Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 96 of 100
Found at i:16740738 original size:476 final size:473
Alignment explanation
Indices: 16739868--16740887 Score: 1110
Period size: 476 Copynumber: 2.1 Consensus size: 473
16739858 CGGCTAGTTA
* * *
16739868 GTGGGTTCAGGAACATCTTCATATTTTTATCATGCCAATG-CTTTTTTATGGCTTGTAAATTCAT
1 GTGGGTTCA-GCACATCTTCATATTTTT-GCATGCCAATGCCATTTTTATGGCTTGTAAATTCAT
* * *
16739932 ATAAACACTCACTAGCACCCATATCTGAGCTTGCCTCAATTCTGTAAACATGAACACTATGCTTG
64 ATAAGCACTCACCAGCACCCATATCTGAGCTTGCCTCAATTCTGTAAACATGAACAATATGCTTG
* * * * *
16739997 AGCCTCTTAAGTCTTGGTCACTGCCCAAACCACTATTCTAGGCTAGTTCCCTATGACTCAGGCCT
129 AGCCTCTTAAGTCTCGATCACTACCAAAACCACTATTCTAAGCTAGTTCCCTATGACTCAGGCCT
* * * * *
16740062 CTAGTAGGCCTTAAGGCATAGTCCCCCTTACTATCGACCTTGTCCTGCTAGAACTCTTAGGCATG
194 CCAGTAGGCCTTAAGGCATAGTCCCCCTTACTATCGACCTTATCCTACTAGAACCCCTAGGCATG
** ** * *
16740127 GACCAGTTTGTAGACTATGACACATGCACATACCTCAACCACCATCAGGGCATGTTGGCCCTTGG
259 GACCAACTTACAGACTATGACACATGCACATACCTCAACCACCATCAAGACATGTTGGCCCTTGG
* * * * * * * *
16740192 TCTCGGTACATGCTCTGACTACCATTGGCATATGCTAGGTCTTTGTGTAGGTAGGTCCCTTGAGC
324 TCTCGGCACATGCTCTCAATACCATTGGCACATGCTAGGCCTTTATGTAGGTAGGTCCCTCGAAC
* * *
16740257 ACCATTGGCACATGCTTAGGCAAACACCACAT-ACAGGTATCCTAAGCCCGAGCTATGCACCATG
389 ACCATTGGCACATGCTGAGGCAAACACCAC-TCACAGGTATCCTAAGCCCAAGCCATGCACCATG
* **
16740321 TGTAGC-ATGACTGGGCAGTG-
453 TGCA-CTACAACTGGGCAGTGT
* *
16740341 GATGGGTTCAGCACATGTTCATATTTTTGCCATGCCAATGCCATTTTTATGGTTTGTAAATTCAT
1 G-TGGGTTCAGCACATCTTCATATTTTTG-CATGCCAATGCCATTTTTATGGCTTGTAAATTCAT
* ** * * * * * *
16740406 ATAAGCATTCACCAGTGCCCGTAGT-TGGGCTTGGCTGAATTCTGTGGAACATGAACAATGTG-T
64 ATAAGCACTCACCAGCACCCATA-TCTGAGCTTGCCTCAATTCTGT-AAACATGAACAATATGCT
* * * **
16740469 TGGAGCCTCTTGAGTCTCGATCGCTACTAAAACCACTATTCTAAGCTAGTTCCCTATGACTTGGG
127 T-GAGCCTCTTAAGTCTCGATCACTACCAAAACCACTATTCTAAGCTAGTTCCCTATGACTCAGG
* * **
16740534 CCTCCAGTAGGCCTTAAGGCTTGGTCTTCC-TAGCTATCGAACCTTAT-CTCACTAGAACCCCTA
191 CCTCCAGTAGGCCTTAAGGCATAGTCCCCCTTA-CTATCG-ACCTTATCCT-ACTAGAACCCCTA
* * * *
16740597 GGCGTGGACCAACTTACAGACTATGACACATGTACATACTTCGACCACCATCAAGACATGTTGGC
253 GGCATGGACCAACTTACAGACTATGACACATGCACATACCTCAACCACCATCAAGACATGTTGGC
* * *
16740662 CCTTGGTCTTGGCATATGCT-TCAAT-CGTCATTGGCACATGCT-GGCCCTTTATGT-GGATAGT
318 CCTTGGTCTCGGCACATGCTCTCAATAC--CATTGGCACATGCTAGG-CCTTTATGTAGG-TAGG
* *** * * * **
16740723 TCCCTCGAACACCATTGGCACATGCTGGGGTGGACACCACTCATAGGTGTCTTGGGCCCAAGCCA
379 TCCCTCGAACACCATTGGCACATGCTGAGGCAAACACCACTCACAGGTATCCTAAGCCCAAGCCA
* *
16740788 TGCACTATGTGCACTACAACTGGGTAGTGT
444 TGCACCATGTGCACTACAACTGGGCAGTGT
* *
16740818 GTGGGTTTAAGCACATCTTCATATTTTTGCAGTGCCAATGCCATTTTTATTGCTTGTAAATTCAT
1 GTGGG-TTCAGCACATCTTCATATTTTTGCA-TGCCAATGCCATTTTTATGGCTTGTAAATTCAT
16740883 ATAAG
64 ATAAG
16740888 TGCTCACTAG
Statistics
Matches: 451, Mismatches: 78, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
473 27 0.06
474 69 0.15
475 109 0.24
476 188 0.42
477 58 0.13
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (473 bp):
GTGGGTTCAGCACATCTTCATATTTTTGCATGCCAATGCCATTTTTATGGCTTGTAAATTCATAT
AAGCACTCACCAGCACCCATATCTGAGCTTGCCTCAATTCTGTAAACATGAACAATATGCTTGAG
CCTCTTAAGTCTCGATCACTACCAAAACCACTATTCTAAGCTAGTTCCCTATGACTCAGGCCTCC
AGTAGGCCTTAAGGCATAGTCCCCCTTACTATCGACCTTATCCTACTAGAACCCCTAGGCATGGA
CCAACTTACAGACTATGACACATGCACATACCTCAACCACCATCAAGACATGTTGGCCCTTGGTC
TCGGCACATGCTCTCAATACCATTGGCACATGCTAGGCCTTTATGTAGGTAGGTCCCTCGAACAC
CATTGGCACATGCTGAGGCAAACACCACTCACAGGTATCCTAAGCCCAAGCCATGCACCATGTGC
ACTACAACTGGGCAGTGT
Found at i:16742799 original size:250 final size:252
Alignment explanation
Indices: 16742317--16742810 Score: 785
Period size: 250 Copynumber: 2.0 Consensus size: 252
16742307 CAAGGACCAA
* * * *
16742317 CACCTATCATAAATCATGTGTGCACACCCCTGGCCCTTACCCTTAATCATTGGAAGCCTAAATGT
1 CACCTATCACAAATCATGTGCGCACACCCCTGGCCCCTACCCTTAATCATTGGAACCCTAAATGT
* * *
16742382 CATTAGTCAGGTTCTTCGATGATGCTCTGACAATGGTGCTCCAAGCAAAAAAATGTGACCCCCAG
66 CATTAGTCAGGTTCTCCGATGATACTCTGACAATGGTGCTCCAAGCAAAAAAATGTGACCACCAG
* * * * *
16742447 AACATGCTTGAGCCCAGCATGTTCATTTTGTCCTAGAATCAAACTTTGGCTAAGGCCTCAATCAT
131 AACATGCTTGAGCCCAGCATGTTCACTGTGGCCTAGAATCAAACTTCGACTAAGGCCTCAATCAT
*
16742512 CAACAGCCCATGTTGGTGCATGGTGTAGGCATATGCCTCAACCATCATCGACACAAC
196 CAACAACCCATGTTGGTGCATGGTGTAGGCATATGCCTCAACCATCATCGACACAAC
* * *
16742569 CACC-ATCACAAATCATGTGCGCACACCTCTGGCCCCTACCCTTGATCGTTGGAACCCTAAATGT
1 CACCTATCACAAATCATGTGCGCACACCCCTGGCCCCTACCCTTAATCATTGGAACCCTAAATGT
* * *
16742633 CATTGGTTAGGTTCTCCGATGATACTCTGATAATGGTGCTCCAAGCAAAAAAATGTGA-CACCAG
66 CATTAGTCAGGTTCTCCGATGATACTCTGACAATGGTGCTCCAAGCAAAAAAATGTGACCACCAG
* *
16742697 CACATGCTTGAGCCCAGCATGTTCACTGTGGCCTAGAATCGAACTTCGACTAAGGCCTCAATCAT
131 AACATGCTTGAGCCCAGCATGTTCACTGTGGCCTAGAATCAAACTTCGACTAAGGCCTCAATCAT
16742762 CAACAACCCATGTTGGTGCATGGTGTAGGCATATGCCTCAACCATCATC
196 CAACAACCCATGTTGGTGCATGGTGTAGGCATATGCCTCAACCATCATC
16742811 AACATAAATT
Statistics
Matches: 221, Mismatches: 21, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
250 111 0.50
251 106 0.48
252 4 0.02
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (252 bp):
CACCTATCACAAATCATGTGCGCACACCCCTGGCCCCTACCCTTAATCATTGGAACCCTAAATGT
CATTAGTCAGGTTCTCCGATGATACTCTGACAATGGTGCTCCAAGCAAAAAAATGTGACCACCAG
AACATGCTTGAGCCCAGCATGTTCACTGTGGCCTAGAATCAAACTTCGACTAAGGCCTCAATCAT
CAACAACCCATGTTGGTGCATGGTGTAGGCATATGCCTCAACCATCATCGACACAAC
Found at i:16743023 original size:110 final size:110
Alignment explanation
Indices: 16742825--16743074 Score: 295
Period size: 110 Copynumber: 2.3 Consensus size: 110
16742815 TAAATTGGCA
* ** * * * * ** *
16742825 TTTGGTATGGGCAGTTGCCTTGACCACCATTGGCATAAGCTAGCTCTTGCTATGGGCAGTTGCCT
1 TTTGGTATAGGCACATGCCTTGACCACCATCGACACAAGCTAGCCCTTGCTATAAGCAGTTACCT
* * * *
16742890 TGACCACCATCAGTGTATTTTGGACTACCATCAACGCATGTTGCC
66 TGACCACCATCAGTGCATGTTGGACTACCATCAACGCATGCTACC
* *
16742935 TTTGGTATAGGCACATGCCTCGACCACCATCGACACAAGCTAGCCCTTGCTATAAGCATTTACCT
1 TTTGGTATAGGCACATGCCTTGACCACCATCGACACAAGCTAGCCCTTGCTATAAGCAGTTACCT
**
16743000 TGACCACCATC-GATGCATGTTGGACTACCATCAGTGCATGCTACC
66 TGACCACCATCAG-TGCATGTTGGACTACCATCAACGCATGCTACC
* * *
16743045 CTTGGTACAGGCACATGCTTTGACCACCAT
1 TTTGGTATAGGCACATGCCTTGACCACCAT
16743075 TGGCACATGC
Statistics
Matches: 117, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
109 1 0.01
110 116 0.99
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (110 bp):
TTTGGTATAGGCACATGCCTTGACCACCATCGACACAAGCTAGCCCTTGCTATAAGCAGTTACCT
TGACCACCATCAGTGCATGTTGGACTACCATCAACGCATGCTACC
Found at i:16743108 original size:23 final size:23
Alignment explanation
Indices: 16743076--16743128 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
16743066 GACCACCATT
16743076 GGCACATGCTGGCCTTTAGTGTA
1 GGCACATGCTGGCCTTTAGTGTA
*
16743099 GTCACATGCTGGCCTTTAGTGTA
1 GGCACATGCTGGCCTTTAGTGTA
16743122 GGCACAT
1 GGCACAT
16743129 ACCTCGATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCACATGCTGGCCTTTAGTGTA
Found at i:16751133 original size:21 final size:21
Alignment explanation
Indices: 16751109--16751156 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
16751099 CCATGTGCCT
16751109 GCACCTTGATCATTAGTGCTA
1 GCACCTTGATCATTAGTGCTA
16751130 GCACCTTGATCATTAGTGCTA
1 GCACCTTGATCATTAGTGCTA
16751151 GCACCT
1 GCACCT
16751157 CGATTTGACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (21 bp):
GCACCTTGATCATTAGTGCTA
Found at i:16757212 original size:52 final size:52
Alignment explanation
Indices: 16757150--16757254 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
16757140 TAAATAGAAA
* *
16757150 AGATAACACTTTCCAAGGCCCCCATGTCTCTAGACTCCCTAATGTTGCTGTC
1 AGATAACACTTTCCAAGGCCCCCACGTCTCTAGACTCCCTAACGTTGCTGTC
* *
16757202 AGATAACACTTTCCAAGGCCCCCACGTCTTTAGACTCCCTAACGTTGTTGTC
1 AGATAACACTTTCCAAGGCCCCCACGTCTCTAGACTCCCTAACGTTGCTGTC
16757254 A
1 A
16757255 ACCATCGCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (52 bp):
AGATAACACTTTCCAAGGCCCCCACGTCTCTAGACTCCCTAACGTTGCTGTC
Found at i:16764745 original size:3 final size:3
Alignment explanation
Indices: 16764727--16764778 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
16764717 ATAAAATTTA
*
16764727 TTG TTA TTG TTG -TG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
16764774 TTG TT
1 TTG TT
16764779 ATTATTACTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.02, C:0.00, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:16764980 original size:18 final size:19
Alignment explanation
Indices: 16764943--16764979 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
16764933 TATATATATA
16764943 TATTTATTTATTTATCTTT
1 TATTTATTTATTTATCTTT
16764962 TATTT-TTTATTTA-CTTT
1 TATTTATTTATTTATCTTT
16764979 T
1 T
16764980 TGGTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 8 0.44
19 5 0.28
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (19 bp):
TATTTATTTATTTATCTTT
Found at i:16765056 original size:15 final size:14
Alignment explanation
Indices: 16765039--16765085 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
16765029 GAAATTCTTA
16765039 TTATTGTTATTATT
1 TTATTGTTATTATT
16765053 ATTATCTAGTTATT-TT
1 -TTAT-T-GTTATTATT
16765069 TTATT-TTATTATT
1 TTATTGTTATTATT
16765082 TTAT
1 TTAT
16765086 AAGGTTTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.17
13 6 0.21
14 1 0.03
15 8 0.28
16 3 0.10
17 6 0.21
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (14 bp):
TTATTGTTATTATT
Found at i:16765394 original size:32 final size:33
Alignment explanation
Indices: 16765340--16765401 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
16765330 CAGACTAGTC
* *
16765340 AAAACTTTAAACATACATAAATAATAATAACAA
1 AAAACTTAAAACATACATAAATAACAATAACAA
16765373 AAAACTTAAAACGATA-A-AAATAACAATAA
1 AAAACTTAAAAC-ATACATAAATAACAATAA
16765402 AAATTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 11 0.42
33 12 0.46
34 3 0.12
ACGTcount: A:0.66, C:0.11, G:0.02, T:0.21
Consensus pattern (33 bp):
AAAACTTAAAACATACATAAATAACAATAACAA
Found at i:16765425 original size:110 final size:110
Alignment explanation
Indices: 16765230--16765429 Score: 337
Period size: 110 Copynumber: 1.8 Consensus size: 110
16765220 TAGAAAATTT
* *
16765230 AAAACTTAAAACATACATAAATAATAATAACAAAAAACTTAAAATGATAAAAATTAAATAAAAAA
1 AAAACTTAAAACATACATAAATAATAATAACAAAAAACTTAAAACGATAAAAATAAAATAAAAAA
* *
16765295 TTAAATTAGGAAATTAAAAAAAAAGGTACTTGAACCAGACTAGTC
66 TTAAATCAAGAAATTAAAAAAAAAGGTACTTGAACCAGACTAGTC
*
16765340 AAAACTTTAAACATACATAAATAATAATAACAAAAAACTTAAAACGATAAAAATAACAATAAAAA
1 AAAACTTAAAACATACATAAATAATAATAACAAAAAACTTAAAACGATAAAAATAA-AATAAAAA
*
16765405 TTTAAATCAAGAAATTAAAAAAAAA
65 ATTAAATCAAGAAATTAAAAAAAAA
16765430 AGAACCTGAA
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
110 53 0.64
111 30 0.36
ACGTcount: A:0.64, C:0.09, G:0.05, T:0.22
Consensus pattern (110 bp):
AAAACTTAAAACATACATAAATAATAATAACAAAAAACTTAAAACGATAAAAATAAAATAAAAAA
TTAAATCAAGAAATTAAAAAAAAAGGTACTTGAACCAGACTAGTC
Found at i:16766764 original size:19 final size:18
Alignment explanation
Indices: 16766742--16766882 Score: 76
Period size: 19 Copynumber: 7.6 Consensus size: 18
16766732 TCCTAAATCT
16766742 AACCATAAACCGTAAACCA
1 AACCATAAACC-TAAACCA
* * *
16766761 AACCTTTAACCCTAAACCT
1 AACC-ATAAACCTAAACCA
*
16766780 AACCGTAAATCCTAAACTCTA
1 AACCATAAA-CCTAAAC-C-A
* *
16766801 AACC-T-AACTTAAACCT
1 AACCATAAACCTAAACCA
*
16766817 AA-CATAAACC-AAACCTTC
1 AACCATAAACCTAAACC--A
*
16766835 AACCTTAAACCTAAACCA
1 AACCATAAACCTAAACCA
* *
16766853 AATCGTAAACCCTAAACCTA
1 AACCATAAA-CCTAAACC-A
16766873 AACCA-AAACC
1 AACCATAAACC
16766883 CAAAATCAAA
Statistics
Matches: 94, Mismatches: 16, Indels: 25
0.70 0.12 0.19
Matches are distributed among these distances:
15 1 0.01
16 8 0.09
17 4 0.04
18 20 0.21
19 41 0.44
20 16 0.17
21 4 0.04
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (18 bp):
AACCATAAACCTAAACCA
Found at i:16766815 original size:11 final size:11
Alignment explanation
Indices: 16766773--16766826 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 11
16766763 CCTTTAACCC
*
16766773 TAAACCTAACCG
1 TAAACCTAA-CT
16766785 TAAATCCTAAACT
1 TAAA-CCT-AACT
16766798 CTAAACCTAACT
1 -TAAACCTAACT
*
16766810 TAAACCTAACA
1 TAAACCTAACT
16766821 TAAACC
1 TAAACC
16766827 AAACCTTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
11 16 0.43
12 8 0.22
13 7 0.19
14 6 0.16
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (11 bp):
TAAACCTAACT
Found at i:16766851 original size:6 final size:6
Alignment explanation
Indices: 16766733--16766882 Score: 89
Period size: 6 Copynumber: 24.3 Consensus size: 6
16766723 TAATCGAAAT
* *
16766733 CCTAAA TCT-AA CCATAAA CCGTAAA CC-AAA CCTTTAAC CCTAAA CCT-AA
1 CCTAAA CCTAAA CC-TAAA CC-TAAA CCTAAA CC--TAAA CCTAAA CCTAAA
* *
16766782 CCGTAAA TCCTAAA CTCTAAA CCT-AA CTTAAA CCT-AA CATAAA CC-AAA
1 CC-TAAA -CCTAAA C-CTAAA CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA
* * *
16766830 CCTTCAA CCTTAAA CCTAAA CC-AAA TCGTAAA CCCTAAA CCTAAA CCAAAA
1 CC-TAAA CC-TAAA CCTAAA CCTAAA -CCTAAA -CCTAAA CCTAAA CCTAAA
16766881 CC
1 CC
16766883 CAAAATCAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 30
0.72 0.09 0.19
Matches are distributed among these distances:
5 28 0.25
6 40 0.35
7 40 0.35
8 6 0.05
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (6 bp):
CCTAAA
Found at i:16766851 original size:25 final size:24
Alignment explanation
Indices: 16766771--16766879 Score: 105
Period size: 25 Copynumber: 4.5 Consensus size: 24
16766761 AACCTTTAAC
*
16766771 CCTAAACCTAACCGTAAATCCTAAA
1 CCTAAACCAAACCGTAAA-CCTAAA
* *
16766796 CTCTAAACCTAA-CTTAAACCT-AA
1 C-CTAAACCAAACCGTAAACCTAAA
* * *
16766819 CATAAACCAAACCTTCAACCTTAAA
1 CCTAAACCAAACCGTAAACC-TAAA
*
16766844 CCTAAACCAAATCGTAAACCCTAAA
1 CCTAAACCAAACCGTAAA-CCTAAA
16766869 CCTAAACCAAA
1 CCTAAACCAAA
16766880 ACCCAAAATC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.11
23 10 0.14
24 4 0.06
25 37 0.52
26 12 0.17
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (24 bp):
CCTAAACCAAACCGTAAACCTAAA
Found at i:16766882 original size:67 final size:66
Alignment explanation
Indices: 16766754--16766882 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 66
16766744 CCATAAACCG
* * **
16766754 TAAACCAAACCTTTAACCCTAAACCTAACCGTAAATCCTAAACTCTAAACCTAACTTAAACCTAA
1 TAAACCAAACCTTCAACCCTAAACCTAACCG-AAATCCTAAACCCTAAACCTAACCAAAACCTAA
16766819 CA
65 CA
* *
16766821 TAAACCAAACCTTCAACCTTAAACCTAAACC-AAATCGTAAACCCTAAACCTAAACCAAAACC
1 TAAACCAAACCTTCAACCCTAAACCT-AACCGAAATCCTAAACCCTAAACCT-AACCAAAACC
16766883 CAAAATCAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
66 18 0.33
67 32 0.59
68 4 0.07
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.19
Consensus pattern (66 bp):
TAAACCAAACCTTCAACCCTAAACCTAACCGAAATCCTAAACCCTAAACCTAACCAAAACCTAAC
A
Found at i:16766912 original size:25 final size:25
Alignment explanation
Indices: 16766884--16766932 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
16766874 ACCAAAACCC
16766884 AAAATCAAAACCTAAAACCTACTCT
1 AAAATCAAAACCTAAAACCTACTCT
** *
16766909 AAAATTGAAACCTTAAACCTACTC
1 AAAATCAAAACCTAAAACCTACTC
16766933 AAACCTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (25 bp):
AAAATCAAAACCTAAAACCTACTCT
Found at i:16768442 original size:22 final size:22
Alignment explanation
Indices: 16768417--16768458 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
16768407 GTTGATCTCC
16768417 TAAGCTA-TGATGATGATTAGGT
1 TAAGCTACTGATG-TGATTAGGT
16768439 TAAGCTACTGATGTGATTAG
1 TAAGCTACTGATGTGATTAG
16768459 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (22 bp):
TAAGCTACTGATGTGATTAGGT
Found at i:16773911 original size:23 final size:24
Alignment explanation
Indices: 16773863--16773910 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
16773853 TGTACATAAT
*
16773863 AATATATACTATAATAATCTGCAA
1 AATAAATACTATAATAATCTGCAA
*
16773887 AATAAATA-TATAAT-ATCTTCAA
1 AATAAATACTATAATAATCTGCAA
16773909 AA
1 AA
16773911 ACCAAGTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 6 0.27
24 7 0.32
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AATAAATACTATAATAATCTGCAA
Found at i:16776657 original size:34 final size:33
Alignment explanation
Indices: 16776609--16776675 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
16776599 GCATTTTAAT
* *
16776609 GTTTTTTAAGGGTATTATTTAAGGCCTTTTTTA
1 GTTTTTTAAAGGTATTATTTAAGGCATTTTTTA
*
16776642 GTTTTTTGAAAGGTATTATTTAAGGTATTTTTTA
1 GTTTTTT-AAAGGTATTATTTAAGGCATTTTTTA
16776676 TTAAAAATGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 7 0.23
34 23 0.77
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (33 bp):
GTTTTTTAAAGGTATTATTTAAGGCATTTTTTA
Found at i:16776956 original size:62 final size:62
Alignment explanation
Indices: 16776853--16777018 Score: 228
Period size: 62 Copynumber: 2.7 Consensus size: 62
16776843 TTTTTTTTTA
* * * ** *
16776853 GGATTATTTAAGGCGTCTCTAG-CTAGTAAACACCTTAAATAATGTTGATCAAATTTTTAGT
1 GGATTATTTAAGGCGTTTTTAGCCAAAAAAACACCTTAAATAATGTTAATCAAATTTTTAGT
*
16776914 GGATTATTTAAGGCGTTTTTAGCCAAAAAAACACCTTAAATAACGTTAATCAAATTTTTAGT
1 GGATTATTTAAGGCGTTTTTAGCCAAAAAAACACCTTAAATAATGTTAATCAAATTTTTAGT
* **
16776976 GGATTATTTAAGGCCTTTTTA-CCAAAAAAATGCCTTAAATAAT
1 GGATTATTTAAGGCGTTTTTAGCCAAAAAAACACCTTAAATAAT
16777019 CCCATTCAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 39 0.42
62 54 0.58
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (62 bp):
GGATTATTTAAGGCGTTTTTAGCCAAAAAAACACCTTAAATAATGTTAATCAAATTTTTAGT
Found at i:16784268 original size:62 final size:62
Alignment explanation
Indices: 16784149--16784331 Score: 199
Period size: 62 Copynumber: 3.0 Consensus size: 62
16784139 TGTAAGAAAC
* * * * * * * * *
16784149 TCAATTATTATGTTTATTTGAAGATAAATGTAGTATTTGATCACTATAATTTATTTAAAATAT
1 TCAATTACTATGTTT-TTTCAAGCTAAACGTAGTAATTGTTCATTATAATTTTTTTAAAATAA
* * *
16784212 TCAATTACTATGTTTTTTTAAGCTAAACGTAGTAATTGTTTATTGTAATTTTTTTAAAATAA
1 TCAATTACTATGTTTTTTCAAGCTAAACGTAGTAATTGTTCATTATAATTTTTTTAAAATAA
* * *
16784274 TCAATTACTATGTATCTTTCAA-CTAAACGTTG-AATTATTCATTATAATTTTTTTAAAA
1 TCAATTACTATGT-TTTTTCAAGCTAAACGTAGTAATTGTTCATTATAATTTTTTTAAAA
16784332 CATATGTATA
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
61 23 0.23
62 59 0.58
63 20 0.20
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (62 bp):
TCAATTACTATGTTTTTTCAAGCTAAACGTAGTAATTGTTCATTATAATTTTTTTAAAATAA
Found at i:16796023 original size:4 final size:4
Alignment explanation
Indices: 16796016--16796067 Score: 79
Period size: 4 Copynumber: 12.8 Consensus size: 4
16796006 TATATAAATC
16796016 TTAT TTAT CTTGA- TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT -TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
16796065 TTA
1 TTA
16796068 GTTTTGGTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 1 0.02
4 41 0.91
5 2 0.04
6 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:16796632 original size:20 final size:20
Alignment explanation
Indices: 16796591--16796632 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
16796581 CTTCGAATTG
*
16796591 AATTTCTGAAAATATTTTGA
1 AATTTCTGAAAATATTTGGA
*
16796611 AATTTTTGAAAA-ATTATGGA
1 AATTTCTGAAAATATT-TGGA
16796631 AA
1 AA
16796633 ATGTTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.45, C:0.02, G:0.12, T:0.40
Consensus pattern (20 bp):
AATTTCTGAAAATATTTGGA
Found at i:16802714 original size:10 final size:10
Alignment explanation
Indices: 16802691--16802725 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
16802681 CTCATGCAAG
*
16802691 AAAAAAAGGCA
1 AAAAAAATG-A
16802702 AAAAAAATGA
1 AAAAAAATGA
16802712 AAAAAAATGA
1 AAAAAAATGA
16802722 AAAA
1 AAAA
16802726 GGTCAAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.80, C:0.03, G:0.11, T:0.06
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:16809020 original size:61 final size:61
Alignment explanation
Indices: 16808895--16809023 Score: 215
Period size: 61 Copynumber: 2.1 Consensus size: 61
16808885 TCATTCAGTC
* *
16808895 ATGAAGCTTTAAAGATCAAGAATAAGCTCATATATTTGTATTTGAATTGAAAACAAACTCT
1 ATGAAGCTTTAAAGATCAAGAATAAGCTCATACATTTGTATTTAAATTGAAAACAAACTCT
*
16808956 ATGAAGCTTTAGAGATCAAGAATAAGCTCAT-CATTTGTATTTAAATTGAAAACAAACTCTT
1 ATGAAGCTTTAAAGATCAAGAATAAGCTCATACATTTGTATTTAAATTGAAAACAAACTC-T
16809017 ATGAAGC
1 ATGAAGC
16809024 CTATACCACC
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
60 26 0.41
61 38 0.59
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (61 bp):
ATGAAGCTTTAAAGATCAAGAATAAGCTCATACATTTGTATTTAAATTGAAAACAAACTCT
Found at i:16812678 original size:8 final size:8
Alignment explanation
Indices: 16812665--16812711 Score: 76
Period size: 8 Copynumber: 5.9 Consensus size: 8
16812655 TTTAAAAAGT
16812665 ATAATTAA
1 ATAATTAA
16812673 ATAATTAA
1 ATAATTAA
*
16812681 ATGATTAA
1 ATAATTAA
16812689 ATAATTAA
1 ATAATTAA
16812697 ATAATTAA
1 ATAATTAA
*
16812705 TTAATTA
1 ATAATTA
16812712 TTATTATAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (8 bp):
ATAATTAA
Found at i:16812737 original size:13 final size:13
Alignment explanation
Indices: 16812721--16812780 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
16812711 ATTATTATAG
16812721 TAAATAATTATTT
1 TAAATAATTATTT
*
16812734 TAAATAATAATTAT
1 TAAATAATTATT-T
16812748 T---TAATTATTT
1 TAAATAATTATTT
*
16812758 TAAA-AACTTTTTT
1 TAAATAA-TTATTT
16812771 TAAATAATTA
1 TAAATAATTA
16812781 AATTTTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
10 2 0.05
11 7 0.19
12 2 0.05
13 22 0.59
14 4 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATAATTATTT
Found at i:16814309 original size:3 final size:3
Alignment explanation
Indices: 16814301--16814328 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
16814291 CATTTACAAA
16814301 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16814329 TAAATAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16816654 original size:2 final size:2
Alignment explanation
Indices: 16816647--16816673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16816637 TGTGACGTTA
16816647 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
16816674 AAGATTTTCT
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:16819580 original size:22 final size:22
Alignment explanation
Indices: 16819554--16819597 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16819544 TGTATATTTA
16819554 TATTTGTATCCCTAAAATTAAG
1 TATTTGTATCCCTAAAATTAAG
*
16819576 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAAAATTAAG
16819598 GACAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (22 bp):
TATTTGTATCCCTAAAATTAAG
Found at i:16823532 original size:22 final size:22
Alignment explanation
Indices: 16823506--16823549 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
16823496 TGTATATTTA
*
16823506 TATTTGTATTCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
16823528 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
16823550 GACAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:16825577 original size:36 final size:36
Alignment explanation
Indices: 16825520--16825605 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
16825510 AAAAAGATAG
*
16825520 ATAAAATAGCAGTTTACACTTTAAACATGTGTTAAT
1 ATAAAATAGCAGTTCACACTTTAAACATGTGTTAAT
* * *
16825556 ATAAAATAGTAGTGTCA-ACTTTAAACTTGTGTTCAT
1 ATAAAATAGCAGT-TCACACTTTAAACATGTGTTAAT
16825592 ATAAAATAGCAGTT
1 ATAAAATAGCAGTT
16825606 TACCTCAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
35 1 0.02
36 41 0.93
37 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (36 bp):
ATAAAATAGCAGTTCACACTTTAAACATGTGTTAAT
Found at i:16832274 original size:262 final size:264
Alignment explanation
Indices: 16831788--16832306 Score: 721
Period size: 262 Copynumber: 2.0 Consensus size: 264
16831778 CTATTGGACA
* ** * * * *
16831788 TTTACCCAAACCAAGGAAATGAACATTAGAACCAAAATTAACGCAATATTCAATTCATCATCAGT
1 TTTACACAAACCAAGGAAACCAACATTAGAACCAAAATCAACACAATATTAAATTCATCAGCAGT
* *
16831853 GAAACTCGGGAGGCCAACGACATACAGAATTACAGATCAAAAAAGATTTCAATCAAATTCAATCA
66 GAAACTAGGGAGGCCAACGACATACAGAATTACAGATCAAAAAAGATTTCAATCAAATGCAATCA
* * *
16831918 TAATTCAAATACAGCAACACATTCTAACACGGAATCCAGAGAGATAATTTAAGGTGTTTATTCTT
131 CAATTCAAATACAGCAACACATTCTAACACGGAATCCAGAGAGATAATTTAAGATGTTTATTCTC
*
16831983 AGCAATCAAAATATATATTTTATAGAACTAA-GAAACATTAATTGACATAGTCAA-GTGAATATC
196 AGAAATCAAAATATATATTTTATAGAACTAACG-AACATTAATTGACATAGTCAAGGTGAATATC
16832046 AGATG
260 AGATG
16832051 TTTACACAAACC-AGGAAACCAACATTAGAACCAAAATCAACACAATATTAAATTCATCAGCAGT
1 TTTACACAAACCAAGGAAACCAACATTAGAACCAAAATCAACACAATATTAAATTCATCAGCAGT
*
16832115 GAAACTAGGGAGAG-CAA-GAATATACAGAATTACAGATCAAAAAA-ATTTTCAATCAAATGCAA
66 GAAACTAGGGAG-GCCAACG-ACATACAGAATTACAGATCAAAAAAGA-TTTCAATCAAATGCAA
* * * * *
16832177 TCACGATTCAAATACAGCAACACATTTTAACACGGAATTCATAGA-ATTAATTTAAGATGTTTCT
128 TCACAATTCAAATACAGCAACACATTCTAACACGGAATCCAGAGAGA-TAATTTAAGATGTTTAT
* * **
16832241 TCTCAGAAATCGAAAA-ATATATTTTATAGAACTAACGCATATTAATTGATGTAGTCAAGGTGAA
192 TCTCAGAAATC-AAAATATATATTTTATAGAACTAACGAACATTAATTGACATAGTCAAGGTGAA
16832305 TA
256 TA
16832307 GACATGATTC
Statistics
Matches: 226, Mismatches: 23, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
261 3 0.01
262 199 0.88
263 24 0.11
ACGTcount: A:0.45, C:0.17, G:0.13, T:0.26
Consensus pattern (264 bp):
TTTACACAAACCAAGGAAACCAACATTAGAACCAAAATCAACACAATATTAAATTCATCAGCAGT
GAAACTAGGGAGGCCAACGACATACAGAATTACAGATCAAAAAAGATTTCAATCAAATGCAATCA
CAATTCAAATACAGCAACACATTCTAACACGGAATCCAGAGAGATAATTTAAGATGTTTATTCTC
AGAAATCAAAATATATATTTTATAGAACTAACGAACATTAATTGACATAGTCAAGGTGAATATCA
GATG
Found at i:16842207 original size:174 final size:176
Alignment explanation
Indices: 16841915--16842261 Score: 626
Period size: 174 Copynumber: 2.0 Consensus size: 176
16841905 TACAGTTAAG
*
16841915 CAGTTAAGCATTTCACTGCCTTCTTTCTAATAAAGTAGCCAAAAAAAAAAAAAAAAACTGCCTCT
1 CAGTTAAGCATTTCACTGCCTTCTTTCTAATAAAGTAGCCAAAAAAAAAAAAAAAAACTGCATCT
16841980 TAACAATAAGGGAATTGACTATCAACAGGAAATATTAAAATTTAAAAAAGAAAATGTTTACTTCC
66 TAACAATAAGGGAATTGACTATCAACAGGAAATATTAAAATTTAAAAAAGAAAATGTTTACTTCC
16842045 TCATTGAAAACTTAAACCTACATGAGTACACAAAAACTACATAGTA
131 TCATTGAAAACTTAAACCTACATGAGTACACAAAAACTACATAGTA
*
16842091 CAGTTAAGCATTTCACTGCCTTCTTTCTTATAAAGTAG-C-AAAAAAAAAAAAAAAACTGCATCT
1 CAGTTAAGCATTTCACTGCCTTCTTTCTAATAAAGTAGCCAAAAAAAAAAAAAAAAACTGCATCT
* * *
16842154 TAACGATAAGGGAGTTGACTATCAACAGGAAATATTAAAATTTTAAAAAGAAAATGTTTACTTCC
66 TAACAATAAGGGAATTGACTATCAACAGGAAATATTAAAATTTAAAAAAGAAAATGTTTACTTCC
*
16842219 TCATTGAAAAGTTAAACCTACATGAGTACACAAAAACTACATA
131 TCATTGAAAACTTAAACCTACATGAGTACACAAAAACTACATA
16842262 ATGCGAGTGA
Statistics
Matches: 165, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
174 127 0.77
175 1 0.01
176 37 0.22
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (176 bp):
CAGTTAAGCATTTCACTGCCTTCTTTCTAATAAAGTAGCCAAAAAAAAAAAAAAAAACTGCATCT
TAACAATAAGGGAATTGACTATCAACAGGAAATATTAAAATTTAAAAAAGAAAATGTTTACTTCC
TCATTGAAAACTTAAACCTACATGAGTACACAAAAACTACATAGTA
Found at i:16843398 original size:33 final size:33
Alignment explanation
Indices: 16843356--16843419 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
16843346 TTAAGCCTAT
16843356 GACCACTAGAAACATAAAAGAAACCACTAATAA
1 GACCACTAGAAACATAAAAGAAACCACTAATAA
* *
16843389 GACCACTAGAAACATAGAAGAAACCATTAAT
1 GACCACTAGAAACATAAAAGAAACCACTAAT
16843420 GACCTGGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.55, C:0.20, G:0.11, T:0.14
Consensus pattern (33 bp):
GACCACTAGAAACATAAAAGAAACCACTAATAA
Found at i:16849854 original size:30 final size:30
Alignment explanation
Indices: 16849820--16849896 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
16849810 GCTCTTAACT
* *
16849820 TTTAATTTATACTTAAAAAAGCCTTCAACC
1 TTTAATTTGTACATAAAAAAGCCTTCAACC
** * * *
16849850 TTTAATTTGTACCCAAATAAGCCTTTAATC
1 TTTAATTTGTACATAAAAAAGCCTTCAACC
16849880 TTTAATTTGTACATAAA
1 TTTAATTTGTACATAAA
16849897 TTAAATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.38, C:0.17, G:0.05, T:0.40
Consensus pattern (30 bp):
TTTAATTTGTACATAAAAAAGCCTTCAACC
Found at i:16866117 original size:70 final size:72
Alignment explanation
Indices: 16866043--16866178 Score: 179
Period size: 71 Copynumber: 1.9 Consensus size: 72
16866033 TATAAAAGTA
* *
16866043 ATTTTCTCAACAAAAACTA-CCTTTTATTTTTAAAATGTCATTTTTATTGAA-TT-TAAAAAATA
1 ATTTTCTCAACAAAAACTATCCTTTTATCTTTAAAACGTCATTTTTATT-AAGTTCTAAAAAATA
16866105 TATTTTTT
65 TATTTTTT
* * * **
16866113 ATTTTTTTAACGAAAACTATGTTTTTATCTTTAAAACGTCATTTTTATTAAGTTCTAAAAAATAT
1 ATTTTCTCAACAAAAACTATCCTTTTATCTTTAAAACGTCATTTTTATTAAGTTCTAAAAAATAT
16866178 A
66 A
16866179 AATATTTTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 18 0.32
71 27 0.48
72 11 0.20
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.49
Consensus pattern (72 bp):
ATTTTCTCAACAAAAACTATCCTTTTATCTTTAAAACGTCATTTTTATTAAGTTCTAAAAAATAT
ATTTTTT
Found at i:16866459 original size:73 final size:70
Alignment explanation
Indices: 16866272--16866459 Score: 180
Period size: 74 Copynumber: 2.6 Consensus size: 70
16866262 AATGTTGTCT
* * * * * *
16866272 TTGTTGAATTATGAAATTTTTTTTTATGTTTTTAATAAAGATTGTGTTTTCTATCTTAGAAGCAT
1 TTGTTGAATTATGAAATTTTTTTTCATGTTTTCAATAAAAAATGTGTTTTCTATCTTACAAACAT
*
16866337 TATTT
66 TATTA
** * * *
16866342 TTGTTGAATTTTAAAAAATAACTTTTTTCATGTTTTCAACAAAAAATGCAT-TTTATTTATCTTA
1 TTGTTGAA--TTATGAAAT--TTTTTTTCATGTTTTCAATAAAAAATG--TGTTT-TCTATCTTA
*
16866406 CAAACATTGTTA
59 CAAACATTATTA
16866418 TTGTTGAATTATGAAATTTTTTTGTCATGTTTTCAATAAAAA
1 TTGTTGAATTATGAAATTTTTTT-TCATGTTTTCAATAAAAA
16866460 CTACATCTTA
Statistics
Matches: 93, Mismatches: 17, Indels: 13
0.76 0.14 0.11
Matches are distributed among these distances:
70 8 0.09
72 12 0.13
73 17 0.18
74 28 0.30
75 3 0.03
76 25 0.27
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (70 bp):
TTGTTGAATTATGAAATTTTTTTTCATGTTTTCAATAAAAAATGTGTTTTCTATCTTACAAACAT
TATTA
Found at i:16867732 original size:21 final size:22
Alignment explanation
Indices: 16867694--16867737 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
16867684 TAATTTTGAA
* * *
16867694 TTTATATTTAAATTAATTTATT
1 TTTATATTAAAATAAATTAATT
16867716 TTTATA-TAAAATAAATTAATT
1 TTTATATTAAAATAAATTAATT
16867737 T
1 T
16867738 AAAATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTATATTAAAATAAATTAATT
Found at i:16877500 original size:15 final size:15
Alignment explanation
Indices: 16877480--16877510 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16877470 TCGAACCGAA
*
16877480 TCGATTTTGATCGGT
1 TCGATTATGATCGGT
16877495 TCGATTATGATCGGT
1 TCGATTATGATCGGT
16877510 T
1 T
16877511 ATTTAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.13, G:0.26, T:0.45
Consensus pattern (15 bp):
TCGATTATGATCGGT
Found at i:16881533 original size:93 final size:93
Alignment explanation
Indices: 16881286--16881533 Score: 254
Period size: 94 Copynumber: 2.6 Consensus size: 93
16881276 GCCTAATCAG
* * **
16881286 ATTTCATTTTTTCAAATAAAATTCTTCAATAATTTG-GTAGAATTAATTTCAAAATTTTATTTCT
1 ATTTTATTTTTT-AAATAAAATTCTCCAATAATTTGAGTAG-ATTAATTT-AAAAAATTATTTCT
* * *
16881350 AAACTCATGAAATTTTCCAATAGTTTGGTAAG
63 AAACTCATAAAATTTT-CAATAATTTGGTAAA
* * * * ** *
16881382 ATTTTA-TTTTTAAGTAAAATCCTCTAATTATTT-AGTAGGATTAATGAAAAAAATTTATTT-TT
1 ATTTTATTTTTTAAATAAAATTCTCCAATAATTTGAGTA-GATTAATTTAAAAAA-TTATTTCTA
16881444 AACTCATAAAATCTCTT-AATAATTTGGTAAA
64 AACTCATAAAAT-T-TTCAATAATTTGGTAAA
*
16881475 ATTTTATTTTTTAAATAAAATTCTCCAATAATTTGATTAGATTAATTTAAAAAATTATT
1 ATTTTATTTTTTAAATAAAATTCTCCAATAATTTGAGTAGATTAATTTAAAAAATTATT
16881534 ATTATTATTA
Statistics
Matches: 124, Mismatches: 21, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
93 39 0.31
94 69 0.56
95 11 0.09
96 5 0.04
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.46
Consensus pattern (93 bp):
ATTTTATTTTTTAAATAAAATTCTCCAATAATTTGAGTAGATTAATTTAAAAAATTATTTCTAAA
CTCATAAAATTTTCAATAATTTGGTAAA
Found at i:16881536 original size:3 final size:3
Alignment explanation
Indices: 16881528--16881569 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
16881518 AATTTAAAAA
*
16881528 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
16881570 TCCTCATGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:16893614 original size:26 final size:26
Alignment explanation
Indices: 16893584--16893647 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
16893574 TCATGATTTT
16893584 ATTTTATTTTTATTCTTATTTTATCA
1 ATTTTATTTTTATTCTTATTTTATCA
***
16893610 ATTTT-TTAAAGATTCTTATTTTATCA
1 ATTTTATT-TTTATTCTTATTTTATCA
16893636 ATTTTTATTTTT
1 A-TTTTATTTTT
16893648 CCTATATTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.07
26 21 0.72
27 4 0.14
28 2 0.07
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (26 bp):
ATTTTATTTTTATTCTTATTTTATCA
Found at i:16902589 original size:8 final size:8
Alignment explanation
Indices: 16902572--16902612 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
16902562 TTCAGTAACA
16902572 TATTTCTT
1 TATTTCTT
*
16902580 TATTTTTT
1 TATTTCTT
16902588 TATTTCTTT
1 TATTTC-TT
16902597 TATTCTCTT
1 TATT-TCTT
16902606 TATTTCT
1 TATTTCT
16902613 AGAGGTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 15 0.52
9 12 0.41
10 2 0.07
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTCTT
Found at i:16906725 original size:12 final size:12
Alignment explanation
Indices: 16906708--16906734 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
16906698 CCGTTTCATC
16906708 ATTATTATTGTT
1 ATTATTATTGTT
16906720 ATTATTATTGTT
1 ATTATTATTGTT
16906732 ATT
1 ATT
16906735 TGTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:16909754 original size:17 final size:17
Alignment explanation
Indices: 16909732--16909765 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16909722 TCCTAATGGA
16909732 TTGCATAATTTAAACAT
1 TTGCATAATTTAAACAT
16909749 TTGCATAATTTAAACAT
1 TTGCATAATTTAAACAT
16909766 GAACTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
TTGCATAATTTAAACAT
Found at i:16911540 original size:19 final size:21
Alignment explanation
Indices: 16911488--16911538 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 21
16911478 TTTGATGATC
16911488 TTTATATTTATTTA-AGTTAT
1 TTTATATTTATTTAGAGTTAT
**
16911508 TTTA-GGTTATTTAGA-TTAT
1 TTTATATTTATTTAGAGTTAT
16911527 TTTATATTTATT
1 TTTATATTTATT
16911539 AGTTTTTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (21 bp):
TTTATATTTATTTAGAGTTAT
Found at i:16914930 original size:27 final size:27
Alignment explanation
Indices: 16914892--16914969 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
16914882 GGTTGGGTAG
16914892 GTTGAGAATCTAGTTTTCAAGGGGCTA
1 GTTGAGAATCTAGTTTTCAAGGGGCTA
* *
16914919 GTTGAGATTCTAGTTTTGAAGGGGCTA
1 GTTGAGAATCTAGTTTTCAAGGGGCTA
* * * *
16914946 GTTGGGAATATGGTTTTGAAGGGG
1 GTTGAGAATCTAGTTTTCAAGGGG
16914970 TTGGTTGGGA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.06, G:0.36, T:0.35
Consensus pattern (27 bp):
GTTGAGAATCTAGTTTTCAAGGGGCTA
Found at i:16916870 original size:25 final size:25
Alignment explanation
Indices: 16916841--16916891 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
16916831 GAAATCAAGC
* *
16916841 TGCACTAATGTAGGAGAATTAGATT
1 TGCACTAATGTAAGAGAATCAGATT
16916866 TGCACTAATGTAAGAGAATCAGATT
1 TGCACTAATGTAAGAGAATCAGATT
16916891 T
1 T
16916892 CTACACAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (25 bp):
TGCACTAATGTAAGAGAATCAGATT
Found at i:16917780 original size:28 final size:26
Alignment explanation
Indices: 16917744--16917816 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 26
16917734 AATTGATACC
*
16917744 ATAATTAAAAATAATTATAAAAACAATA
1 ATAAATAAAAATAATTA-AAAAACAA-A
* *
16917772 ATAAATAAAATTAA-TAAAAAATAAA
1 ATAAATAAAAATAATTAAAAAACAAA
*
16917797 ATATTAATAAAAATGATTAA
1 ATA--AATAAAAATAATTAA
16917817 TTATTTGACC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.11
26 7 0.19
27 11 0.30
28 15 0.41
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (26 bp):
ATAAATAAAAATAATTAAAAAACAAA
Found at i:16917798 original size:16 final size:18
Alignment explanation
Indices: 16917768--16917809 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16917758 TTATAAAAAC
*
16917768 AATAATAAAT-AAA-ATT
1 AATAAAAAATAAAATATT
16917784 AATAAAAAATAAAATATT
1 AATAAAAAATAAAATATT
16917802 AATAAAAA
1 AATAAAAA
16917810 TGATTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 3 0.13
18 11 0.48
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAAAAATAAAATATT
Found at i:16931124 original size:23 final size:23
Alignment explanation
Indices: 16931088--16931142 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
16931078 AGATGAGTGT
*
16931088 ACACTCAAAAGAACAACTGAAAG
1 ACACTTAAAAGAACAACTGAAAG
* *
16931111 ATACTTAAAAGAACAACTTAAAG
1 ACACTTAAAAGAACAACTGAAAG
16931134 ACACTTAAA
1 ACACTTAAA
16931143 GTAAGAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.56, C:0.18, G:0.09, T:0.16
Consensus pattern (23 bp):
ACACTTAAAAGAACAACTGAAAG
Found at i:16933356 original size:72 final size:69
Alignment explanation
Indices: 16933078--16933424 Score: 229
Period size: 72 Copynumber: 4.9 Consensus size: 69
16933068 CTGAAACTAT
*
16933078 ATTTTTGAAAATTTAAAAATTTAACAAAAATCACATTTTTAAGATAAAAACATAATGGATG-TAA
1 ATTTTTGAAAATTTAAAAATTTAACAAAAATCACA-TTTTAAGATAAAAACGTAATGGATGTTAA
16933142 AACTTA
65 AA-TTA
* * * ** * * * * *
16933148 ATTTTTG-AAATTT-TAGATTTAAAAAAAAATCATGTTTTGAAGATAAAAATGTAGTTGATATTG
1 ATTTTTGAAAATTTAAAAATTT-AACAAAAATCACATTTT-AAGATAAAAACGTAATGGATGTTA
*
16933211 AAA-CA
64 AAATTA
* * * * * * * * * *
16933216 ATATTTTGAAAATTTTGAAATTTTAACAAATACCGCATTTTTAAAATAAGAAACATAGTAGTTGT
1 AT-TTTTGAAAA-TTTAAAAATTTAACAAAAATCACA-TTTTAAGATAA-AAACGTAATGGATGT
*
16933281 TAAAATTT
62 TAAAATTA
*
16933289 TTTTTTGAAAATTTAAAAATTTAACAAAAATCACATTTTAAGGATAAAGAACGTAATGGATGCTT
1 ATTTTTGAAAATTTAAAAATTTAACAAAAATCACATTTTAA-GATAAA-AACGTAATGGATG-TT
* *
16933354 AAACTTT
63 AAAATTA
* * * * * *
16933361 ATTTTCG-AAATTATGAAATTTTAA-TAAAATCCACATTTTGAAGTTAAAAAACGTAATGCATGT
1 ATTTTTGAAAATT-TAAAAATTTAACAAAAAT-CACATTTT-AAGAT-AAAAACGTAATGGATGT
16933424 T
62 T
16933425 GGTACTCAAA
Statistics
Matches: 211, Mismatches: 49, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
68 12 0.06
69 37 0.18
70 21 0.10
71 60 0.28
72 75 0.36
73 6 0.03
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (69 bp):
ATTTTTGAAAATTTAAAAATTTAACAAAAATCACATTTTAAGATAAAAACGTAATGGATGTTAAA
ATTA
Found at i:16933448 original size:11 final size:12
Alignment explanation
Indices: 16933432--16933460 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
16933422 GTTGGTACTC
16933432 AAAATAAAAT-T
1 AAAATAAAATGT
16933443 AAAATAAAATGT
1 AAAATAAAATGT
16933455 AAAATA
1 AAAATA
16933461 TATTTACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AAAATAAAATGT
Found at i:16935995 original size:22 final size:22
Alignment explanation
Indices: 16935935--16935998 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 22
16935925 CTACAAAAAA
*
16935935 TTAATTTTAAATGAAATAAATTTT
1 TTAATTTT-AAT-AAATAAATTAT
*
16935959 TATAATTTGGAATAAA-AAATTAT
1 T-TAATTT-TAATAAATAAATTAT
16935982 TTAATTTTATATAAATA
1 TTAATTTTA-ATAAATA
16935999 TTATTGTTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 1 0.03
22 11 0.33
23 8 0.24
24 4 0.12
25 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
TTAATTTTAATAAATAAATTAT
Found at i:16965802 original size:11 final size:11
Alignment explanation
Indices: 16965784--16965817 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16965774 AAAAGAATAG
16965784 GAAAGGAAAAT
1 GAAAGGAAAAT
*
16965795 GAAGGGAAAAT
1 GAAAGGAAAAT
16965806 -AAAGGAAAAT
1 GAAAGGAAAAT
16965816 GA
1 GA
16965818 CACATAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.29, T:0.09
Consensus pattern (11 bp):
GAAAGGAAAAT
Found at i:16972852 original size:25 final size:25
Alignment explanation
Indices: 16972818--16972870 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
16972808 TTTCCCTTTA
* *
16972818 CTATTCGATGTGGGATTAATGTATC
1 CTATTCGATGTGAGATTAATGTACC
16972843 CTATTCGATGTGAGATTAATGTACC
1 CTATTCGATGTGAGATTAATGTACC
16972868 CTA
1 CTA
16972871 CTTGCATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (25 bp):
CTATTCGATGTGAGATTAATGTACC
Found at i:16981916 original size:2 final size:2
Alignment explanation
Indices: 16981909--16981939 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
16981899 TTGATGTGTT
16981909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16981940 GTTAATTTAG
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16982332 original size:21 final size:20
Alignment explanation
Indices: 16982282--16982333 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
16982272 TAAAAAAAGG
*
16982282 TATTATGATGAAATTTTAAC
1 TATTATGAAGAAATTTTAAC
* *
16982302 CATTGCTGAAGAAATTTTAAC
1 TATT-ATGAAGAAATTTTAAC
16982323 TATTATTGAAG
1 TATTA-TGAAG
16982334 GATTTTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (20 bp):
TATTATGAAGAAATTTTAAC
Found at i:16983786 original size:20 final size:21
Alignment explanation
Indices: 16983737--16983791 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
16983727 ATTCATGCAC
16983737 CCTTTTAAAACAAAAGGTTAA
1 CCTTTTAAAACAAAAGGTTAA
16983758 CCTTTTAAAACAAAAGGTTAA
1 CCTTTTAAAACAAAAGGTTAA
*
16983779 CCTTTAAAAACAA
1 CCTTTTAAAACAA
16983792 TGCCATTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.27
Consensus pattern (21 bp):
CCTTTTAAAACAAAAGGTTAA
Found at i:16989021 original size:22 final size:22
Alignment explanation
Indices: 16988993--16989034 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16988983 TTTTCTATCT
*
16988993 TTAATTCTAGGGATACAAATAC
1 TTAATTCTAGAGATACAAATAC
*
16989015 TTAATTCTAGAGATATAAAT
1 TTAATTCTAGAGATACAAAT
16989035 GTAAATATAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTAATTCTAGAGATACAAATAC
Found at i:16991622 original size:14 final size:14
Alignment explanation
Indices: 16991603--16991630 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16991593 AAAATATGAG
16991603 ATTAATAATTAGTC
1 ATTAATAATTAGTC
16991617 ATTAATAATTAGTC
1 ATTAATAATTAGTC
16991631 TAATAATCCT
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:0.07, T:0.43
Consensus pattern (14 bp):
ATTAATAATTAGTC
Found at i:16995038 original size:21 final size:20
Alignment explanation
Indices: 16995008--16995046 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16994998 ATAGTCATAA
*
16995008 TTATAGTTCAAGTTTTTTAGG
1 TTATAATTC-AGTTTTTTAGG
*
16995029 TTATAATTCATTTTTTTA
1 TTATAATTCAGTTTTTTA
16995047 CAAGTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (20 bp):
TTATAATTCAGTTTTTTAGG
Found at i:16995404 original size:16 final size:17
Alignment explanation
Indices: 16995383--16995421 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
16995373 TATTTGATGA
*
16995383 AATAAAA-ATTAGTTAT
1 AATAAAAGATTAATTAT
16995399 AATAAAAGATTAATTAT
1 AATAAAAGATTAATTAT
*
16995416 ATTAAA
1 AATAAA
16995422 GATAAAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
AATAAAAGATTAATTAT
Found at i:16996355 original size:3 final size:3
Alignment explanation
Indices: 16996341--16996384 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
16996331 ATCAACACCT
*
16996341 TTC TTA TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
16996385 ATCATTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16997916 original size:119 final size:119
Alignment explanation
Indices: 16997705--16997934 Score: 379
Period size: 119 Copynumber: 1.9 Consensus size: 119
16997695 CAAATAAATG
*
16997705 TATGCACCCAATGCCAGTCTCAATATGATAGATATTTGCCTATGCCATGCCACCTTCATTTGTTT
1 TATGCACCCAATGCCAGTCTCAATATGATAGATATTTGCCTATGCCACGCCACCTTCATTTGTTT
**
16997770 TAGTCTCAATTCTTCCCATATATCTGCAATTGAGTTCCCAATTCTTTCCATATA
66 TAGTCTCAATTCTTCCCATATATCTGCAATCAAGTTCCCAATTCTTTCCATATA
** * * *
16997824 TATGCACCCCCTGCCAGTCTCAATATGATAGATATTTGCCTATGTCACGCCATCTTCGTTTGTTT
1 TATGCACCCAATGCCAGTCTCAATATGATAGATATTTGCCTATGCCACGCCACCTTCATTTGTTT
*
16997889 TAGTCTTAATTCTTCCCATATATCTGCAATCAAGTTCCCAATTCTT
66 TAGTCTCAATTCTTCCCATATATCTGCAATCAAGTTCCCAATTCTT
16997935 CCCACATTCC
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 102 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (119 bp):
TATGCACCCAATGCCAGTCTCAATATGATAGATATTTGCCTATGCCACGCCACCTTCATTTGTTT
TAGTCTCAATTCTTCCCATATATCTGCAATCAAGTTCCCAATTCTTTCCATATA
Found at i:16999280 original size:93 final size:93
Alignment explanation
Indices: 16999097--16999277 Score: 290
Period size: 93 Copynumber: 1.9 Consensus size: 93
16999087 CACAATACTC
* * * * *
16999097 CATACAGTTTTGAAAAAGTACGCATTATACCCGTCAAGGCCTGGTTCTTTATCACTATGTGTGAA
1 CATACAGTTTTGAAAAAGTACACATTATACCCGACAAGGCCTAGTGCTTTACCACTATGTGTGAA
16999162 AAGATACCTTGCTGAATTTCTTTCCTGG
66 AAGATACCTTGCTGAATTTCTTTCCTGG
*
16999190 CATACAGTTTTGAAAAAGTGCACATTATACCCGACAAGGCCTAGTGCTTTACCACTATGTTGTGA
1 CATACAGTTTTGAAAAAGTACACATTATACCCGACAAGGCCTAGTGCTTTACCACTATG-TGTGA
*
16999255 AAAGATACCTTGTTGAATTTCTT
65 AAAGATACCTTGCTGAATTTCTT
16999278 CCTTGGTTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 53 0.66
94 27 0.34
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (93 bp):
CATACAGTTTTGAAAAAGTACACATTATACCCGACAAGGCCTAGTGCTTTACCACTATGTGTGAA
AAGATACCTTGCTGAATTTCTTTCCTGG
Found at i:17002084 original size:19 final size:20
Alignment explanation
Indices: 17002056--17002094 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17002046 TAATTTTGTA
17002056 TTATTATT-AAGTTTATTTT
1 TTATTATTAAAGTTTATTTT
*
17002075 TTATTTTTAAAGTTTATTTT
1 TTATTATTAAAGTTTATTTT
17002095 AAAGATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (20 bp):
TTATTATTAAAGTTTATTTT
Found at i:17002284 original size:17 final size:17
Alignment explanation
Indices: 17002254--17002294 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
17002244 ACTGAACCGG
17002254 ATAAGAAAAGAAG-AAGA
1 ATAA-AAAAGAAGAAAGA
17002271 ATAAAAAAGAAAGAAAGA
1 ATAAAAAAG-AAGAAAGA
17002289 A-AAAAA
1 ATAAAAA
17002295 TATAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 5 0.23
17 12 0.55
18 5 0.23
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (17 bp):
ATAAAAAAGAAGAAAGA
Found at i:17002304 original size:17 final size:18
Alignment explanation
Indices: 17002284--17002317 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
17002274 AAAAAGAAAG
17002284 AAAGAAAAAA-ATATAAA
1 AAAGAAAAAATATATAAA
17002301 AAAGAAAAAATATATAA
1 AAAGAAAAAATATATAA
17002318 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (18 bp):
AAAGAAAAAATATATAAA
Found at i:17002322 original size:3 final size:3
Alignment explanation
Indices: 17002309--17002361 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
17002299 AAAAAGAAAA
17002309 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17002355 AAT AAT A
1 AAT AAT A
17002362 CAAAATGGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:17005580 original size:19 final size:20
Alignment explanation
Indices: 17005543--17005583 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
17005533 TTATCAATGG
* *
17005543 TGATTCAAGATTAGCTCTTT
1 TGATTCAAGATGAGATCTTT
17005563 TGATT-AAGATGAGATCTTT
1 TGATTCAAGATGAGATCTTT
17005582 TG
1 TG
17005584 GTCGAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (20 bp):
TGATTCAAGATGAGATCTTT
Found at i:17005720 original size:27 final size:27
Alignment explanation
Indices: 17005659--17005729 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
17005649 TAGGTAATTT
*
17005659 ATCGAGATGAGCTTTTTGATCGAGGTG
1 ATCGAGATGAGCTCTTTGATCGAGGTG
* * *
17005686 -GCTTAGATGAGCTCTTTGATTGAGGTG
1 ATC-GAGATGAGCTCTTTGATCGAGGTG
17005713 ATCGAGATGAGCTCTTT
1 ATCGAGATGAGCTCTTT
17005730 TGGCTAAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.03
27 34 0.94
28 1 0.03
ACGTcount: A:0.21, C:0.13, G:0.31, T:0.35
Consensus pattern (27 bp):
ATCGAGATGAGCTCTTTGATCGAGGTG
Found at i:17005744 original size:19 final size:19
Alignment explanation
Indices: 17005720--17005756 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
17005710 GTGATCGAGA
17005720 TGAGCTCTTTTGGCTAAGG
1 TGAGCTCTTTTGGCTAAGG
17005739 TGAGCTCTTTTGGCTAAG
1 TGAGCTCTTTTGGCTAAG
17005757 CTAATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.16, G:0.30, T:0.38
Consensus pattern (19 bp):
TGAGCTCTTTTGGCTAAGG
Found at i:17006332 original size:85 final size:85
Alignment explanation
Indices: 17006022--17006336 Score: 328
Period size: 85 Copynumber: 3.7 Consensus size: 85
17006012 GGCTGAGTTG
* * * * * * * *
17006022 TTTTATCAAATTAGGCTTTTATGAAGGCATTTTATAGATCTAAGCTATTTTGGTCAAGTTGAGTC
1 TTTTGTCAAATTAGGCCTTTATGAAGGTATTTCATAGATCCAAGCTCTTTTGGTCGAGCTGAGTC
* *
17006087 TGAGCTCTTTGGTCGAGTTA
66 TGAGCTCTTTGGTAGAGCTA
** * * * * ** * ** *
17006107 TTTTGTGGAATTATGCATTTATGAATGAATTTTGTAGATCCAAGCTCTTTCGG-CTGAAATAAGT
1 TTTTGTCAAATTAGGCCTTTATGAAGGTATTTCATAGATCCAAGCTCTTTTGGTC-GAGCTGAGT
* *
17006171 CTGAGCTCTTTAGTTGAGCTA
65 CTGAGCTCTTTGGTAGAGCTA
* * *
17006192 TTTTGTTAAATTAGGCCTTTATGAAGGTATTTCGTAGATCCAAGCTCTTTTGGTCGAGCTGAGTT
1 TTTTGTCAAATTAGGCCTTTATGAAGGTATTTCATAGATCCAAGCTCTTTTGGTCGAGCTGAGTC
* *
17006257 TGAGCTCCTTGGTAGAGCTG
66 TGAGCTCTTTGGTAGAGCTA
*
17006277 TTTTGTCAAATTAAGCCTTTATGAAGGTATTTCATAGATCCTAA-CTCTTTTGGTCGAGCT
1 TTTTGTCAAATTAGGCCTTTATGAAGGTATTTCATAGATCC-AAGCTCTTTTGGTCGAGCT
17006337 AAATCCAAGC
Statistics
Matches: 190, Mismatches: 37, Indels: 6
0.82 0.16 0.03
Matches are distributed among these distances:
84 1 0.01
85 186 0.98
86 3 0.02
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (85 bp):
TTTTGTCAAATTAGGCCTTTATGAAGGTATTTCATAGATCCAAGCTCTTTTGGTCGAGCTGAGTC
TGAGCTCTTTGGTAGAGCTA
Found at i:17006568 original size:85 final size:85
Alignment explanation
Indices: 17006412--17006952 Score: 308
Period size: 85 Copynumber: 6.4 Consensus size: 85
17006402 CTATTTGACA
* * * * * **
17006412 GAGCTATTTTGTCGAATTAGGCCTTTATAAATGTATTTTATAAATTTAAGCTCTTTTGGTCGAGC
1 GAGCTATTTTGTCGAATTAGGCCTTTATGAAGGTATTTTATAGATTCAAGCTCTTTTAGTAAAGC
* *
17006477 TGAGTTTGAA-CTTTTTGGCT
66 TAAGTTT-AAGCTCTTTGGCT
* * *
17006497 GAGCTATTTTATTGAATTAAGCCTTTATGAAGGTATTTTATAGATTCAAGCTCTTTTAGTAAAGC
1 GAGCTATTTTGTCGAATTAGGCCTTTATGAAGGTATTTTATAGATTCAAGCTCTTTTAGTAAAGC
17006562 TAAGTTTAAGCTCTTTGGCT
66 TAAGTTTAAGCTCTTTGGCT
* * * * * * ** *
17006582 AAGCTATTTTGTCAAATTAGGCCTTTATGAAGGTATTTTATAGATCCGAGCTCCTTTGGTTGAGT
1 GAGCTATTTTGTCGAATTAGGCCTTTATGAAGGTATTTTATAGATTCAAGCTCTTTTAGTAAAGC
* ** * *
17006647 TGAGTCCAAGATCTTTGGCC
66 TAAGTTTAAGCTCTTTGGCT
* * * * * **
17006667 GAGTTATTTTTTCGAATT-GGACCTTTATAAAGGCATTTTGTAGATAT-AAGCTCTTTT-GATTG
1 GAGCTATTTTGTCGAATTAGG-CCTTTATGAAGGTATTTTATAGAT-TCAAGCTCTTTTAG-TAA
* * * * *
17006729 TGTTGAGTCTAAGCTCTTTGAC-
63 AGCTAAGTTTAAGCTCTTTGGCT
* * * * * ** * * ***
17006751 CAACTTGTTTTGTCAAATT-GAACCTTTATGAAGACATTTTGTAGATTCGAGCTC-TTTAGGCCT
1 GAGC-TATTTTGTCGAATTAG-GCCTTTATGAAGGTATTTTATAGATTCAAGCTCTTTTA-GTAA
* ** *
17006814 AGTTGTGTTCAAGCTCTTTGGCT
63 AGCTAAGTTTAAGCTCTTTGGCT
* * * * * * *
17006837 AAGCTGTTTTGT-GAAATT-GAGCTTTTATGAAGGTATTTTTATAGATCCGAGCTCTTTTGGTCA
1 GAGCTATTTTGTCG-AATTAG-GCCTTTATGAAGGTA-TTTTATAGATTCAAGCTCTTTTAGTAA
* * ** *
17006900 AGCTGAGTTTAAGCTATTTAACC
63 AGCTAAGTTTAAGCTCTTTGGCT
* * *
17006923 GAACTGTTTTGTCAAATTAGGCCTTTATGA
1 GAGCTATTTTGTCGAATTAGGCCTTTATGA
17006953 TTGAGTCTGA
Statistics
Matches: 357, Mismatches: 84, Indels: 29
0.76 0.18 0.06
Matches are distributed among these distances:
84 10 0.03
85 283 0.79
86 60 0.17
87 4 0.01
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.42
Consensus pattern (85 bp):
GAGCTATTTTGTCGAATTAGGCCTTTATGAAGGTATTTTATAGATTCAAGCTCTTTTAGTAAAGC
TAAGTTTAAGCTCTTTGGCT
Found at i:17006720 original size:170 final size:170
Alignment explanation
Indices: 17006413--17006723 Score: 378
Period size: 170 Copynumber: 1.8 Consensus size: 170
17006403 TATTTGACAG
* * ** *
17006413 AGCTATTTTGTCGAATTAGGCCTTTATAAATGTATTTTATAAATTTAAGCTCTTTTGGTCGAGCT
1 AGCTATTTTGTCAAATTAGGCCTTTATAAAGGTATTTTATAAATCCAAGCTCCTTTGGTCGAGCT
** * * * * *
17006478 GAGTTTGAACTTTTTGGCTGAGCTATTTTATTGAATTAAGCCTTTATGAAGGTATTTTATAGATT
66 GAGTTCCAAATCTTTGGCCGAGCTATTTTATTGAATTAAGCCTTTATAAAGGCATTTTATAGATT
17006543 CAAGCTCTTTTAGTAAAGCTAAGTTTAAGCTCTTTGGCTA
131 CAAGCTCTTTTAGTAAAGCTAAGTTTAAGCTCTTTGGCTA
* * * * *
17006583 AGCTATTTTGTCAAATTAGGCCTTTATGAAGGTATTTTATAGATCCGAGCTCCTTTGGTTGAGTT
1 AGCTATTTTGTCAAATTAGGCCTTTATAAAGGTATTTTATAAATCCAAGCTCCTTTGGTCGAGCT
* * *
17006648 GAG-TCCAAGATCTTTGGCCGAGTTATTTT-TTCGAATT-GGACCTTTATAAAGGCATTTTGTAG
66 GAGTTCCAA-ATCTTTGGCCGAGCTATTTTATT-GAATTAAG-CCTTTATAAAGGCATTTTATAG
17006710 ATAT-AAGCTCTTTT
128 AT-TCAAGCTCTTTT
17006724 GATTGTGTTG
Statistics
Matches: 117, Mismatches: 20, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
169 6 0.05
170 110 0.94
171 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.42
Consensus pattern (170 bp):
AGCTATTTTGTCAAATTAGGCCTTTATAAAGGTATTTTATAAATCCAAGCTCCTTTGGTCGAGCT
GAGTTCCAAATCTTTGGCCGAGCTATTTTATTGAATTAAGCCTTTATAAAGGCATTTTATAGATT
CAAGCTCTTTTAGTAAAGCTAAGTTTAAGCTCTTTGGCTA
Found at i:17007224 original size:85 final size:85
Alignment explanation
Indices: 17006956--17007227 Score: 235
Period size: 85 Copynumber: 3.2 Consensus size: 85
17006946 TTTATGATTG
* * * * * * ** * *
17006956 AGTCTGAGCTTTTTGGCTAAACAATTTTGTCTAATTAAGCCTTTATGAAGGCATTTTATAGATCC
1 AGTCTGAGCTTTTTGGCTGAGCTAGTTTATCAAATTGGGCCTTTATGAAGGTATTTTATAGATTC
*
17007021 AAGCTCTTTTGGTTGAGCTGA
66 AAGCTCTTTTGGTAGAGCT-A
* * * * * * *
17007042 A-TCTGAGCTCTTTAGCTGAGTTAGTTTGTCTAATTGGGTCTTTATGAAGGTATTTTGTAGATTC
1 AGTCTGAGCTTTTTGGCTGAGCTAGTTTATCAAATTGGGCCTTTATGAAGGTATTTTATAGATTC
* * *
17007106 AAACTCTTTTGGTCA-AGTTT
66 AAGCTCTTTTGGT-AGAGCTA
* ** * * *
17007126 TGTCAAAGCTTTTTGG-TCGAGCTATTTTATCAAATTTGGCCTTTATGAAGGTATTTTCTAGATT
1 AGTCTGAGCTTTTTGGCT-GAGCTAGTTTATCAAATTGGGCCTTTATGAAGGTATTTTATAGATT
* *
17007190 CGAGCTCTTTTGATAGAGCTA
65 CAAGCTCTTTTGGTAGAGCTA
17007211 AGTCTGAGCTTTTTGGC
1 AGTCTGAGCTTTTTGGC
17007228 CTAGCTTTCC
Statistics
Matches: 144, Mismatches: 37, Indels: 10
0.75 0.19 0.05
Matches are distributed among these distances:
84 2 0.01
85 141 0.98
86 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (85 bp):
AGTCTGAGCTTTTTGGCTGAGCTAGTTTATCAAATTGGGCCTTTATGAAGGTATTTTATAGATTC
AAGCTCTTTTGGTAGAGCTA
Found at i:17008803 original size:18 final size:19
Alignment explanation
Indices: 17008780--17008824 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
17008770 GTAAATTAAT
* *
17008780 AAATAACACAT-AAAACTA
1 AAATAAAACATAAAAAATA
*
17008798 AAATAAAACTTAAAAAATA
1 AAATAAAACATAAAAAATA
17008817 AAATAAAA
1 AAATAAAA
17008825 TAAAAAACCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (19 bp):
AAATAAAACATAAAAAATA
Found at i:17008831 original size:19 final size:19
Alignment explanation
Indices: 17008791--17008831 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17008781 AATAACACAT
* *
17008791 AAAACTAAAATAAAACTTA
1 AAAAATAAAATAAAACTAA
17008810 AAAAATAAAATAAAA-TAA
1 AAAAATAAAATAAAACTAA
17008828 AAAA
1 AAAA
17008832 CCAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAATAAAATAAAACTAA
Found at i:17008856 original size:19 final size:18
Alignment explanation
Indices: 17008809--17008856 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
17008799 AATAAAACTT
* *
17008809 AAAAAATAAAATAAAATA
1 AAAAAACAAAATAAAAAA
*
17008827 AAAAACCAAAATTAAAAAA
1 AAAAAACAAAA-TAAAAAA
*
17008846 AAAAAAGAAAA
1 AAAAAACAAAA
17008857 AAATTGATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (18 bp):
AAAAAACAAAATAAAAAA
Found at i:17013898 original size:62 final size:61
Alignment explanation
Indices: 17013832--17013948 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 61
17013822 CCCCTCTTCA
17013832 CATAATTACTA-AAAT-GTGCCTCTGACCAT-AGTTGACCAAAATTACTATGACGCCCCTACAAC
1 CATAATTAC-ACAAATGGT-CCTCT-ACCATCAGTTG-CCAAAATTACTATGACGCCCCTACAAC
* * * *
17013894 CATAATTACACAAATGGTCTTCTACCATCATTTGCTAAAATTACTATGATGCCCC
1 CATAATTACACAAATGGTCCTCTACCATCAGTTGCCAAAATTACTATGACGCCCC
17013949 CTAGCATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
61 25 0.52
62 21 0.44
63 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.29
Consensus pattern (61 bp):
CATAATTACACAAATGGTCCTCTACCATCAGTTGCCAAAATTACTATGACGCCCCTACAAC
Found at i:17015153 original size:415 final size:410
Alignment explanation
Indices: 17014632--17015427 Score: 1023
Period size: 414 Copynumber: 1.9 Consensus size: 410
17014622 TAATTGACTA
* * *
17014632 AAATTACTATAATACCCTTTAACCATAATTATAAAAAAAAAATCCCTTTTGATTACTTGATATAA
1 AAATTACTATAATACCCCTTAACCATAATTAAAAAAAAAAAAACCCTTTTGATTACTTGATATAA
* ** * *
17014697 TGCCTTACCTATTATAATTATGAAAATACCGTTCATATTATAA-TTAGCTAAAATTATTATAATA
66 TACCTTACCTACCATAATTATGAAAATACCCTTCATATTATAATTTA-CTAAAATTACTA-AATA
* * * * *
17014761 CCTTTTAAGCATAATTACGAAAATATCTTTTTGAA-AGCTTAATAATTA-AGCATTAAATTTTAA
129 CCGTATAAACATAATGACGAAAATA-CTTTTTGAATAGCTTAAGAATTACA-CATTAAATTTTAA
* *
17014824 CATCCATACAATAATATGAAATTAATACACTTAGAAATAATTATAATGCCCTTTTAATTACTTAA
192 CATCCATACAATAATATG-AATTAATACACTTAGAAATAATCATAATGCCCTTTTAATCACTTAA
* ** *
17014889 CGATT-AATTGCATGCATTTAAATTGATTGTAATG-CTCTTCTTTCAATGATT-ATCTAAAATTA
256 CGATTGAATTACATGCATCCAAATTGATTGTAATGTC-CTTCTTTCAATAATTAAT-TAAAATTA
* * *
17014951 CTATAATGTCCCTCTCAACATATTTACTAAAATAGC-CCTCTTACCATAACTGGTCAAAATTAAA
319 CTATAATGCCCCTCTCAACATATTTACTAAAATA-CTCCTCTTAACATAACTAGTCAAAATTAAA
17015015 ATTATATCCCTACAACCATCATTTTTTG
383 ATTATATCCCTACAACCATCATTTTTTG
* * * *
17015043 AAATTACTATAATACCCCTTAGCCATAATTACCAAAAAAAAAAAAAACCTTTTTGATTGCTTTAT
1 AAATTACTATAATACCCCTTAACCATAATT----AAAAAAAAAAAAACCCTTTTGATTACTTGAT
* * *
17015108 ATAATACCTGT-CCTACCATAATTATGAAAATACCCTTCATATTATAATTTATTGAAATTACTAC
62 ATAATACCT-TACCTACCATAATTATGAAAATACCCTTCATATTATAATTTACTAAAATTACTAA
** * * *
17015172 ATACCGTATAAATGTAATGATGAAAATACTTTTTTAATTGCTTAAGAATTACACATTAAATTTTA
126 ATACCGTATAAACATAATGACGAAAATACTTTTTGAATAGCTTAAGAATTACACATTAAATTTTA
* * ** *
17015237 ACATCCATATAATAATATGAATTAATCCTTTTAGAAATAATCATAATGCCCTTTTAATCACTTGA
191 ACATCCATACAATAATATGAATTAATACACTTAGAAATAATCATAATGCCCTTTTAATCACTTAA
* *
17015302 CGATTGAATTACATGCATCCAAATTGATTTTAATGTCCTTTTTTCAATAATTAATTAAAATTACT
256 CGATTGAATTACATGCATCCAAATTGATTGTAATGTCCTTCTTTCAATAATTAATTAAAATTACT
* * *
17015367 ATAATGCCCCTTTCAACATATTTACTAAAATACTCCTCTTAACATAATTAGTCAAAGTTAA
321 ATAATGCCCCTCTCAACATATTTACTAAAATACTCCTCTTAACATAACTAGTCAAAATTAA
17015428 TATAATACTC
Statistics
Matches: 329, Mismatches: 44, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
411 28 0.09
413 54 0.16
414 163 0.50
415 80 0.24
416 4 0.01
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (410 bp):
AAATTACTATAATACCCCTTAACCATAATTAAAAAAAAAAAAACCCTTTTGATTACTTGATATAA
TACCTTACCTACCATAATTATGAAAATACCCTTCATATTATAATTTACTAAAATTACTAAATACC
GTATAAACATAATGACGAAAATACTTTTTGAATAGCTTAAGAATTACACATTAAATTTTAACATC
CATACAATAATATGAATTAATACACTTAGAAATAATCATAATGCCCTTTTAATCACTTAACGATT
GAATTACATGCATCCAAATTGATTGTAATGTCCTTCTTTCAATAATTAATTAAAATTACTATAAT
GCCCCTCTCAACATATTTACTAAAATACTCCTCTTAACATAACTAGTCAAAATTAAAATTATATC
CCTACAACCATCATTTTTTG
Found at i:17016156 original size:113 final size:112
Alignment explanation
Indices: 17015953--17016162 Score: 253
Period size: 113 Copynumber: 1.9 Consensus size: 112
17015943 ATTCTTACCG
* * * * * *
17015953 TAATTACGAAACTATCCCTCATATTATATTTGGATAAAATTACTATGATACTCTCTAACCATAAT
1 TAATTACAAAAATACCCCTCATATTATAATTGGACAAAATTACTATAATACTCTCTAACCATAAT
* * *
17016018 TACAAAAATATCCCTTTTTTTATTGCTTCATATAATGCATCTCTTATT
66 TACAAAAAAAACCC-TTTTTAATTGCTTCATATAATGCATCTCTTATT
* * **
17016066 TAATTACAAAAATACCCCTCATATTATAATTGGCCAAAATTACTATAATGC-CTTCTAAGTATAA
1 TAATTACAAAAATACCCCTCATATTATAATTGGACAAAATTACTATAATACTC-TCTAACCATAA
17016130 TTACAAAAAAAAAACCC-TTTTAATTGCTTCATA
65 TTAC--AAAAAAAACCCTTTTTAATTGCTTCATA
17016163 ATTACACATT
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
112 1 0.01
113 71 0.88
115 9 0.11
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.38
Consensus pattern (112 bp):
TAATTACAAAAATACCCCTCATATTATAATTGGACAAAATTACTATAATACTCTCTAACCATAAT
TACAAAAAAAACCCTTTTTAATTGCTTCATATAATGCATCTCTTATT
Found at i:17017641 original size:23 final size:24
Alignment explanation
Indices: 17017605--17017653 Score: 82
Period size: 23 Copynumber: 2.1 Consensus size: 24
17017595 TTGGTTTGGT
17017605 TTTTAGGGTTTAAGGTAGGTTCAA
1 TTTTAGGGTTTAAGGTAGGTTCAA
*
17017629 TTTTA-GGTTTAAGGTTGGTTCAA
1 TTTTAGGGTTTAAGGTAGGTTCAA
17017652 TT
1 TT
17017654 CAATTTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.22, C:0.04, G:0.27, T:0.47
Consensus pattern (24 bp):
TTTTAGGGTTTAAGGTAGGTTCAA
Found at i:17017809 original size:20 final size:19
Alignment explanation
Indices: 17017786--17018022 Score: 128
Period size: 20 Copynumber: 11.9 Consensus size: 19
17017776 GTTAGTTTCA
17017786 GTTTAGGATTTATGGTTTTG
1 GTTTAGG-TTTATGGTTTTG
*
17017806 GTTTAGGGTTTA-GG-GTTG
1 GTTTA-GGTTTATGGTTTTG
* *
17017824 GGTTAGGGTTTA-GGGTTTG
1 GTTTA-GGTTTATGGTTTTG
*
17017843 GTTTAAGGTTTAAGGTTAGGTTTAG
1 GTTT-AGGTTT-A---T-GGTTTTG
*
17017868 GTTTAGGTTTAGGGTTTTG
1 GTTTAGGTTTATGGTTTTG
** *
17017887 GTTTAGGATTTGGGGATTTG
1 GTTTAGG-TTTATGGTTTTG
* *
17017907 GTTTAGGGTTTGA-AGATTTG
1 GTTTA-GGTTT-ATGGTTTTG
*
17017927 GTTTAGGGTTTATGTTTTTG
1 GTTTA-GGTTTATGGTTTTG
*
17017947 GTTTAGAGTTTATGGTTTAAG
1 GTTTAG-GTTTATGGTTT-TG
*
17017968 GTTTAGGTTTGA-GGTTTAGG
1 GTTTAGGTTT-ATGGTTT-TG
*
17017988 GTTT-GGTTTATGGTTTAG
1 GTTTAGGTTTATGGTTTTG
*
17018006 GATTT-GGTTTAAGGTTT
1 G-TTTAGGTTTATGGTTT
17018023 CAATTTAGGG
Statistics
Matches: 179, Mismatches: 20, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
18 19 0.11
19 52 0.29
20 80 0.45
21 12 0.07
23 1 0.01
24 6 0.03
25 9 0.05
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (19 bp):
GTTTAGGTTTATGGTTTTG
Found at i:17018002 original size:19 final size:19
Alignment explanation
Indices: 17017802--17018022 Score: 142
Period size: 19 Copynumber: 11.8 Consensus size: 19
17017792 GATTTATGGT
*
17017802 TTTGGTTTAGGGTTTAGGG
1 TTTGGTTTATGGTTTAGGG
* *
17017821 -TTGGGTTAGGGTTTAGGG
1 TTTGGTTTATGGTTTAGGG
* *
17017839 TTTGGTTTAAGGTTTAAGG
1 TTTGGTTTATGGTTTAGGG
*
17017858 TTAGGTTTA-GGTTTA-GG
1 TTTGGTTTATGGTTTAGGG
*
17017875 TTTAGGGTTT-TGGTTTAGGA
1 TTT--GGTTTATGGTTTAGGG
*
17017895 TTTGGGGATT-TGGTTTAGGG
1 TTT--GGTTTATGGTTTAGGG
*
17017915 TTTGAAGATT-TGGTTTAGGG
1 TTTG--GTTTATGGTTTAGGG
* *
17017935 TTTATGTTTTTGGTTTA--G
1 TTT-GGTTTATGGTTTAGGG
* *
17017953 ---AGTTTATGGTTTAAGG
1 TTTGGTTTATGGTTTAGGG
17017969 TTTAGGTTTGA-GGTTTAGGG
1 TTT-GGTTT-ATGGTTTAGGG
*
17017989 TTTGGTTTATGGTTTAGGA
1 TTTGGTTTATGGTTTAGGG
*
17018008 TTTGGTTTAAGGTTT
1 TTTGGTTTATGGTTT
17018023 CAATTTAGGG
Statistics
Matches: 167, Mismatches: 18, Indels: 34
0.76 0.08 0.16
Matches are distributed among these distances:
14 11 0.07
16 1 0.01
17 4 0.02
18 26 0.16
19 64 0.38
20 60 0.36
21 1 0.01
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (19 bp):
TTTGGTTTATGGTTTAGGG
Found at i:17018021 original size:7 final size:6
Alignment explanation
Indices: 17017786--17018022 Score: 137
Period size: 7 Copynumber: 36.7 Consensus size: 6
17017776 GTTAGTTTCA
* * *
17017786 GTTTAG GATTTATG GTTTTG GTTTAGG GTTTAG GGTT-G GGTTAGG GTTTAGG
1 GTTTAG G-TTTA-G GTTTAG GTTTA-G GTTTAG GTTTAG GTTTA-G GTTTA-G
*
17017838 GTTT-G GTTTAAG GTTTAAG G-TTAG GTTTAG GTTTAG GTTTAGG GTTTTG
1 GTTTAG GTTT-AG GTTT-AG GTTTAG GTTTAG GTTTAG GTTTA-G GTTTAG
* *
17017887 GTTTAG GATTTGGG GATTT-G GTTTAGG GTTTGAAG ATTT-G GTTTAGG
1 GTTTAG G-TTT-AG G-TTTAG GTTTA-G GTTT--AG GTTTAG GTTTA-G
* *
17017934 GTTTATG TTTTTG GTTTAG AGTTTATG GTTTAAG GTTTAG GTTTGAG GTTTAGG
1 GTTTA-G GTTTAG GTTTAG -GTTTA-G GTTT-AG GTTTAG GTTT-AG GTTTA-G
17017988 GTTT-G GTTTATG GTTTAG GATTT-G GTTTAAG GTTT
1 GTTTAG GTTTA-G GTTTAG G-TTTAG GTTT-AG GTTT
17018023 CAATTTAGGG
Statistics
Matches: 190, Mismatches: 14, Indels: 53
0.74 0.05 0.21
Matches are distributed among these distances:
5 28 0.15
6 52 0.27
7 95 0.50
8 14 0.07
9 1 0.01
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.49
Consensus pattern (6 bp):
GTTTAG
Found at i:17020892 original size:14 final size:15
Alignment explanation
Indices: 17020873--17020901 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17020863 TTATGTAAAA
17020873 CCTTTTTT-ACTTTT
1 CCTTTTTTCACTTTT
17020887 CCTTTTTTCACTTTT
1 CCTTTTTTCACTTTT
17020902 TTTGAATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (15 bp):
CCTTTTTTCACTTTT
Found at i:17021663 original size:26 final size:25
Alignment explanation
Indices: 17021608--17021674 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
17021598 ATCCTTTAAC
* * *
17021608 CATAATTATGAAGATGCTCTCTTAT
1 CATAATTATGAAAATACCCTCTTAT
17021633 CATAATTATGAAAATACCCTTCTTAT
1 CATAATTATGAAAATACCC-TCTTAT
* *
17021659 TATAATTGATTAAAAT
1 CATAATT-ATGAAAAT
17021675 TATTATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
25 16 0.46
26 12 0.34
27 7 0.20
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.40
Consensus pattern (25 bp):
CATAATTATGAAAATACCCTCTTAT
Found at i:17022135 original size:35 final size:35
Alignment explanation
Indices: 17022068--17022136 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
17022058 CCTCTACAAT
*
17022068 CATAATTACAAAAATACCATCATACCACCATTTGC
1 CATAATTACAAAAATACCATCACACCACCATTTGC
* * * *
17022103 CATAATTACAAAAATGCCTTCCCACCATCATTTG
1 CATAATTACAAAAATACCATCACACCACCATTTG
17022137 TGAAAATTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.29, G:0.04, T:0.28
Consensus pattern (35 bp):
CATAATTACAAAAATACCATCACACCACCATTTGC
Found at i:17025873 original size:12 final size:11
Alignment explanation
Indices: 17025854--17025885 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
17025844 ATAATGATAG
17025854 ATAAAATAAAA
1 ATAAAATAAAA
17025865 ATGAAAATAAAA
1 AT-AAAATAAAA
17025877 ATAAAATAA
1 ATAAAATAA
17025886 GAAAAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (11 bp):
ATAAAATAAAA
Found at i:17025877 original size:18 final size:18
Alignment explanation
Indices: 17025838--17025960 Score: 57
Period size: 18 Copynumber: 6.9 Consensus size: 18
17025828 CAAAATTAAT
* *
17025838 AAAATAATAATGATAGAT-
1 AAAATAAAAATGA-AAATA
17025856 AAAATAAAAATGAAAATA
1 AAAATAAAAATGAAAATA
17025874 AAAAT-AAAAT-AAGAA-A
1 AAAATAAAAATGAA-AATA
* *
17025890 AAAGCTAAAAGAATGAAAATTGT
1 AAA-AT-AAA-AATGAAAA-T-A
17025913 AAAA-AAAAAT--AAATA
1 AAAATAAAAATGAAAATA
*
17025928 AATAA-AGAAATGAAAATA
1 AA-AATAAAAATGAAAATA
*
17025946 AAAAGAAAAA-GAAAA
1 AAAATAAAAATGAAAA
17025961 ACATGTGATT
Statistics
Matches: 83, Mismatches: 8, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
15 2 0.02
16 14 0.17
17 21 0.25
18 28 0.34
19 5 0.06
20 8 0.10
21 2 0.02
23 3 0.04
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (18 bp):
AAAATAAAAATGAAAATA
Found at i:17025956 original size:22 final size:22
Alignment explanation
Indices: 17025918--17025959 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
17025908 ATTGTAAAAA
*
17025918 AAAATAAATAAATAAAGAAATG
1 AAAATAAATAAAAAAAGAAATG
17025940 AAAATAAA-AAGAAAAAGAAA
1 AAAATAAATAA-AAAAAGAAA
17025960 AACATGTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATAAATAAAAAAAGAAATG
Found at i:17026367 original size:21 final size:20
Alignment explanation
Indices: 17026307--17026375 Score: 86
Period size: 20 Copynumber: 3.4 Consensus size: 20
17026297 ATTTTTTCAA
*
17026307 AAATTC-AACTCTAAACCTAG
1 AAATTCAAAC-CTAAACCCAG
*
17026327 AAATTCAAACCTAGACCCAG
1 AAATTCAAACCTAAACCCAG
*
17026347 AAATTTAAACCTACAACCCAG
1 AAATTCAAACCTA-AACCCAG
17026368 AAATTCAA
1 AAATTCAA
17026376 GCCACCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.48, C:0.26, G:0.06, T:0.20
Consensus pattern (20 bp):
AAATTCAAACCTAAACCCAG
Found at i:17026584 original size:52 final size:52
Alignment explanation
Indices: 17026517--17026621 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
17026507 TGGATTTTGT
* * * * *
17026517 CCAACGTGATTTAGGCTTAGGTTTTGCCTGATTTGATTTTGAATTGAAAACC
1 CCAACGTGATTTAGGCCTAGGTTCTGCCTCATTTGATTCTAAATTGAAAACC
* *
17026569 CCAATGTGATTTAGGCCTAGGTTCTGCTTCATTTGATTCTAAATTGAAAACC
1 CCAACGTGATTTAGGCCTAGGTTCTGCCTCATTTGATTCTAAATTGAAAACC
17026621 C
1 C
17026622 TTTGGTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (52 bp):
CCAACGTGATTTAGGCCTAGGTTCTGCCTCATTTGATTCTAAATTGAAAACC
Found at i:17026688 original size:3 final size:3
Alignment explanation
Indices: 17026680--17026732 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
17026670 AAGGAAAGAA
17026680 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17026728 AAT AA
1 AAT AA
17026733 CAGTTGACCC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17028241 original size:2 final size:2
Alignment explanation
Indices: 17028229--17028258 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17028219 TACCGAACGC
*
17028229 AT AT CT 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
17028259 TGAGATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17030837 original size:3 final size:3
Alignment explanation
Indices: 17030829--17030869 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
17030819 ATCCTATTGT
*
17030829 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17030870 TTTTTTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:17031547 original size:6 final size:6
Alignment explanation
Indices: 17031532--17031563 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
17031522 AGAGAGCATG
*
17031532 TGCAAC TGCAAA TGCAAA TGCAAA TGCAAA TG
1 TGCAAA TGCAAA TGCAAA TGCAAA TGCAAA TG
17031564 GGGGGCAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (6 bp):
TGCAAA
Found at i:17038538 original size:31 final size:29
Alignment explanation
Indices: 17038487--17038547 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
17038477 CACTTAACTA
17038487 AGTATTATCCTTTGATTTTGATAAAAAAAAT
1 AGTATTAT-CTTTGATTTTGA-AAAAAAAAT
*
17038518 AGTATTAT-TTTCGATGTTTGAAAAATAAAT
1 AGTATTATCTTT-GAT-TTTGAAAAAAAAAT
17038548 TTTTTTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 3 0.11
30 11 0.41
31 13 0.48
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (29 bp):
AGTATTATCTTTGATTTTGAAAAAAAAAT
Found at i:17039488 original size:25 final size:26
Alignment explanation
Indices: 17039453--17039502 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
17039443 AATAAAATTT
* *
17039453 AAAATCACAAAAATAATATTTTTTAA
1 AAAATCACAAAAAAAAAATTTTTTAA
17039479 AAAATC-CAAAAAAAAAATTTTTTA
1 AAAATCACAAAAAAAAAATTTTTTA
17039503 CCTAAACCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAATCACAAAAAAAAAATTTTTTAA
Found at i:17039580 original size:19 final size:18
Alignment explanation
Indices: 17039552--17039587 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17039542 CTAGTCCGAC
*
17039552 GATTCGATCTGGTGTCAGT
1 GATTCAATCTGG-GTCAGT
17039571 GATTCAATCTGGGTCAG
1 GATTCAATCTGGGTCAG
17039588 CTCAGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (18 bp):
GATTCAATCTGGGTCAGT
Found at i:17040121 original size:19 final size:20
Alignment explanation
Indices: 17040076--17040126 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
17040066 GTGGTTTTTT
*
17040076 ATTTTTTTTTTTTGACAGAA
1 ATTTTTTTTTTCTGACAGAA
* *
17040096 AGCTTTTTTTTTCTGGCA-AA
1 A-TTTTTTTTTTCTGACAGAA
17040116 ATTTTTTTTTT
1 ATTTTTTTTTT
17040127 TTCTTTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 9 0.35
20 4 0.15
21 13 0.50
ACGTcount: A:0.20, C:0.08, G:0.10, T:0.63
Consensus pattern (20 bp):
ATTTTTTTTTTCTGACAGAA
Found at i:17040698 original size:44 final size:44
Alignment explanation
Indices: 17040592--17040822 Score: 254
Period size: 44 Copynumber: 5.2 Consensus size: 44
17040582 TTAACAACAT
* * * *
17040592 TTTTAAAAATTTAAAA-AGCTTCTCTGAGCAAAGGCTCAATAAC
1 TTTTAAAAATTTAAAATGGCTCCTCTAAGCAGAGGCTCAATAAC
* * * * *
17040635 -TTTGAAAATTTAAAGTGGCTCCTCTAAGTAGAGACTCAATGAC
1 TTTTAAAAATTTAAAATGGCTCCTCTAAGCAGAGGCTCAATAAC
*
17040678 TTTTAAAAATTTAAAATGGCTCCTCTAAGAAGAGGCTCAATAAC
1 TTTTAAAAATTTAAAATGGCTCCTCTAAGCAGAGGCTCAATAAC
* * *
17040722 TTTTAAAAATTTAAAAAGGCTCCTCTAAGCAGAGTCTCAACAAC
1 TTTTAAAAATTTAAAATGGCTCCTCTAAGCAGAGGCTCAATAAC
* *
17040766 TTTAAAAATCTATCTTGAAAA-AGCTCCTCTAAGCAGAGGCTCAATAAC
1 TTTTAAAA---AT-TT-AAAATGGCTCCTCTAAGCAGAGGCTCAATAAC
17040814 -TTTAAAAAT
1 TTTTAAAAAT
17040823 CCATCTTGAA
Statistics
Matches: 158, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
42 13 0.08
43 20 0.13
44 87 0.55
47 8 0.05
48 26 0.16
49 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (44 bp):
TTTTAAAAATTTAAAATGGCTCCTCTAAGCAGAGGCTCAATAAC
Found at i:17040798 original size:48 final size:48
Alignment explanation
Indices: 17040696--17041024 Score: 363
Period size: 48 Copynumber: 6.9 Consensus size: 48
17040686 ATTTAAAATG
* * *
17040696 GCTCCTCTAAGAAGAGGCTCAATAACTTTTAAAA---AT-TT-AAAAA
1 GCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCTATCTTGAAAAA
*
17040739 GGCTCCTCTAAGCAGAGTCTCAACAACTTTAAAAATCTATCTTGAAAAA
1 -GCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCTATCTTGAAAAA
* *
17040788 GCTCCTCTAAGCAGAGGCTCAATAACTTTAAAAATCCATCTTGAAAAA
1 GCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCTATCTTGAAAAA
* *
17040836 GCTCATCTCAA-CAGAGGTTCAACAACTTTTAAAAAATCTCATCTTGAAAAA
1 GCTCCTCT-AAGCAGAGGCTCAACAAC-TTT-AAAAATCT-ATCTTGAAAAA
* *
17040887 GCTCCT-TCAAGCAGAGGCTTCAA-AACTTTAAAAATCCAT-TCGAAAAAA
1 GCTCCTCT-AAGCAGAGGC-TCAACAACTTTAAAAATCTATCTTG-AAAAA
* *
17040935 GCTCCTGTAAGCAGAGGCTCAACAACTTTAAAAATCTTAT-ATGAAAAA
1 GCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATC-TATCTTGAAAAA
* **
17040983 GCTCTTGAAAGCAGAGGCTCAACAACTTTAAAAATCTCATCT
1 GCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCT-ATCT
17041025 GTTCTTGAAA
Statistics
Matches: 247, Mismatches: 21, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
44 30 0.12
47 9 0.04
48 144 0.58
49 21 0.09
50 14 0.06
51 25 0.10
52 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.26
Consensus pattern (48 bp):
GCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCTATCTTGAAAAA
Found at i:17041007 original size:147 final size:146
Alignment explanation
Indices: 17040734--17041024 Score: 380
Period size: 147 Copynumber: 2.0 Consensus size: 146
17040724 TTAAAAATTT
* * *
17040734 AAAAAGGCTCCTCTAAGCAGAGTCTCAACAACTTTAAAAATCTATCTTGAAAAAGCTCCTCTAAG
1 AAAAAGGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCCATCTCGAAAAAGCTCCTCTAAG
* * * *
17040799 CAGAGGCTCAATAACTTTAAAAATCCATCTTGAAAAAGCTCATCTCAACAGAGGTTCAACAACTT
66 CAGAGGCTCAACAACTTTAAAAATCCATCATGAAAAAGCTCATCTAAACAGAGGCTCAACAAC-T
17040864 TTAAAAAATCTCATCTTG
130 TT-AAAAATCTCATCTTG
*
17040882 AAAAA-GCTCCT-TCAAGCAGAGGCTTCAA-AACTTTAAAAATCCAT-TCGAAAAAAGCTCCTGT
1 AAAAAGGCTCCTCT-AAGCAGAGGC-TCAACAACTTTAAAAATCCATCTCG-AAAAAGCTCCTCT
*
17040943 AAGCAGAGGCTCAACAACTTTAAAAATCTTAT-ATGAAAAAGCTC-T-TGAAAGCAGAGGCTCAA
63 AAGCAGAGGCTCAACAACTTTAAAAATC-CATCATGAAAAAGCTCATCT-AAA-CAGAGGCTCAA
17041005 CAACTTTAAAAATCTCATCT
125 CAACTTTAAAAATCTCATCT
17041025 GTTCTTGAAA
Statistics
Matches: 128, Mismatches: 9, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
145 14 0.11
146 9 0.07
147 94 0.73
148 11 0.09
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (146 bp):
AAAAAGGCTCCTCTAAGCAGAGGCTCAACAACTTTAAAAATCCATCTCGAAAAAGCTCCTCTAAG
CAGAGGCTCAACAACTTTAAAAATCCATCATGAAAAAGCTCATCTAAACAGAGGCTCAACAACTT
TAAAAATCTCATCTTG
Found at i:17045311 original size:15 final size:16
Alignment explanation
Indices: 17045285--17045323 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
17045275 ATTGGCAACA
*
17045285 AAAATGGATTGATA-AG
1 AAAAT-GATTGAAAGAG
17045301 AAAATGATTGAAAGAG
1 AAAATGATTGAAAGAG
17045317 AAAATGA
1 AAAATGA
17045324 AAGGCAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (16 bp):
AAAATGATTGAAAGAG
Found at i:17053278 original size:18 final size:20
Alignment explanation
Indices: 17053255--17053294 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
17053245 TAAATTTTTT
17053255 TTTATATT-TTTTTA-TTAA
1 TTTATATTATTTTTATTTAA
17053273 TTTATATTATTTTTATTTAA
1 TTTATATTATTTTTATTTAA
17053293 TT
1 TT
17053295 ATAACTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATATTATTTTTATTTAA
Found at i:17054423 original size:16 final size:16
Alignment explanation
Indices: 17054402--17054453 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
17054392 AGTTAAACCG
17054402 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
17054418 AAAAAGAGAAAGAGAAAGA
1 AAAAAGA-AAAGA-AAA-A
*
17054437 AAGAAA-AAGAGAAAAA
1 AA-AAAGAAAAGAAAAA
17054453 A
1 A
17054454 TATAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 9 0.29
17 8 0.26
18 7 0.23
19 4 0.13
20 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAGAAAAA
Found at i:17054443 original size:22 final size:22
Alignment explanation
Indices: 17054404--17054450 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
17054394 TTAAACCGAA
17054404 AAAGAAAAGAAAAAAAAAAGAG
1 AAAGAAAAGAAAAAAAAAAGAG
*
17054426 AAAGAGAAAG-AAAGAAAAAGAG
1 AAAGA-AAAGAAAAAAAAAAGAG
17054448 AAA
1 AAA
17054451 AAATATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAGAAAAGAAAAAAAAAAGAG
Found at i:17056512 original size:20 final size:21
Alignment explanation
Indices: 17056472--17056512 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17056462 GCCATTTACA
* *
17056472 ATTCTCTAAACCACTTCAATC
1 ATTCTATAAAACACTTCAATC
17056493 ATTCTATAAAACAC-TCAATC
1 ATTCTATAAAACACTTCAATC
17056513 TACTCCTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTCTATAAAACACTTCAATC
Found at i:17060634 original size:12 final size:11
Alignment explanation
Indices: 17060615--17060649 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
17060605 GGAAGACAAG
17060615 AAAGAAAAAAA
1 AAAGAAAAAAA
17060626 AATAG-AAAAAA
1 AA-AGAAAAAAA
17060637 AAAGAAAAAAA
1 AAAGAAAAAAA
17060648 AA
1 AA
17060650 GATTTTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.09
11 18 0.82
12 2 0.09
ACGTcount: A:0.89, C:0.00, G:0.09, T:0.03
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:17060636 original size:11 final size:10
Alignment explanation
Indices: 17060615--17060651 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
17060605 GGAAGACAAG
17060615 AAAGAAAAAAA
1 AAAG-AAAAAA
17060626 AATAGAAAAAA
1 AA-AGAAAAAA
17060637 AAAGAAAAAA
1 AAAGAAAAAA
17060647 AAAGA
1 AAAGA
17060652 TTTTTTCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 13 0.52
11 10 0.40
12 2 0.08
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (10 bp):
AAAGAAAAAA
Found at i:17066065 original size:21 final size:21
Alignment explanation
Indices: 17066041--17066083 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
17066031 AACAGAAAGA
17066041 GAAGAAGAACATGCTAGAATT
1 GAAGAAGAACATGCTAGAATT
**
17066062 GAAGAAGAATGTGCTAGAATT
1 GAAGAAGAACATGCTAGAATT
17066083 G
1 G
17066084 TGCAAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.07, G:0.28, T:0.21
Consensus pattern (21 bp):
GAAGAAGAACATGCTAGAATT
Found at i:17075284 original size:11 final size:11
Alignment explanation
Indices: 17075268--17075293 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17075258 AGGTTGTGAA
17075268 CTTGTAATTGG
1 CTTGTAATTGG
17075279 CTTGTAATTGG
1 CTTGTAATTGG
17075290 CTTG
1 CTTG
17075294 ATATTTGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.27, T:0.46
Consensus pattern (11 bp):
CTTGTAATTGG
Found at i:17080003 original size:3 final size:3
Alignment explanation
Indices: 17079995--17080020 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17079985 AACTAAGGTT
17079995 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
17080021 TAACCATTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17083714 original size:83 final size:83
Alignment explanation
Indices: 17083604--17083768 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 83
17083594 GAGTGGTAAG
* * *
17083604 ACTAGAAGAGACAAAATTTAAAAAAAAAAAAAAAAGTAAAAATTTCAAGAAAATTAGGGATAATC
1 ACTAGAAGAGACAAAATTAAAAAAAAAAAAAAAAAGTAAAAATTTCAAGAAAATTAGGGACAACC
*
17083669 CGAATTGAGGAAAAGATT
66 CAAATTGAGGAAAAGATT
* *
17083687 ACTAGAAGAGACAAAATTAAAAAAAAAAAAAAAAAGTAAAAATTTCGAGAAAATTAGGGGCAACC
1 ACTAGAAGAGACAAAATTAAAAAAAAAAAAAAAAAGTAAAAATTTCAAGAAAATTAGGGACAACC
17083752 CAAATTGAGGAAAAGAT
66 CAAATTGAGGAAAAGAT
17083769 AAGAAAGGGC
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 76 1.00
ACGTcount: A:0.59, C:0.07, G:0.16, T:0.17
Consensus pattern (83 bp):
ACTAGAAGAGACAAAATTAAAAAAAAAAAAAAAAAGTAAAAATTTCAAGAAAATTAGGGACAACC
CAAATTGAGGAAAAGATT
Found at i:17090043 original size:61 final size:62
Alignment explanation
Indices: 17089975--17090122 Score: 189
Period size: 61 Copynumber: 2.4 Consensus size: 62
17089965 AATTCCCGTG
* *
17089975 TTTCTTTTAATTAAATGTCATAATTGAGT-ATTT-AAAATTTTTAC-TTAACTCAATTATGA-CA
1 TTTCTTTTAATTAAATGTCATAATTGACTAATTTGAAAA-TTTTACATT-ACTCAATTA-CATCA
*
17090036 TTTCTTTT-ATTAAATGTCATAATTGCCTAATTTGAAAATTTTACATTACTCAATTACATCA
1 TTTCTTTTAATTAAATGTCATAATTGACTAATTTGAAAATTTTACATTACTCAATTACATCA
**
17090097 TTTCTTTTAATTAAACATCATAATTG
1 TTTCTTTTAATTAAATGTCATAATTG
17090123 GCTCTTATTT
Statistics
Matches: 77, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
60 19 0.25
61 37 0.48
62 21 0.27
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.47
Consensus pattern (62 bp):
TTTCTTTTAATTAAATGTCATAATTGACTAATTTGAAAATTTTACATTACTCAATTACATCA
Done.