
1 AATAATATATTAATA
5400275 AATAATATATTAATA
1 AATAATATATTAATA
5400290 AATAATAT
1 AATAATAT
5400298 TATAATATAT
Statistics
Matches: 113, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
12 10 0.09
13 14 0.12
14 13 0.12
15 45 0.40
16 6 0.05
17 6 0.05
18 18 0.16
19 1 0.01
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:5400236 original size:7 final size:7
Alignment explanation
Indices: 5400184--5400326 Score: 63
Period size: 8 Copynumber: 18.6 Consensus size: 7
5400174 AATATACTAT
5400184 TAATAAA
1 TAATAAA
* *
5400191 CAATATTA
1 TAATA-AA
*
5400199 TAATATAT
1 TAATA-AA
5400207 TAATAAA
1 TAATAAA
5400214 TAATATATTA
1 TAATA-A--A
5400224 TTAATAAA
1 -TAATAAA
*
5400232 GAATATAA
1 TAATA-AA
5400240 TAATAAA
1 TAATAAA
5400247 TAATATTAA
1 TAATA--AA
* *
5400256 T-TTAAC
1 TAATAAA
5400262 TAATAAA
1 TAATAAA
*
5400269 TATTATAA
1 TAATA-AA
*
5400277 TAATATAT
1 TAATA-AA
5400285 TAATAAA
1 TAATAAA
*
5400292 TAATATTA
1 TAATA-AA
*
5400300 TAATATAT
1 TAATA-AA
5400308 TAATAAA
1 TAATAAA
5400315 TAATAAAA
1 TAAT-AAA
5400323 TAAT
1 TAAT
5400327 TTTATTTTAA
Statistics
Matches: 104, Mismatches: 20, Indels: 23
0.71 0.14 0.16
Matches are distributed among these distances:
6 2 0.02
7 39 0.38
8 53 0.51
9 3 0.03
10 2 0.02
11 5 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (7 bp):
TAATAAA
Found at i:5400302 original size:23 final size:23
Alignment explanation
Indices: 5400233--5400319 Score: 106
Period size: 23 Copynumber: 3.8 Consensus size: 23
5400223 ATTAATAAAG
*
5400233 AATATAATAATAAATAATA-T-T
1 AATATATTAATAAATAATATTAT
* * * *
5400254 AATTTAACTAATAAATATTATAAT
1 AATAT-ATTAATAAATAATATTAT
5400278 AATATATTAATAAATAATATTAT
1 AATATATTAATAAATAATATTAT
5400301 AATATATTAATAAATAATA
1 AATATATTAATAAATAATA
5400320 AAATAATTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
21 4 0.07
22 12 0.22
23 34 0.62
24 5 0.09
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATATTAATAAATAATATTAT
Found at i:5400303 original size:15 final size:15
Alignment explanation
Indices: 5400136--5400331 Score: 92
Period size: 15 Copynumber: 12.9 Consensus size: 15
5400126 ATTTTACCTT
*
5400136 TAAATAATATTATAT
1 TAAATAATATTATAA
5400151 TAACA-AATCATATATTAA
1 TAA-ATAAT-AT-TA-TAA
5400169 TAAATAATATACTATTAA
1 TAAATAATAT--TA-TAA
*
5400187 TAAACAATATTATAA
1 TAAATAATATTATAA
* *
5400202 T--ATATTAATA-AA
1 TAAATAATATTATAA
5400214 T-AAT-ATATTATTAA
1 TAAATAATATTA-TAA
* *
5400228 TAAAGAATATAATAA
1 TAAATAATATTATAA
5400243 TAAATAATATTAATTTAA
1 TAAATAATATT-A--TAA
5400261 CT-AATAAATATTATAA
1 -TAAAT-AATATTATAA
5400277 T-AAT-ATA-T-TAA
1 TAAATAATATTATAA
5400288 TAAATAATATTATAA
1 TAAATAATATTATAA
* *
5400303 TATATTAATA-AATAA
1 TA-AATAATATTATAA
*
5400318 TAAAATAATTTTAT
1 T-AAATAATATTAT
5400332 TTTAAGTATT
Statistics
Matches: 141, Mismatches: 17, Indels: 45
0.69 0.08 0.22
Matches are distributed among these distances:
11 4 0.03
12 11 0.08
13 14 0.10
14 4 0.03
15 43 0.30
16 23 0.16
17 5 0.04
18 30 0.21
19 7 0.05
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (15 bp):
TAAATAATATTATAA
Found at i:5400360 original size:78 final size:78
Alignment explanation
Indices: 5400136--5400297 Score: 203
Period size: 74 Copynumber: 2.1 Consensus size: 78
5400126 ATTTTACCTT
* ** * *
5400136 TAAATAATAT-TATATTAACAAATCATATATTAATAAATAATA-TACTATTAA-TAA-ACAATA-
1 TAAATAATATAT-TATTAATAAAGAATATAATAATAAATAATATTAAT-TTAACTAATA-AATAT
5400196 T-T-ATAATATATTAA
63 TATAATAATATATTAA
5400210 TAAATAATATATTATTAATAAAGAATATAATAATAAATAATATTAATTTAACTAATAAATATTAT
1 TAAATAATATATTATTAATAAAGAATATAATAATAAATAATATTAATTTAACTAATAAATATTAT
5400275 AATAATATATTAA
66 AATAATATATTAA
5400288 TAAATAATAT
1 TAAATAATAT
5400298 TATAATATAT
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
74 40 0.53
75 11 0.14
76 2 0.03
77 1 0.01
78 22 0.29
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (78 bp):
TAAATAATATATTATTAATAAAGAATATAATAATAAATAATATTAATTTAACTAATAAATATTAT
AATAATATATTAA
Found at i:5400406 original size:16 final size:15
Alignment explanation
Indices: 5400385--5400435 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
5400375 TTATTATTAA
*
5400385 AATATAATTATTTTTT
1 AATATAAATA-TTTTT
*
5400401 AATATAAATAATTTT
1 AATATAAATATTTTT
5400416 AATAATAAATAATTTTT
1 AAT-ATAAAT-ATTTTT
5400433 AAT
1 AAT
5400436 GTTTTAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 7 0.23
16 15 0.50
17 8 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATAAATATTTTT
Found at i:5400417 original size:15 final size:16
Alignment explanation
Indices: 5400397--5400431 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
5400387 TATAATTATT
5400397 TTTTAAT-ATAAATAA
1 TTTTAATAATAAATAA
5400412 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
5400428 TTTT
1 TTTT
5400432 TAATGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:5400600 original size:15 final size:14
Alignment explanation
Indices: 5400564--5400599 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5400554 AAAATGTAAA
*
5400564 TATTTTTTAAAATT
1 TATTTTTTAAAAGT
*
5400578 TATTTTTTGAAAGT
1 TATTTTTTAAAAGT
5400592 TATTTTTT
1 TATTTTTT
5400600 TACGAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (14 bp):
TATTTTTTAAAAGT
Found at i:5408553 original size:20 final size:19
Alignment explanation
Indices: 5408524--5408561 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5408514 AAAAAGATAA
5408524 TAAATGTTTAATTTTTTAAT
1 TAAATGTTT-ATTTTTTAAT
*
5408544 TAAATTTTTATTTTTTAA
1 TAAATGTTTATTTTTTAA
5408562 AATATATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TAAATGTTTATTTTTTAAT
Found at i:5410424 original size:2 final size:2
Alignment explanation
Indices: 5410417--5410441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5410407 TATGAAAGCT
5410417 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
5410442 CATAATTTGA
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:5412761 original size:7 final size:7
Alignment explanation
Indices: 5412749--5412775 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5412739 TTTTTCTTGT
5412749 ATTGTTG
1 ATTGTTG
5412756 ATTGTTG
1 ATTGTTG
5412763 ATTGTTG
1 ATTGTTG
5412770 ATTGTT
1 ATTGTT
5412776 ATTTATTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (7 bp):
ATTGTTG
Found at i:5424833 original size:13 final size:13
Alignment explanation
Indices: 5424815--5424839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5424805 GAAATGTTTT
5424815 ATAAAAAAAAAAA
1 ATAAAAAAAAAAA
5424828 ATAAAAAAAAAA
1 ATAAAAAAAAAA
5424840 TGAAACAAAA
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (13 bp):
ATAAAAAAAAAAA
Found at i:5425087 original size:18 final size:18
Alignment explanation
Indices: 5425045--5425098 Score: 67
Period size: 17 Copynumber: 3.0 Consensus size: 18
5425035 TTATTTTCTG
*
5425045 ATTTGATTTCAAATAAAAT
1 ATTT-ATTTTAAATAAAAT
5425064 -TTTATTTTAAATAAAAT
1 ATTTATTTTAAATAAAAT
5425081 ATTTA-TTTAAATACAAAT
1 ATTTATTTTAAATA-AAAT
5425099 TAAAAGTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (18 bp):
ATTTATTTTAAATAAAAT
Found at i:5425134 original size:24 final size:24
Alignment explanation
Indices: 5425107--5425157 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
5425097 ATTAAAAGTT
* *
5425107 AAGGTTTTATTTAAATATAAATTA
1 AAGGGTTTATTTAAACATAAATTA
**
5425131 AAGGGTTTATTTTGACATAAATTA
1 AAGGGTTTATTTAAACATAAATTA
5425155 AAG
1 AAG
5425158 ATCAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (24 bp):
AAGGGTTTATTTAAACATAAATTA
Found at i:5425201 original size:23 final size:23
Alignment explanation
Indices: 5425175--5425219 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5425165 TTTTATTTGA
*
5425175 ATGTAATTAAAAAT-ATAAAATTT
1 ATGTAAAT-AAAATGATAAAATTT
5425198 ATGTAAATAAAATGATAAAATT
1 ATGTAAATAAAATGATAAAATT
5425220 CATATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
ATGTAAATAAAATGATAAAATTT
Found at i:5425562 original size:18 final size:18
Alignment explanation
Indices: 5425536--5425899 Score: 161
Period size: 18 Copynumber: 20.8 Consensus size: 18
5425526 AGTATAGTTT
*
5425536 TATTTATAAATAATATTA
1 TATTAATAAATAATATTA
5425554 TATTAATAAA-AAGTATTA
1 TATTAATAAATAA-TATTA
5425572 TATTAATAAAATAATATTA
1 TATTAAT-AAATAATATTA
*
5425591 TA-T--T--GT-A-A-TA
1 TATTAATAAATAATATTA
5425601 TATTAATAAATAATATTA
1 TATTAATAAATAATATTA
*
5425619 TATGAATAAATAATA-TA
1 TATTAATAAATAATATTA
* * *
5425636 CAATCAATATGAT-ATATTA
1 -TATTAATA-AATAATATTA
* * *
5425655 -ATGAA-AATATTATAATA
1 TATTAATAA-ATAATATTA
5425672 TATTAATAAATAATATTA
1 TATTAATAAATAATATTA
* *
5425690 T-TATATATTAATAAATAATA
1 TAT-TA-ATAAAT-AATATTA
* *
5425710 TATT-ATTAATAATACTA
1 TATTAATAAATAATATTA
5425727 TATTAATAAATAATA--A
1 TATTAATAAATAATATTA
* * *
5425743 TA-AAATAATATTATAATA
1 TATTAATAA-ATAATATTA
*
5425761 TATTAATAAATAATATAA
1 TATTAATAAATAATATTA
* * *
5425779 TAATAATTATTAAT-TTA
1 TATTAATAAATAATATTA
*
5425796 -ATTAATCAATATTACAATAATA
1 TATTAAT-AA-A-T--AATATTA
*
5425818 TATGAATAAATAATA-TA
1 TATTAATAAATAATATTA
5425835 CTATTAAT--AT-A-A-TA
1 -TATTAATAAATAATATTA
*
5425849 TATTAATAAATATTATTA
1 TATTAATAAATAATATTA
* **
5425867 -ATTAATAATATTATAACA
1 TATTAATAA-ATAATATTA
5425885 TATTAATAAATAATA
1 TATTAATAAATAATA
5425900 AAAAGAACAA
Statistics
Matches: 265, Mismatches: 39, Indels: 84
0.68 0.10 0.22
Matches are distributed among these distances:
10 4 0.02
11 2 0.01
12 1 0.00
13 9 0.03
14 3 0.01
15 9 0.03
16 20 0.08
17 39 0.15
18 118 0.45
19 35 0.13
20 11 0.04
21 5 0.02
22 4 0.02
23 5 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TATTAATAAATAATATTA
Done.