Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 15 of 19
Found at i:6384203 original size:30 final size:30
Alignment explanation
Indices: 6384169--6384242 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
6384159 AATAACTAAT
*
6384169 TATAAAAATTTATTTAATTTAAAATT-AAAA
1 TATAAAAATTTATTTAA-ATAAAATTAAAAA
* *
6384199 TATAAAAATTTAATTAAATATAATTAAAAA
1 TATAAAAATTTATTTAAATAAAATTAAAAA
* *
6384229 GATAAATATTTATT
1 TATAAAAATTTATT
6384243 GTGGGTAAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 6 0.16
30 31 0.84
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
TATAAAAATTTATTTAAATAAAATTAAAAA
Found at i:6405071 original size:15 final size:15
Alignment explanation
Indices: 6405047--6405076 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6405037 TAATAATATT
6405047 TTTTAATTTTATTAA
1 TTTTAATTTTATTAA
*
6405062 TTTTATTTTTATTAA
1 TTTTAATTTTATTAA
6405077 AAAGTTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATTTTATTAA
Found at i:6405773 original size:20 final size:20
Alignment explanation
Indices: 6405748--6405796 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
6405738 TTAGTAATAA
*
6405748 TATTTTCAAAAATTTTAAAT
1 TATTTTAAAAAATTTTAAAT
6405768 TATTTTAAAAAATTTTAAAT
1 TATTTTAAAAAATTTTAAAT
6405788 TA-TTTAAAA
1 TATTTTAAAA
6405797 TTTTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 7 0.25
20 21 0.75
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTTTAAAAAATTTTAAAT
Found at i:6405795 original size:9 final size:10
Alignment explanation
Indices: 6405759--6405803 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
6405749 ATTTTCAAAA
6405759 ATTTTAAATT
1 ATTTTAAATT
**
6405769 ATTTTAAAAA
1 ATTTTAAATT
6405779 ATTTTAAATT
1 ATTTTAAATT
*
6405789 ATTTAAAATT
1 ATTTTAAATT
6405799 -TTTTA
1 ATTTTA
6405804 TTAACTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
9 4 0.14
10 25 0.86
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:6406012 original size:14 final size:15
Alignment explanation
Indices: 6405993--6406025 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
6405983 AATAATAAAT
6405993 AATATTTTAA-TTAA
1 AATATTTTAATTTAA
6406007 AATATTTTAATTTAA
1 AATATTTTAATTTAA
6406022 AATA
1 AATA
6406026 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTTTAATTTAA
Found at i:6449413 original size:2 final size:2
Alignment explanation
Indices: 6449406--6449441 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6449396 GGAAATATGC
6449406 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6449442 TTAATTAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6452077 original size:3 final size:3
Alignment explanation
Indices: 6452069--6452097 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6452059 ATTGCCTCTT
6452069 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6452098 TTCATACGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6462573 original size:30 final size:28
Alignment explanation
Indices: 6462537--6462612 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 28
6462527 AGCTATTAGT
6462537 TATAAAAATTTATTTAACTTAAAATAAAAA
1 TATAAAAATTTATTTAAC--AAAATAAAAA
* *
6462567 TATAAAAATTTAATTGAACATAATAAAAA
1 TATAAAAATTT-ATTTAACAAAATAAAAA
* *
6462596 AATAAACATTTATTTAA
1 TATAAAAATTTATTTAA
6462613 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.12
29 18 0.45
30 11 0.28
31 6 0.15
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (28 bp):
TATAAAAATTTATTTAACAAAATAAAAA
Found at i:6474164 original size:20 final size:20
Alignment explanation
Indices: 6474126--6474164 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
6474116 AAAATTTTAT
* *
6474126 ATTTTAAATATGTTAAATTC
1 ATTTAAAATATATTAAATTC
*
6474146 ATTTAAAATATATTTAATT
1 ATTTAAAATATATTAAATT
6474165 AATTGTATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTTAAAATATATTAAATTC
Found at i:6500506 original size:2 final size:2
Alignment explanation
Indices: 6500499--6500526 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6500489 GTTTGATGTG
6500499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6500527 TAGATACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6506132 original size:17 final size:17
Alignment explanation
Indices: 6506107--6506147 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
6506097 TAGATCTTAT
* *
6506107 ATAAGTTATTTTTTTAA
1 ATAATTTATTTATTTAA
6506124 ATAATTTATTTATTTAA
1 ATAATTTATTTATTTAA
6506141 ATAATTT
1 ATAATTT
6506148 TAACTTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATAATTTATTTATTTAA
Found at i:6512203 original size:1 final size:1
Alignment explanation
Indices: 6512197--6512223 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6512187 ACCAACCACA
6512197 CCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCC
6512224 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:6515078 original size:2 final size:2
Alignment explanation
Indices: 6515071--6515107 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6515061 CCCTTCTCGT
6515071 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6515108 TTGTCATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6515178 original size:101 final size:101
Alignment explanation
Indices: 6515003--6515192 Score: 362
Period size: 101 Copynumber: 1.9 Consensus size: 101
6514993 TAGCAGAAAG
*
6515003 ATATTTGTCATCATCTGCAACGGTGAGGAAGACTATTAACTAGGACTAGCATGTCCTACCCTTCT
1 ATATTTGTCATCATCTGCAACGATGAGGAAGACTATTAACTAGGACTAGCATGTCCTACCCTTCT
6515068 CGTTATATATATATATATATATATATATATATATAT
66 CGTTATATATATATATATATATATATATATATATAT
*
6515104 ATATTTGTCATCATCTGCAACGATGAGGAAGACTATTGACTAGGACTAGCATGTCCTACCCTTCT
1 ATATTTGTCATCATCTGCAACGATGAGGAAGACTATTAACTAGGACTAGCATGTCCTACCCTTCT
6515169 CGTTATATATATATATATATATAT
66 CGTTATATATATATATATATATAT
6515193 TCTGAAAGAC
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (101 bp):
ATATTTGTCATCATCTGCAACGATGAGGAAGACTATTAACTAGGACTAGCATGTCCTACCCTTCT
CGTTATATATATATATATATATATATATATATATAT
Found at i:6515362 original size:2 final size:2
Alignment explanation
Indices: 6515355--6515385 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6515345 GCCGAAGCTT
*
6515355 TA TA TA TA TA CA 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
6515386 TAAAGGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6530651 original size:19 final size:19
Alignment explanation
Indices: 6530623--6530685 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
6530613 GTAAAGTTTT
*
6530623 TTTATTTTATTTTT-TCTTA
1 TTTATATTATTTTTAT-TTA
6530642 TTTATATTATTATTTATTTA
1 TTTATATTATT-TTTATTTA
*
6530662 TTTTTA-TATTTTTATTCTA
1 TTTATATTATTTTTATT-TA
6530681 TTTAT
1 TTTAT
6530686 CCATATGTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
18 6 0.16
19 20 0.53
20 11 0.29
21 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATATTATTTTTATTTA
Found at i:6531633 original size:11 final size:11
Alignment explanation
Indices: 6531614--6531645 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
6531604 ATTAACAAAA
*
6531614 TAATATTATTT
1 TAATTTTATTT
6531625 TAATTTTATTT
1 TAATTTTATTT
6531636 TAATTTTATT
1 TAATTTTATT
6531646 GGACATTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTTTATTT
Found at i:6544577 original size:52 final size:52
Alignment explanation
Indices: 6544512--6544616 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
6544502 TATTTTATTG
6544512 TATTGAAATGTGGATAAAGTCAAACAAATATATATATTTTTTATTGTCTAAC
1 TATTGAAATGTGGATAAAGTCAAACAAATATATATATTTTTTATTGTCTAAC
6544564 TATTGAAATGTGGATAAAGTCAAACAAATATATATATTTTTTATTGTCTAAC
1 TATTGAAATGTGGATAAAGTCAAACAAATATATATATTTTTTATTGTCTAAC
6544616 T
1 T
6544617 GAGTCAATGC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (52 bp):
TATTGAAATGTGGATAAAGTCAAACAAATATATATATTTTTTATTGTCTAAC
Found at i:6545187 original size:15 final size:16
Alignment explanation
Indices: 6545169--6545201 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
6545159 ATGTGAGAGA
6545169 AAATAGATA-TTTATT
1 AAATAGATATTTTATT
6545184 AAATAGATATTTTATT
1 AAATAGATATTTTATT
6545200 AA
1 AA
6545202 TTATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
AAATAGATATTTTATT
Found at i:6552336 original size:15 final size:15
Alignment explanation
Indices: 6552316--6552371 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
6552306 AATAAAATAT
6552316 ATAATATATTTAAAA
1 ATAATATATTTAAAA
*
6552331 ATAATATTATATAAAA
1 ATAATA-TATTTAAAA
*
6552347 ATTAATA-A-TAAAAA
1 A-TAATATATTTAAAA
6552361 ATAAGTATATT
1 ATAA-TATATT
6552372 AAATTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.09
14 7 0.21
15 8 0.24
16 10 0.30
17 5 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAATATATTTAAAA
Found at i:6552351 original size:23 final size:22
Alignment explanation
Indices: 6552297--6552359 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
6552287 ATTTTTTTAA
6552297 AAAAATT-AAAATAAAATATAT
1 AAAAATTAAAAATAAAATATAT
* *
6552318 AATATATTTAAAAATAATATTATAT
1 AA-A-AATTAAAAATAA-AATATAT
*
6552343 AAAAATTAATAATAAAA
1 AAAAATTAAAAATAAAA
6552360 AATAAGTATA
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 13 0.39
24 8 0.24
25 8 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAAATTAAAAATAAAATATAT
Found at i:6552391 original size:46 final size:47
Alignment explanation
Indices: 6552279--6552423 Score: 111
Period size: 46 Copynumber: 3.0 Consensus size: 47
6552269 ATTGTCAATA
*
6552279 AAATTTATATTTTTTTAA-AAAAATTAAAATAAAATATATAATATATTT
1 AAATTTATA--TTTTAAATAAAAATTAAAATAAAATATATAATATATTT
** * *
6552327 AAAAATA-ATATTATATAAAAATTAATAATAAAA-A-ATAAGTATA-TT
1 AAATTTATATTTTAAATAAAAATTAA-AATAAAATATATAA-TATATTT
* *
6552372 AAATTTATATTTTAAATAAAGTATTTATAAATCAAATATTATAATATTATTT
1 AAATTTATATTTTAAATAAA--AATTA-AAATAAAATA-TATAATA-TATTT
6552424 TATTAAAAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 20
0.70 0.10 0.19
Matches are distributed among these distances:
45 15 0.20
46 24 0.32
47 8 0.11
48 15 0.20
49 2 0.03
50 2 0.03
51 6 0.08
52 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (47 bp):
AAATTTATATTTTAAATAAAAATTAAAATAAAATATATAATATATTT
Found at i:6552465 original size:23 final size:22
Alignment explanation
Indices: 6552409--6552467 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 22
6552399 TAAATCAAAT
6552409 ATTATAATATTATTTTATTAAAA
1 ATTA-AATATTATTTTATTAAAA
* *
6552432 ATTTAATTATTATTTTATTTATATA
1 A-TTAAATATTATTTTA-TTA-AAA
6552457 A-TAAATATTAT
1 ATTAAATATTAT
6552468 AATATTATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 21 0.70
24 6 0.20
25 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTAAATATTATTTTATTAAAA
Found at i:6552485 original size:28 final size:27
Alignment explanation
Indices: 6552395--6552486 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 27
6552385 AAATAAAGTA
6552395 TTTATAAATCAAATATTATAATATTATTT
1 TTTAT-AAT-AAATATTATAATATTATTT
* *
6552424 TAT-TAA-AAAT-TTA-ATTATTATTTTAT
1 TTTATAATAAATATTATAATATTA--TT-T
6552450 TTATATAATAAATATTATAATATTATCTT
1 TT-TATAATAAATATTATAATATTAT-TT
6552479 TTTATAAT
1 TTTATAAT
6552487 TACATTACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 19
0.68 0.05 0.26
Matches are distributed among these distances:
23 6 0.12
24 3 0.06
25 6 0.12
26 2 0.04
27 3 0.06
28 10 0.20
29 10 0.20
30 4 0.08
31 6 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTATAATAAATATTATAATATTATTT
Found at i:6558303 original size:9 final size:9
Alignment explanation
Indices: 6558289--6558315 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6558279 AACCAGTAAC
6558289 AGTTGTGGG
1 AGTTGTGGG
6558298 AGTTGTGGG
1 AGTTGTGGG
6558307 AGTTGTGGG
1 AGTTGTGGG
6558316 GAACAGGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.56, T:0.33
Consensus pattern (9 bp):
AGTTGTGGG
Found at i:6559128 original size:2 final size:2
Alignment explanation
Indices: 6559074--6559109 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6559064 TATCACACCA
* *
6559074 TC TC TC TC TC TC TC TC TC TC TC TG TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6559110 AATCTCTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.44, G:0.03, T:0.53
Consensus pattern (2 bp):
TC
Found at i:6565762 original size:9 final size:9
Alignment explanation
Indices: 6565731--6565773 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
6565721 AAATTATTTT
6565731 ATAATATAAA
1 ATAATA-AAA
6565741 ATATATAAAAA
1 ATA-AT-AAAA
6565752 ATAATAAAA
1 ATAATAAAA
*
6565761 ATAATTAAA
1 ATAATAAAA
6565770 ATAA
1 ATAA
6565774 GTGAAATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 16 0.53
10 5 0.17
11 8 0.27
12 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
ATAATAAAA
Found at i:6566609 original size:22 final size:21
Alignment explanation
Indices: 6566568--6566643 Score: 82
Period size: 21 Copynumber: 3.6 Consensus size: 21
6566558 AAATTAGTTC
*
6566568 AATTCATAAAATATTAAAATT
1 AATTCATAAAATTTTAAAATT
*
6566589 AATTTATAAAATTTTTAAAATT
1 AATTCATAAAA-TTTTAAAATT
*
6566611 TATTCACT-AAATTTTAAAATT
1 AATTCA-TAAAATTTTAAAATT
* *
6566632 AATCCACAAAAT
1 AATTCATAAAAT
6566644 CTTCAATATC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 28 0.62
22 16 0.36
23 1 0.02
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTCATAAAATTTTAAAATT
Found at i:6566716 original size:21 final size:21
Alignment explanation
Indices: 6566668--6566719 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
6566658 TATCAAACTT
*
6566668 TTATAAAATCGGTTTAAAAAA
1 TTATAAAATCGATTTAAAAAA
* * *
6566689 CTCTAAAATCGATTTAAAATA
1 TTATAAAATCGATTTAAAAAA
6566710 TTATAAAATC
1 TTATAAAATC
6566720 TGTTCATCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (21 bp):
TTATAAAATCGATTTAAAAAA
Found at i:6567369 original size:19 final size:20
Alignment explanation
Indices: 6567338--6567381 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
6567328 TTCATCAAAG
*
6567338 AAAAAAATATAAA-TCTTTT
1 AAAAAAATATAAATTATTTT
6567357 AAAAGAAAT-TAAATTATTTT
1 AAAA-AAATATAAATTATTTT
6567377 AAAAA
1 AAAAA
6567382 TTTTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAAAATATAAATTATTTT
Found at i:6568144 original size:11 final size:11
Alignment explanation
Indices: 6568130--6568157 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
6568120 TTTTTAGTAT
6568130 TTTTTTTTGAA
1 TTTTTTTTGAA
6568141 TTTTTTTTGAA
1 TTTTTTTTGAA
6568152 TTTTTT
1 TTTTTT
6568158 CCAGCTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:6570179 original size:15 final size:16
Alignment explanation
Indices: 6570159--6570188 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6570149 AGAAATTCTA
6570159 TTAGTTCATA-TTTTT
1 TTAGTTCATACTTTTT
6570174 TTAGTTCATACTTTT
1 TTAGTTCATACTTTT
6570189 AACCATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.63
Consensus pattern (16 bp):
TTAGTTCATACTTTTT
Found at i:6598339 original size:20 final size:21
Alignment explanation
Indices: 6598316--6598354 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
6598306 TATTTAATAA
6598316 AAAATTTAAT-TATTTTTAAT
1 AAAATTTAATATATTTTTAAT
*
6598336 AAAATTTTATATATTTTTA
1 AAAATTTAATATATTTTTA
6598355 TTTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAAATTTAATATATTTTTAAT
Found at i:6598344 original size:21 final size:22
Alignment explanation
Indices: 6598308--6598354 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
6598298 AAGTATAATA
6598308 TTTAATAAAAAATTTA-ATTATT
1 TTTAATAAAAAATTTATA-TATT
*
6598330 TTTAAT-AAAATTTTATATATT
1 TTTAATAAAAAATTTATATATT
6598351 TTTA
1 TTTA
6598355 TTTTAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTAATAAAAAATTTATATATT
Found at i:6598388 original size:32 final size:32
Alignment explanation
Indices: 6598333--6598398 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
6598323 AATTATTTTT
* *
6598333 AATAAAATTTTATATATTTTTATT-TTAAATTA
1 AATAAAAATTTATATATTATTATTATT-AATTA
6598365 AATAAAAATTTATA-ATTAATTATTATTAATTA
1 AATAAAAATTTATATATT-ATTATTATTAATTA
6598397 AA
1 AA
6598399 ATATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 3 0.10
32 25 0.83
33 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
AATAAAAATTTATATATTATTATTATTAATTA
Found at i:6598754 original size:2 final size:2
Alignment explanation
Indices: 6598747--6598779 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6598737 AACTTCATCA
6598747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6598780 GCAAGAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6598940 original size:2 final size:2
Alignment explanation
Indices: 6598933--6598969 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
6598923 TTATACATAA
6598933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6598970 ATCGTCAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6604169 original size:68 final size:68
Alignment explanation
Indices: 6604094--6604220 Score: 182
Period size: 68 Copynumber: 1.9 Consensus size: 68
6604084 TTTTAATTTA
* * *
6604094 TTTTATTTAAATTTTATTCTTTAAACAGGAAAATAATGCACTAATTAATTAATCAAATATTTAAA
1 TTTTATTTAAATTTTATTCTTTAAACAAGAAAATAATACACTAATTAATAAATCAAATATTTAAA
6604159 TGT
66 TGT
* * * * *
6604162 TTTTATTTGAATTTTATTTTTTAAACAAGAAGATAATATATTAATTAATAAATCAAATA
1 TTTTATTTAAATTTTATTCTTTAAACAAGAAAATAATACACTAATTAATAAATCAAATA
6604221 CTCGTGCTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (68 bp):
TTTTATTTAAATTTTATTCTTTAAACAAGAAAATAATACACTAATTAATAAATCAAATATTTAAA
TGT
Found at i:6627453 original size:26 final size:26
Alignment explanation
Indices: 6627416--6627487 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 26
6627406 ATATTACACA
* *
6627416 TCATGTTGAAAAAATATTGTTTCATG
1 TCATGTTAAAAAAATATTGTTACATG
*
6627442 TCATAGTTAAAAAGAAGATTGTTACATG
1 TCAT-GTTAAAAA-AATATTGTTACATG
*
6627470 TTATGTTAAAAAAATATT
1 TCATGTTAAAAAAATATT
6627488 ATTATTTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 9 0.23
27 15 0.38
28 15 0.38
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (26 bp):
TCATGTTAAAAAAATATTGTTACATG
Found at i:6644110 original size:17 final size:18
Alignment explanation
Indices: 6644086--6644130 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
6644076 ATATATATAT
6644086 ATTTAAATTTAGATGT-AA
1 ATTTAAATTTAGAT-TAAA
6644104 A-TTAAA-TTAGATTAAA
1 ATTTAAATTTAGATTAAA
6644120 ATTTAAATTTA
1 ATTTAAATTTA
6644131 ATCATCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.04
16 9 0.38
17 10 0.42
18 4 0.17
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (18 bp):
ATTTAAATTTAGATTAAA
Found at i:6645030 original size:2 final size:2
Alignment explanation
Indices: 6645023--6645049 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6645013 CTCCCTCCTG
6645023 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
6645050 GAGAGAGAGA
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:6668226 original size:4 final size:4
Alignment explanation
Indices: 6668217--6668243 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6668207 CCAAAAAAGA
6668217 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
6668244 ACTAAAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:6670945 original size:3 final size:3
Alignment explanation
Indices: 6670937--6670970 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6670927 GAAAGAATAA
6670937 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
6670971 GAATGTGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6678302 original size:147 final size:148
Alignment explanation
Indices: 6678125--6678395 Score: 361
Period size: 147 Copynumber: 1.8 Consensus size: 148
6678115 AAAATAAACT
** *
6678125 AAAATAAAAGTAAATAATCATAATAACATTTAAATTACAA-ACAAAAATTAATATTTTAAAACAT
1 AAAATAAAAGTAAATAATCATAATAACATTTAAATTACAATA-AAAAAGAAATATATTAAAACAT
* *
6678189 TAATGATTAAAATGTAAATAAAATATTAACATTTAAATGATCT-ATTATTAATATTTTAAATAAA
65 CAATGATTAAAATATAAATAAAATATTAACATTTAAATGAT-TAATTATTAATATTTTAAATAAA
6678253 TTATAAATTATTAATATTGA
129 TTATAAATTATTAATATTGA
* * * * *
6678273 AAAATAAAA-TAAATAA-CAATAATAGCATTTAAATTATAATAAAATAGAAATATATTATAATAT
1 AAAATAAAAGTAAATAATC-ATAATAACATTTAAATTACAATAAAAAAGAAATATATTAAAACAT
* * * *
6678336 CAATTATTAAATTATAAATAAAATATTAATATTTAAATTATTAATTATTAATATTTTAAA
65 CAATGATTAAAATATAAATAAAATATTAACATTTAAATGATTAATTATTAATATTTTAAA
6678396 AATAAAATAA
Statistics
Matches: 106, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
146 2 0.02
147 94 0.89
148 10 0.09
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (148 bp):
AAAATAAAAGTAAATAATCATAATAACATTTAAATTACAATAAAAAAGAAATATATTAAAACATC
AATGATTAAAATATAAATAAAATATTAACATTTAAATGATTAATTATTAATATTTTAAATAAATT
ATAAATTATTAATATTGA
Found at i:6678346 original size:41 final size:41
Alignment explanation
Indices: 6678301--6678404 Score: 113
Period size: 41 Copynumber: 2.5 Consensus size: 41
6678291 ATAATAGCAT
6678301 TTAAATTAT-AATAAAATAGAAATATATTATAA-TATCAATTA
1 TTAAATTATAAATAAAATAGAAATAT-TTA-AATTATCAATTA
** *
6678342 TTAAATTATAAATAAAATATTAATATTTAAATTATTAATTA
1 TTAAATTATAAATAAAATAGAAATATTTAAATTATCAATTA
*
6678383 TTAATATTTTAAAAATAAAATA
1 TTAA-A--TTATAAATAAAATA
6678405 AAAAATTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 2 0.04
41 24 0.44
42 15 0.28
44 13 0.24
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (41 bp):
TTAAATTATAAATAAAATAGAAATATTTAAATTATCAATTA
Found at i:6678403 original size:44 final size:42
Alignment explanation
Indices: 6678301--6678423 Score: 108
Period size: 41 Copynumber: 2.8 Consensus size: 42
6678291 ATAATAGCAT
*
6678301 TTAAATT-ATAATAAAATAGAAATATATTATAATATCAATTA
1 TTAAATTAAAAATAAAATAGAAATATATTATAATATCAATTA
* ** *
6678342 TTAAATTATAAATAAAATATTAATAT-TTA-AATTATTAATTA
1 TTAAATTAAAAATAAAATAGAAATATATTATAA-TATCAATTA
*
6678383 TTAATATTTTAAAAATAAAATAAAAAATTATATATATAATA
1 TTAA-A--TTAAAAATAAAAT-AGAAA-TATAT-TATAATA
6678424 ATAGGTTTTT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
40 2 0.03
41 22 0.34
42 15 0.23
44 12 0.19
45 3 0.05
46 3 0.05
47 1 0.02
48 4 0.06
49 2 0.03
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (42 bp):
TTAAATTAAAAATAAAATAGAAATATATTATAATATCAATTA
Found at i:6683886 original size:13 final size:14
Alignment explanation
Indices: 6683886--6683924 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
6683876 AATAAAAATT
*
6683886 AAATTAATAAATAA
1 AAATTAATTAATAA
*
6683900 AAATTAATTCATAA
1 AAATTAATTAATAA
*
6683914 AAATAAATTAA
1 AAATTAATTAA
6683925 AGTTTAAAAT
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:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATTAATTAATAA
Found at i:6683900 original size:19 final size:19
Alignment explanation
Indices: 6683876--6683925 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
6683866 ATATATTATT
6683876 AATAAAAATTAAATTAATA
1 AATAAAAATTAAATTAATA
*
6683895 AATAAAAATT-AATTCATA
1 AATAAAAATTAAATTAATA
6683913 AA-AATAAATTAAA
1 AATAA-AAATTAAA
6683926 GTTTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 14 0.50
19 12 0.43
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAAAAATTAAATTAATA
Found at i:6694885 original size:138 final size:139
Alignment explanation
Indices: 6694631--6694913 Score: 433
Period size: 138 Copynumber: 2.0 Consensus size: 139
6694621 TTCAGATGGT
6694631 TTTTAGGAGAGAAATGAGAAATGTGAAAGCGAGGTGAAGACAGTGGTGGTGGTGGTGGTTTGTTG
1 TTTTAGGAGAGAAATGAGAAATGTGAAAGCGAGGTGAAGACA-----GGTGGTGGTGGTTTGTTG
* *
6694696 AAGAACGTTGAAAAGTAGCAAGAGCAGGGTTTAAGATTTGGTTTATGTAGAGGAGGATAAAAGTG
61 AAGAACGTTGAAAAGTAGCAAGAGCAGGGTTTAAGATTTGGGTTATGTAGAGGAGGATAAAAGAG
* *
6694761 GGTTCTGGCTTGCA
126 GGTACCGGCTTGCA
* *
6694775 TTTTAGGAGGGAAATGAGAAATGTGAAAGCGAGTTGAAGACA-GTGGTGGTGGTTTGTTGAAGAA
1 TTTTAGGAGAGAAATGAGAAATGTGAAAGCGAGGTGAAGACAGGTGGTGGTGGTTTGTTGAAGAA
* * *
6694839 TGTTGAAAAGTAGCAAGAGCAGGGTTTAGGATTTGGGTTATGTAGAGGAGGGTAAAAGAGGGTAC
66 CGTTGAAAAGTAGCAAGAGCAGGGTTTAAGATTTGGGTTATGTAGAGGAGGATAAAAGAGGGTAC
6694904 CGGCTTGCA
131 CGGCTTGCA
6694913 T
1 T
6694914 CTCCTGAGCT
Statistics
Matches: 130, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
138 90 0.69
144 40 0.31
ACGTcount: A:0.31, C:0.06, G:0.37, T:0.27
Consensus pattern (139 bp):
TTTTAGGAGAGAAATGAGAAATGTGAAAGCGAGGTGAAGACAGGTGGTGGTGGTTTGTTGAAGAA
CGTTGAAAAGTAGCAAGAGCAGGGTTTAAGATTTGGGTTATGTAGAGGAGGATAAAAGAGGGTAC
CGGCTTGCA
Found at i:6704775 original size:1 final size:1
Alignment explanation
Indices: 6704769--6704795 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
6704759 GGACAAATGC
6704769 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
6704796 CAGAATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6706858 original size:23 final size:21
Alignment explanation
Indices: 6706813--6706884 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
6706803 ATTTTTTTAT
*
6706813 ATTTTTATTTTAAATTAAATA
1 ATTTTTATATTAAATTAAATA
*
6706834 ATTTTTATAATTAATATTAATTA
1 ATTTTTAT-ATTAA-ATTAAATA
* *
6706857 ATTATTA-ATTAAA--ATATA
1 ATTTTTATATTAAATTAAATA
6706875 ATTTTT-TATT
1 ATTTTTATATT
6706885 TTTATATGCT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
18 11 0.26
20 1 0.02
21 13 0.31
22 4 0.10
23 13 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTATATTAAATTAAATA
Found at i:6710635 original size:19 final size:18
Alignment explanation
Indices: 6710611--6710661 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
6710601 GGGCGTAGGA
6710611 AAAAAGAGAAAAAAGAAAG
1 AAAAAGAGAAAAAA-AAAG
**
6710630 AAAAAGAGAAGTAAAAAG
1 AAAAAGAGAAAAAAAAAG
*
6710648 AGAAAG-GAAAAAAA
1 AAAAAGAGAAAAAAA
6710662 CAGGTAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 12 0.44
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (18 bp):
AAAAAGAGAAAAAAAAAG
Found at i:6710639 original size:12 final size:12
Alignment explanation
Indices: 6710617--6710659 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
6710607 AGGAAAAAAG
6710617 AGAAAAA-AGAA
1 AGAAAAAGAGAA
6710628 AGAAAAAGAG-A
1 AGAAAAAGAGAA
6710639 AGTAAAAAGAGAA
1 AG-AAAAAGAGAA
6710652 AGGAAAAA
1 A-GAAAAA
6710660 AACAGGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.36
12 10 0.36
13 7 0.25
14 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:6710793 original size:19 final size:20
Alignment explanation
Indices: 6710752--6710798 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
6710742 ATTTTAAAAT
*
6710752 TTTTATATAAATTATTATTA
1 TTTTATATAAATTATTATAA
6710772 TTTTAT-TAAATTAATTA-AA
1 TTTTATATAAATT-ATTATAA
6710791 TTTTATAT
1 TTTTATAT
6710799 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATATAAATTATTATAA
Found at i:6710799 original size:29 final size:28
Alignment explanation
Indices: 6710758--6710822 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
6710748 AAATTTTTAT
6710758 ATAAATTATTATTATTT-TATTAAATTAA
1 ATAAATTATTATT-TTTATATTAAATTAA
* * * *
6710786 TTAAATTTTATATTTTTATTTTTAATTAA
1 ATAAATTAT-TATTTTTATATTAAATTAA
6710815 ATAAATTA
1 ATAAATTA
6710823 ATTACTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
ATAAATTATTATTTTTATATTAAATTAA
Found at i:6710916 original size:3 final size:3
Alignment explanation
Indices: 6710904--6710957 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
6710894 TGTCATGATA
*
6710904 ATT A-T ATT ATT ATT ATT ATT ATT ATT A-T ATT -TT AAT A-T ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6710947 ATT ATT ATT AT
1 ATT ATT ATT AT
6710958 ATAATATAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
2 10 0.22
3 35 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:6710959 original size:18 final size:18
Alignment explanation
Indices: 6710906--6710965 Score: 74
Period size: 18 Copynumber: 3.5 Consensus size: 18
6710896 TCATGATAAT
6710906 TATATTATTATTATTATTA
1 TATATTA-TATTATTATTA
6710925 T-TATTATATT-TTA--A
1 TATATTATATTATTATTA
6710939 TATATTATATTATTATTA
1 TATATTATATTATTATTA
*
6710957 TATAATATA
1 TATATTATA
6710966 AAAATGATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
14 2 0.06
15 9 0.25
16 6 0.17
17 4 0.11
18 14 0.39
19 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATATTATATTATTATTA
Found at i:6710962 original size:23 final size:22
Alignment explanation
Indices: 6710904--6710965 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 22
6710894 TGTCATGATA
6710904 ATTATATTATTATTAT-TAT-T
1 ATTATATTATTATTATATATAT
*
6710924 A-T-TATTA-TATTTTA-ATAT
1 ATTATATTATTATTATATATAT
6710942 ATTATATTATTATTATATAATAT
1 ATTATATTATTATTATAT-ATAT
6710965 A
1 A
6710966 AAAATGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 11
0.72 0.04 0.24
Matches are distributed among these distances:
17 7 0.21
18 7 0.21
19 2 0.06
20 6 0.18
21 6 0.18
23 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTATATTATTATTATATATAT
Found at i:6711044 original size:21 final size:21
Alignment explanation
Indices: 6711019--6711068 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
6711009 ATAAAAATTT
6711019 ATTTATTTAAA-AAATATAAAA
1 ATTTATTTAAATAAA-ATAAAA
*
6711040 ATTTAGTTAAATAAAATAAAA
1 ATTTATTTAAATAAAATAAAA
*
6711061 AATTATTT
1 ATTTATTT
6711069 TAATTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
ATTTATTTAAATAAAATAAAA
Found at i:6711068 original size:25 final size:23
Alignment explanation
Indices: 6711009--6711068 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
6710999 ATCTTTAATC
* *
6711009 ATAAAAATTTATTTATTTAAAAA
1 ATAAAAAATTATTTATTAAAAAA
*
6711032 ATATAAAA--ATTTAGTTAAATAAA
1 ATAAAAAATTATTTA-TTAAA-AAA
6711055 ATAAAAAATTATTT
1 ATAAAAAATTATTT
6711069 TAATTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 5 0.17
22 4 0.14
23 16 0.55
25 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
ATAAAAAATTATTTATTAAAAAA
Found at i:6717039 original size:13 final size:13
Alignment explanation
Indices: 6717021--6717046 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6717011 TTGATTAAGT
6717021 TTTTAAACTTTCA
1 TTTTAAACTTTCA
6717034 TTTTAAACTTTCA
1 TTTTAAACTTTCA
6717047 AATAGTCGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAAACTTTCA
Found at i:6723802 original size:21 final size:21
Alignment explanation
Indices: 6723760--6723801 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6723750 TAATATCTAA
* *
6723760 AAAAAATTCTAAAATTATTTT
1 AAAAAATTCAAAAAATATTTT
6723781 AAAAAATTCAAATAAATATTT
1 AAAAAATTCAAA-AAATATTT
6723802 ATTCTCTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATTCAAAAAATATTTT
Found at i:6724104 original size:21 final size:24
Alignment explanation
Indices: 6724075--6724135 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 24
6724065 AATATTAATT
6724075 ATAAAAAAT-T-ATTTAATTTAAA
1 ATAAAAAATATAATTTAATTTAAA
6724097 ATAAAAATATATAAATTTAATTTAAA
1 ATAAAAA-ATAT-AATTTAATTTAAA
6724123 ATAAAAAA-ATAAT
1 ATAAAAAATATAAT
6724136 AATAAAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
22 7 0.20
23 5 0.14
24 3 0.09
25 1 0.03
26 19 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATAAAAAATATAATTTAATTTAAA
Found at i:6724148 original size:27 final size:26
Alignment explanation
Indices: 6724089--6724145 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
6724079 AAAATTATTT
* **
6724089 AATTTAAAATAAAAATATATAAATTT
1 AATTTAAAATAAAAAAATATAAATAA
6724115 AATTTAAAATAAAAAAATA-ATAATAA
1 AATTTAAAATAAAAAAATATA-AATAA
6724141 AATTT
1 AATTT
6724146 TAATATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (26 bp):
AATTTAAAATAAAAAAATATAAATAA
Found at i:6724957 original size:29 final size:28
Alignment explanation
Indices: 6724925--6725083 Score: 100
Period size: 29 Copynumber: 5.6 Consensus size: 28
6724915 ATAATATTAT
6724925 AATTAAAATAATATATAATATAAGA-ATAA
1 AATTAAAATAATA-ATAATATAA-ATATAA
6724954 AATTAAAATAA-AA-AATA-AAATATAAA
1 AATTAAAATAATAATAATATAAATAT-AA
* * * *
6724980 AATTAATAT-TTATATAATATAGATAAACA
1 AATTAAAATAATA-ATAATATAAATATA-A
6725009 AATTAAAATAA-AAT-ATAT-AATATAA
1 AATTAAAATAATAATAATATAAATATAA
* * *
6725034 AATATATTAAAGAAATAAAAATAAAATATATAA
1 AAT-TA--AAA-TAATAATAATATAA-ATATAA
*
6725067 AATTATAATAATAATAA
1 AATTAAAATAATAATAA
6725084 AAATAAAATA
Statistics
Matches: 100, Mismatches: 14, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
24 1 0.01
25 8 0.08
26 21 0.21
27 6 0.06
28 11 0.11
29 34 0.34
30 4 0.04
31 3 0.03
32 3 0.03
33 9 0.09
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (28 bp):
AATTAAAATAATAATAATATAAATATAA
Found at i:6724985 original size:55 final size:55
Alignment explanation
Indices: 6724925--6725035 Score: 145
Period size: 55 Copynumber: 2.0 Consensus size: 55
6724915 ATAATATTAT
*
6724925 AATTAAAATAATATATAATATAAGA-ATA-AAATTAAAATAAAAAATAAAATATAAA
1 AATTAAAAT-ATATATAATAT-AGATAAACAAATTAAAATAAAAAATAAAATATAAA
* * * *
6724980 AATTAATATTTATATAATATAGATAAACAAATTAAAATAAAATATATAATATAAA
1 AATTAAAATATATATAATATAGATAAACAAATTAAAATAAAAAATAAAATATAAA
6725035 A
1 A
6725036 TATATTAAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 3 0.06
54 12 0.24
55 34 0.69
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.31
Consensus pattern (55 bp):
AATTAAAATATATATAATATAGATAAACAAATTAAAATAAAAAATAAAATATAAA
Found at i:6725074 original size:23 final size:23
Alignment explanation
Indices: 6725016--6725206 Score: 67
Period size: 24 Copynumber: 8.0 Consensus size: 23
6725006 ACAAATTAAA
*
6725016 ATAAAA-TATATAATATAAAATAT
1 ATAAAATTATA-AAAATAAAATAT
*
6725039 ATTAAAGA-AATAAAAATAAAATAT
1 A-TAAA-ATTATAAAAATAAAATAT
* *
6725063 ATAAAATTATAATAATAATAA-AA
1 ATAAAATTATAAAAATAA-AATAT
* * *
6725086 ATAAAATATATGACATTAAAAATAT
1 ATAAAAT-TATAAAAAT-AAAATAT
* *
6725111 ATTTAAAATATGATATTATATAAAA-AT
1 A--TAAAAT-T-ATA-AAAATAAAATAT
*
6725138 -T--AATAATAAAAATATAAATAT
1 ATAAAATTATAAAAATA-AAATAT
6725159 ATTAAAA--ATAAAATATAAAATATT
1 A-TAAAATTATAAAA-ATAAAATA-T
*
6725183 ATAAAAATAAATAAAAATAAAATA
1 AT-AAAAT-TATAAAAATAAAATA
6725207 CATGATATTA
Statistics
Matches: 128, Mismatches: 17, Indels: 43
0.68 0.09 0.23
Matches are distributed among these distances:
19 4 0.03
20 6 0.05
21 2 0.02
22 4 0.03
23 35 0.27
24 36 0.28
25 10 0.08
26 8 0.06
27 16 0.12
28 6 0.05
29 1 0.01
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (23 bp):
ATAAAATTATAAAAATAAAATAT
Found at i:6725088 original size:38 final size:38
Alignment explanation
Indices: 6725003--6725091 Score: 101
Period size: 38 Copynumber: 2.3 Consensus size: 38
6724993 ATAATATAGA
* * *
6725003 TAAACAAATTAAAATAAAATATATAATATAAAATATAT
1 TAAAAAAATAAAAATAAAATATATAAAATAAAATATAT
* *
6725041 TAAAGAAATAAAAATAAAATATATAAAATTATAATA-A-
1 TAAAAAAATAAAAATAAAATATATAAAA-TAAAATATAT
6725078 TAATAAAAATAAAA
1 TAA-AAAAATAAAA
6725092 TATATGACAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
37 3 0.07
38 35 0.80
39 6 0.14
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (38 bp):
TAAAAAAATAAAAATAAAATATATAAAATAAAATATAT
Found at i:6725108 original size:86 final size:85
Alignment explanation
Indices: 6724934--6725193 Score: 216
Period size: 86 Copynumber: 3.0 Consensus size: 85
6724924 TAATTAAAAT
* *
6724934 AATATATAATATAAGAATAAAATTAAAATA-AAAAATAAAATATA-AAAATTAATATTTATATAA
1 AATATATAATATAA-AATAATATTAAAAAATAAAAATAAAATATATAAAATT-ATA-TTA-ATAA
* * *
6724997 TATAGATAAACA-A-ATTAAAATAA
62 TAAAAATAAA-ATATATGAAAATAA
*
6725020 AATATATAATATAAAAT-ATATTAAAGAAATAAAAATAAAATATATAAAATTATAATAATAATAA
1 AATATATAATATAAAATAATATTAAA-AAATAAAAATAAAATATATAAAATTATATTAATAATAA
* *
6725084 AAATAAAATATATGACATTAA
65 AAATAAAATATATGAAAATAA
* * *
6725105 AA-ATAT-ATTTAAAATATGATATTATATAAAAATTAATAATAAAA-ATAT-AAA-TATATTAAA
1 AATATATAATATAAAATA--ATA-T-TA-AAAAA-TAAAAATAAAATATATAAAATTATATTAAT
*
6725165 AATAAAATATAAAATATTATAAAAATAA
60 AATAAAA-ATAAAATA-TATGAAAATAA
6725193 A
1 A
6725194 TAAAAATAAA
Statistics
Matches: 145, Mismatches: 15, Indels: 26
0.78 0.08 0.14
Matches are distributed among these distances:
83 9 0.06
84 24 0.17
85 16 0.11
86 48 0.33
87 18 0.12
88 18 0.12
89 12 0.08
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.32
Consensus pattern (85 bp):
AATATATAATATAAAATAATATTAAAAAATAAAAATAAAATATATAAAATTATATTAATAATAAA
AATAAAATATATGAAAATAA
Found at i:6725147 original size:113 final size:114
Alignment explanation
Indices: 6725030--6725277 Score: 364
Period size: 113 Copynumber: 2.2 Consensus size: 114
6725020 AATATATAAT
*
6725030 ATAAAATATATTAAAGA-AATAAAAATAAAATATATAAA-ATTATAATAAT-AATAAAAATAAAA
1 ATAAAATATA-TAAAGATAATAAAAATAAAATATA-AAATATTATAAAAATAAATAAAAATAAAA
*
6725092 TATATGACATTAAAAATATATTTA-AAATATGATATTATATAAAAATTAATA
64 TACATGACATTAAAAATATATTTAGAAA-ATGATATTATATAAAAATTAATA
* *
6725143 ATAAAA-ATATAAATATATTAAAAATAAAATATAAAATATTATAAAAATAAATAAAAATAAAATA
1 ATAAAATATATAAAGATAATAAAAATAAAATATAAAATATTATAAAAATAAATAAAAATAAAATA
*
6725207 CATGATATTAAAAATATATTTAGAAAATGATATTATATAAAAATTAATA
66 CATGACATTAAAAATATATTTAGAAAATGATATTATATAAAAATTAATA
* *
6725256 ATAAAA-ATATAAATATATTAAA
1 ATAAAATATATAAAGATAATAAA
6725278 CTTATATTTT
Statistics
Matches: 126, Mismatches: 5, Indels: 8
0.91 0.04 0.06
Matches are distributed among these distances:
111 8 0.06
112 29 0.23
113 86 0.68
114 3 0.02
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (114 bp):
ATAAAATATATAAAGATAATAAAAATAAAATATAAAATATTATAAAAATAAATAAAAATAAAATA
CATGACATTAAAAATATATTTAGAAAATGATATTATATAAAAATTAATA
Found at i:6725149 original size:63 final size:62
Alignment explanation
Indices: 6725075--6725273 Score: 226
Period size: 63 Copynumber: 3.4 Consensus size: 62
6725065 AAAATTATAA
6725075 TAATAATAAAAATAAAATATATGACATTAAAAATATATTTAAAATATGATATTATATAAAAAT
1 TAATAATAAAAATAAAATATATGA-ATTAAAAATATATTTAAAATATGATATTATATAAAAAT
* * **
6725138 TAATAATAAAAATATAA-ATAT--ATTAAAAATA-A---AATATAAAATA-T-TATAAAAA-
1 TAATAATAAAAATAAAATATATGAATTAAAAATATATTTAAAATATGATATTATATAAAAAT
*
6725190 T-A-AATAAAAATAAAATACATGATATTAAAAATATATTTAGAAA-ATGATATTATATAAAAAT
1 TAATAATAAAAATAAAATATATGA-ATTAAAAATATATTTA-AAATATGATATTATATAAAAAT
6725251 TAATAATAAAAATATAAATATAT
1 TAATAATAAAAATA-AAATATAT
6725274 TAAACTTATA
Statistics
Matches: 111, Mismatches: 10, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
50 12 0.11
51 4 0.04
52 1 0.01
53 8 0.07
54 11 0.10
55 9 0.08
58 6 0.05
59 13 0.12
60 8 0.07
61 1 0.01
62 5 0.05
63 26 0.23
64 7 0.06
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (62 bp):
TAATAATAAAAATAAAATATATGAATTAAAAATATATTTAAAATATGATATTATATAAAAAT
Found at i:6725152 original size:21 final size:22
Alignment explanation
Indices: 6725128--6725276 Score: 85
Period size: 21 Copynumber: 6.6 Consensus size: 22
6725118 ATATGATATT
6725128 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATTAATAATAAAA
*
6725149 ATATAAATATATTAAAAAT-AAA
1 ATATAAA-ATATTAATAATAAAA
*
6725171 ATATAAAATATT-ATAAAAATAA
1 ATATAAAATATTAATAATAA-AA
* * *
6725193 ATA-AAAATA-AAATACATGATA
1 ATATAAAATATTAATA-ATAAAA
* * * **
6725214 TTAAAAATATATTTAGAAAATGATATT
1 ATATAAA-ATA-TTA-ATAAT-A-AAA
6725241 ATATAAAA-ATTAATAATAAAA
1 ATATAAAATATTAATAATAAAA
6725262 ATATAAATATATTAA
1 ATATAAA-ATATTAA
6725277 ACTTATATTT
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
20 3 0.03
21 33 0.34
22 23 0.24
23 20 0.21
24 3 0.03
25 4 0.04
26 3 0.03
27 7 0.07
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATAAAA
Found at i:6725198 original size:80 final size:82
Alignment explanation
Indices: 6725048--6725198 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 82
6725038 TATTAAAGAA
* ** *
6725048 ATAAAAATAAAATATATAAAATTATAATAATAATAAAAATAAAATATATGACATTAAAAATATAT
1 ATAAAAATAAAATATATAAAAATATAATAATAATAAAAATAAAATATAAAACATTAAAAATATAA
*
6725113 TTAAAATATGATATTAT
66 ATAAAATATGATATTAT
* * *
6725130 ATAAAAAT-TAATA-ATAAAAATATAA-ATATATTAAAAATAAAATATAAAATATTATAAAA-AT
1 ATAAAAATAAAATATATAAAAATATAATA-ATAATAAAAATAAAATATAAAACATTA-AAAATAT
6725191 AAATAAAA
64 AAATAAAA
6725199 ATAAAATACA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.02
80 42 0.71
81 8 0.14
82 8 0.14
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (82 bp):
ATAAAAATAAAATATATAAAAATATAATAATAATAAAAATAAAATATAAAACATTAAAAATATAA
ATAAAATATGATATTAT
Found at i:6761397 original size:90 final size:89
Alignment explanation
Indices: 6761268--6761440 Score: 258
Period size: 90 Copynumber: 1.9 Consensus size: 89
6761258 GCCAGGCCGC
*
6761268 TTCCTCCATAACCCCAATTTGCTCCGCCACAACACCCACCTCTGCTGCCTCAGCAATTCCC-CTT
1 TTCCTCCATAACCACAATTTGCTCCGCCACAACACCCACCTCTGCTGCCTCAGCAA-TCCCTCTT
6761332 TCCTCCACCACGTCAGCCACGCATGT
65 TCCTCCACCACG-CAGCCACGCATGT
* * * * *
6761358 TTCCTCCATAACCACAATTTGCTCTGTCATACCATCCACCTCTGCTGCCTCAGCAATCCCTCTTT
1 TTCCTCCATAACCACAATTTGCTCCGCCACAACACCCACCTCTGCTGCCTCAGCAATCCCTCTTT
*
6761423 CCTCCGCCACGCAGCCAC
66 CCTCCACCACGCAGCCAC
6761441 CTCTTTATCC
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
89 11 0.15
90 64 0.85
ACGTcount: A:0.20, C:0.46, G:0.10, T:0.25
Consensus pattern (89 bp):
TTCCTCCATAACCACAATTTGCTCCGCCACAACACCCACCTCTGCTGCCTCAGCAATCCCTCTTT
CCTCCACCACGCAGCCACGCATGT
Found at i:6762190 original size:2 final size:2
Alignment explanation
Indices: 6762185--6762213 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6762175 ATTGTGTGTG
6762185 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
6762214 TGATATTTTT
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:6769050 original size:14 final size:14
Alignment explanation
Indices: 6769031--6769059 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6769021 TAAATTTTGT
6769031 TGAAAGAAAAGCAA
1 TGAAAGAAAAGCAA
6769045 TGAAAGAAAAGCAA
1 TGAAAGAAAAGCAA
6769059 T
1 T
6769060 AAAAATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.21, T:0.10
Consensus pattern (14 bp):
TGAAAGAAAAGCAA
Found at i:6790137 original size:21 final size:22
Alignment explanation
Indices: 6790102--6790145 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
6790092 CTCTTAAAGT
6790102 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
6790124 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
6790145 A
1 A
6790146 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:6801378 original size:2 final size:2
Alignment explanation
Indices: 6801371--6801405 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6801361 TTCCTGGAAC
6801371 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6801406 ATCCTTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6831509 original size:16 final size:16
Alignment explanation
Indices: 6831468--6831523 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
6831458 TTGATTCATA
6831468 TAATATTAATATTTT-T
1 TAATATT-ATATTTTAT
*
6831484 ATGATGATTATATTTTAT
1 -TAAT-ATTATATTTTAT
*
6831502 TAATATTAAATTTTAT
1 TAATATTATATTTTAT
6831518 T-ATATT
1 TAATATT
6831524 TGATTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.15
16 12 0.35
17 13 0.38
18 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (16 bp):
TAATATTATATTTTAT
Found at i:6853300 original size:12 final size:12
Alignment explanation
Indices: 6853285--6853317 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6853275 AATCAAATTG
6853285 AAATGCAAATCC
1 AAATGCAAATCC
*
6853297 AAATGCAAATTC
1 AAATGCAAATCC
6853309 AAATG-AAAT
1 AAATGCAAAT
6853318 TTATTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.55, C:0.15, G:0.09, T:0.21
Consensus pattern (12 bp):
AAATGCAAATCC
Found at i:6869364 original size:30 final size:28
Alignment explanation
Indices: 6869263--6869746 Score: 112
Period size: 29 Copynumber: 16.9 Consensus size: 28
6869253 ATAATATTAT
*
6869263 AATTAAAAT-AAATATATATATAAGAATAAA
1 AATTAAAATAAAATATATA-AT-ATAA-AAA
6869293 AATTAAAATAAAATA-A-AATAT--AAA
1 AATTAAAATAAAATATATAATATAAAAA
* **
6869317 AATTAATAT-TTATATATAATGATAAAACA
1 AATTAAAATAAAATATATAAT-ATAAAA-A
6869346 AATTAAAATAAAATATATAATATAAAAA
1 AATTAAAATAAAATATATAATATAAAAA
*
6869374 TATATTAAAAATGAAAATA-A-AATAT-ATAA
1 -A-ATT-AAAAT-AAAATATATAATATAAAAA
*
6869403 AATTATAATAATAATA-A-AA-ATAAAATA
1 AATTAAAATAA-AATATATAATATAAAA-A
* * * * *
6869430 TATGACATTAAAA-ATAT-ATTTAAATAA
1 AATTAAAATAAAATATATAATATAAA-AA
* *
6869457 TGATATTATATAA-AATTAATAATAAAATATAAATA
1 --A-ATTA-A-AATAA--AAT-ATATAATATAAAAA
* *
6869492 TATTAAAAATAAAATATAAAATATTATAATAA
1 AATT-AAAATAAAATATATAATA-TA-AA-AA
6869524 TAA-TAAAATAAAATATATGACAT-TAAAAA
1 -AATTAAAATAAAATATAT-A-ATATAAAAA
* * *
6869553 TATATT-TAA-GAAATGATAT--TATATAAA
1 -A-ATTAAAATAAAAT-ATATAATATAAAAA
*
6869580 AATTAATAATAAAA-ATATAAATATATTAAA
1 AATTAA-AATAAAATATAT-AATATA-AAAA
* *
6869610 AATAAAATATAAAATAT-TAGA-AT-AATA
1 AATTAAA-ATAAAATATATA-ATATAAAAA
* * *
6869637 AATAAAAATAAAATCTATGATATTAAAAA
1 AATTAAAATAAAATATATAATA-TAAAAA
* * *
6869666 TATATT-TAA-GAAATGATAT--TATATAAA
1 -A-ATTAAAATAAAAT-ATATAATATAAAAA
*
6869693 AATTAATAATAAAATATA-AATATATTAAA
1 AATTAA-AATAAAATATATAATATA-AAAA
*
6869722 AATAAAATATAAAATAT-TAATATAA
1 AATTAAA-ATAAAATATATAATATAA
6869747 TATAATAATA
Statistics
Matches: 342, Mismatches: 46, Indels: 134
0.66 0.09 0.26
Matches are distributed among these distances:
23 3 0.01
24 12 0.04
25 14 0.04
26 35 0.10
27 45 0.13
28 22 0.06
29 75 0.22
30 67 0.20
31 37 0.11
32 16 0.05
33 6 0.02
35 4 0.01
36 6 0.02
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (28 bp):
AATTAAAATAAAATATATAATATAAAAA
Found at i:6869391 original size:32 final size:32
Alignment explanation
Indices: 6869272--6869776 Score: 106
Period size: 33 Copynumber: 15.6 Consensus size: 32
6869262 TAATTAAAAT
* *
6869272 AAATATATATATAAGAATAAAA-AT-TAAAATA
1 AAATATATAT-TAAAAATAAAATATATAATATA
*
6869303 AAATA-AAATATAAAAATTAATATTTATATATAATGATA
1 AAATATATAT-TAAAAA-TAA-A---ATATATAAT-ATA
*
6869341 AAACA-A-ATT-AAAATAAAATATATAATATA
1 AAATATATATTAAAAATAAAATATATAATATA
*
6869370 AAA-ATATATTAAAAATGAAAATA-AAATATATA
1 AAATATATATTAAAAAT-AAAATATATA-ATATA
6869402 AAATTATAATAATAATAAAAATAAAATATATGACAT-TA
1 AAA-TAT-AT-AT--TAAAAATAAAATATAT-A-ATATA
* *
6869440 AAA-ATATATT-TAAAT--AATGATATTATATA
1 AAATATATATTAAAAATAAAAT-ATATAATATA
* *
6869469 AAAT-TA-ATAATAAAATATAAATATATTAAAAATA
1 AAATATATATTA-AAAATA-AAATATA-T-AATATA
* * ** *
6869503 AAATATAAAAT-ATTATAATAATA-ATAAAATA
1 AAATATATATTAAAAATAA-AATATATAATATA
* *
6869534 AAATATATGACATTAAAAAT---ATATTTAAGA-A
1 AAATATAT---ATTAAAAATAAAATATATAATATA
*
6869565 ATGATAT-TATATAAAAATTAATAATA-A-AA-ATA
1 A-AATATATAT-TAAAAA-TAA-AATATATAATATA
* *
6869597 TAA-ATATATTAAAAATAAAATATAAAATATTA
1 AAATATATATTAAAAATAAAATATATAATA-TA
* * * *
6869629 GAATA-ATAAATAAAAATAAAATCTATGATATTA
1 AAATATAT-ATTAAAAATAAAATATATAATA-TA
* *
6869662 AAA-ATATATTTAAGAAATGATAT-TAT-ATA-A
1 AAATATATA-TTAA-AAATAAAATATATAATATA
* *
6869692 AAAT-TA-ATAATAAAATATAAATATATTAAAAATA
1 AAATATATATTA-AAAATA-AAATATA-T-AATATA
* * ** *
6869726 AAATATAAAATATTAATATAATATAATAATA-A
1 AAATATATATTAAAAATAAAATAT-ATAATATA
*
6869758 ATATATGATATTAAAAATA
1 AAATAT-ATATTAAAAATA
6869777 TATTTAAGAA
Statistics
Matches: 354, Mismatches: 51, Indels: 136
0.65 0.09 0.25
Matches are distributed among these distances:
28 17 0.05
29 32 0.09
30 48 0.14
31 45 0.13
32 48 0.14
33 52 0.15
34 46 0.13
35 21 0.06
36 10 0.03
37 11 0.03
38 21 0.06
39 3 0.01
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.33
Consensus pattern (32 bp):
AAATATATATTAAAAATAAAATATATAATATA
Found at i:6869391 original size:37 final size:37
Alignment explanation
Indices: 6869345--6869746 Score: 134
Period size: 35 Copynumber: 10.7 Consensus size: 37
6869335 ATGATAAAAC
*
6869345 AAATTAAAATAAAATATATAATATAAAAATATATTAA
1 AAATAAAAATAAAATATATAATATAAAAATATATTAA
* * *
6869382 AAATGAAAAT--AA-A-AT-ATATAAAATTATAATAA
1 AAATAAAAATAAAATATATAATATAAAAATATATTAA
*
6869414 TAATAAAAATAAAATATATGACAT-TAAAAATATATTTAA
1 AAATAAAAATAAAATATAT-A-ATATAAAAATATA-TTAA
* * *
6869453 ATAATGATATTATATAAAATTAATAATAAAATATAAATATATTAA
1 A-AAT-A-A--AAATAAAA-T-AT-ATAATATAAAAATATATTAA
6869498 AAATAAAATATAAAATATTATAATAATAATAAA-ATA--AA
1 AAATAAAA-ATAAAATA-TATAAT-ATAA-AAATATATTAA
* * * *
6869536 ATATATGACATTAAAA-ATAT-ATTTAAGAAATGATATT--
1 A-A-ATAAAAATAAAATATATAATATAA-AAAT-ATATTAA
* *
6869573 ATATAAAAATTAATAATA-A-AA-ATATAAATATATTAA
1 AAATAAAAA-TAA-AATATATAATATAAAAATATATTAA
* *
6869609 AAATAAAATATAAAATAT-TAGA-ATAATAAATAAAAATAA
1 AAATAAAA-ATAAAATATATA-ATATAA-AAAT-ATATTAA
* * * *
6869648 AATCTATGATATTAAAA-ATAT-ATTTAAGAAATGATATT--
1 AA---ATAAAAATAAAATATATAATATAA-AAAT-ATATTAA
* * * *
6869686 ATATAAAAAT-TAATA-ATAAAATATAAATATATTAA
1 AAATAAAAATAAAATATATAATATAAAAATATATTAA
6869721 AAATAAAATATAAAATAT-TAATATAA
1 AAATAAAA-ATAAAATATATAATATAA
6869747 TATAATAATA
Statistics
Matches: 265, Mismatches: 49, Indels: 102
0.64 0.12 0.25
Matches are distributed among these distances:
32 23 0.09
33 7 0.03
34 16 0.06
35 37 0.14
36 22 0.08
37 35 0.13
38 19 0.07
39 24 0.09
40 28 0.11
41 16 0.06
42 6 0.02
43 1 0.00
44 10 0.04
45 7 0.03
46 12 0.05
47 2 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (37 bp):
AAATAAAAATAAAATATATAATATAAAAATATATTAA
Found at i:6869428 original size:69 final size:76
Alignment explanation
Indices: 6869394--6869738 Score: 197
Period size: 78 Copynumber: 4.6 Consensus size: 76
6869384 ATGAAAATAA
6869394 AATATATAAAAT-TATAATAATAATAAAAATAAAATATATGACAT-TAAAAATATATTTAAATAA
1 AATA-ATAAAATATA-AAT-ATAATAAAAATAAAATATAT-A-ATATAAAAATATATTTAAATAA
6869457 TGATATTATATAAAATT
61 TGATA-TATATAAAATT
* * * * * *
6869474 AATAATAAAATATAAATATATTAAAAATAAAATATAAAATATTATAATAATAATAAAATAA--A-
1 AATAATAAAATATAAATATAATAAAAATAAAATATATAATATAAAAAT-ATATTTAAATAATGAT
* *
6869536 ATATATGACATT
65 ATATATAAAATT
* * * * * * *
6869548 AAAAAT-ATATTTAAGAAATGATATTATATAAAA-AT-TAATA-ATAAAA-ATA--TAAAT-AT-
1 AATAATAAAATATAA-ATATAATA-AAAATAAAATATATAATATA-AAAATATATTTAAATAATG
* *
6869604 ATTAAAAATAAAA-T
63 A-TATATATAAAATT
* * *
6869618 -ATAA-AATAT-TAGAATAATAAATAAAAATAAAATCTATGATATTAAAAATATATTTAAGA-AA
1 AATAATAAAATATA-AAT-AT-AATAAAAATAAAATATATAATA-TAAAAATATATTTAA-ATAA
6869679 TGATATTATATAAAAATT
61 TGATA-TATAT-AAAATT
* *
6869697 AATAATAAAATATAAATATATTAAAAATAAAATATAAAATAT
1 AATAATAAAATATAAATATAATAAAAATAAAATATATAATAT
6869739 TAATATAATA
Statistics
Matches: 198, Mismatches: 38, Indels: 60
0.67 0.13 0.20
Matches are distributed among these distances:
68 4 0.02
69 22 0.11
70 5 0.03
71 13 0.07
72 4 0.02
73 17 0.09
74 21 0.11
75 11 0.06
76 8 0.04
77 10 0.05
78 33 0.17
79 29 0.15
80 12 0.06
81 7 0.04
82 2 0.01
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.34
Consensus pattern (76 bp):
AATAATAAAATATAAATATAATAAAAATAAAATATATAATATAAAAATATATTTAAATAATGATA
TATATAAAATT
Found at i:6869445 original size:48 final size:48
Alignment explanation
Indices: 6869392--6869557 Score: 138
Period size: 56 Copynumber: 3.2 Consensus size: 48
6869382 AAATGAAAAT
6869392 AAAATATATAAAATTATAATAATAATAAAAATAAAATATATGACATTA
1 AAAATATATAAAATTATAATAATAATAAAAATAAAATATATGACATTA
* *
6869440 AAAATATATTTAAATAATGATATTATATAA-AATTAATAATAAAATATAAAT-ATATTA
1 AAAATATA--T-AA-AAT--TA-TA-ATAATAA-TAAAAATAAAATAT--ATGACATTA
* * *
6869497 AAAATAAAATATAAAATATTATAATAATAATAAAATAAAATATATGACATTA
1 AAAAT-ATATA-AAATTATAATAATAAT-A-AAAATAAAATATATGACATTA
6869549 AAAATATAT
1 AAAATATAT
6869558 TTAAGAAATG
Statistics
Matches: 93, Mismatches: 8, Indels: 31
0.70 0.06 0.23
Matches are distributed among these distances:
48 8 0.09
50 1 0.01
51 12 0.13
52 17 0.18
53 13 0.14
54 2 0.02
55 7 0.08
56 19 0.20
57 10 0.11
58 4 0.04
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (48 bp):
AAAATATATAAAATTATAATAATAATAAAAATAAAATATATGACATTA
Found at i:6869573 original size:109 final size:112
Alignment explanation
Indices: 6869387--6869831 Score: 730
Period size: 109 Copynumber: 4.0 Consensus size: 112
6869377 ATTAAAAATG
6869387 AAAATAAAATATATAAA-ATTATAATAATAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATA-AAATATTATAATAATAATAAAAATAAAATATATGACATTAAAAATATATTT
6869451 AA-ATAATGATATTATAT-AAAATTAATAAT-AAAATATAAATATATTA
65 AAGA-AATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
6869497 AAAATAAAATATAAAATATTATAATAATAAT-AAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATAAAATATTATAATAATAATAAAAATAAAATATATGACATTAAAAATATATTTA
6869561 AGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
66 AGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
* * *
6869608 AAAATAAAATATAAAATATTAGAATAATAAATAAAAATAAAATCTATGATATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATAATAAT-AATAAAAATAAAATATATGACATTAAAAATATATTT
6869673 AAGAAATGATATTATATAAAAATTAATAAT-AAAATATAAATATATTA
65 AAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
* *
6869720 AAAATAAAATATAAAATATTA-ATATAAT-ATAATAAT-AAATATATGATATTAAAAATATATTT
1 AAAATAAAATATAAAATATTATA-ATAATAATAAAAATAAAATATATGACATTAAAAATATATTT
*
6869782 AAGAAATGATATTAT-TACAAATTAATAATAAAAATATAAATATATTA
65 AAGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
6869829 AAA
1 AAA
6869832 TTATATTTTA
Statistics
Matches: 321, Mismatches: 6, Indels: 17
0.93 0.02 0.05
Matches are distributed among these distances:
108 13 0.04
109 110 0.34
110 47 0.15
111 45 0.14
112 46 0.14
113 60 0.19
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (112 bp):
AAAATAAAATATAAAATATTATAATAATAATAAAAATAAAATATATGACATTAAAAATATATTTA
AGAAATGATATTATATAAAAATTAATAATAAAAATATAAATATATTA
Found at i:6869686 original size:222 final size:220
Alignment explanation
Indices: 6869387--6869831 Score: 747
Period size: 222 Copynumber: 2.0 Consensus size: 220
6869377 ATTAAAAATG
*
6869387 AAAATAAAATATATAAAATTATAATAATAATAAAAATAAAATATATGACATTAAAAATATATTTA
1 AAAATAAAATATATAAAATTAGAATAATAATAAAAATAAAATATATGACATTAAAAATATATTTA
6869452 AATAATGATATTATAT-AAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAATAT
66 AATAATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAATAT
6869516 T-ATAATAATAATAA-AATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTATATAA
131 TAAT-ATAAT-ATAATAAT-AAATATATGACATTAAAAATATATTTAAGAAATGATATTAT-TAA
6869579 AAATTAATAATAAAAATATAAATATATTA
192 AAATTAATAATAAAAATATAAATATATTA
* *
6869608 AAAATAAAATATA-AAATATTAGAATAATAAATAAAAATAAAATCTATGATATTAAAAATATATT
1 AAAATAAAATATATAAA-ATTAGAATAAT-AATAAAAATAAAATATATGACATTAAAAATATATT
6869672 TAAGA-AATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAA
64 TAA-ATAATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAA
* *
6869736 TATTAATATAATATAATAATAAATATATGATATTAAAAATATATTTAAGAAATGATATTATTACA
128 TATTAATATAATATAATAATAAATATATGACATTAAAAATATATTTAAGAAATGATATTATTAAA
6869801 AATTAATAATAAAAATATAAATATATTA
193 AATTAATAATAAAAATATAAATATATTA
6869829 AAA
1 AAA
6869832 TTATATTTTA
Statistics
Matches: 213, Mismatches: 5, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
220 3 0.01
221 57 0.27
222 93 0.44
223 58 0.27
224 2 0.01
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (220 bp):
AAAATAAAATATATAAAATTAGAATAATAATAAAAATAAAATATATGACATTAAAAATATATTTA
AATAATGATATTATATAAAAATTAATAATAAAATATAAATATATTAAAAATAAAATATAAAATAT
TAATATAATATAATAATAAATATATGACATTAAAAATATATTTAAGAAATGATATTATTAAAAAT
TAATAATAAAAATATAAATATATTA
Found at i:6869744 original size:13 final size:13
Alignment explanation
Indices: 6869681--6869756 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
6869671 TTAAGAAATG
6869681 ATATT-ATATAAA
1 ATATTAATATAAA
6869693 A-ATTAATAATAAA
1 ATATTAAT-ATAAA
*
6869706 ATATAAATATATTAA
1 ATATTAATATA--AA
* *
6869721 AAATAAAATATAAA
1 ATAT-TAATATAAA
*
6869735 ATATTAATATAAT
1 ATATTAATATAAA
*
6869748 ATAATAATA
1 ATATTAATA
6869757 AATATATGAT
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
11 3 0.06
12 3 0.06
13 24 0.46
14 10 0.19
15 5 0.10
16 7 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATTAATATAAA
Found at i:6869762 original size:30 final size:30
Alignment explanation
Indices: 6869568--6869648 Score: 60
Period size: 30 Copynumber: 2.6 Consensus size: 30
6869558 TTAAGAAATG
* * *
6869568 ATATTATATAAAAATTAATAATAAAAATATAA
1 ATATAATATAAAAATAAAT-AT-AAAATATTA
6869600 ATAT-AT-TAAAAATAAAATATAAAATATTA
1 ATATAATATAAAAAT-AAATATAAAATATTA
6869629 GA-ATAATAAATAAAAATAAA
1 -ATATAAT--ATAAAAATAAA
6869649 ATCTATGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
29 10 0.24
30 12 0.29
31 5 0.12
32 7 0.17
33 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (30 bp):
ATATAATATAAAAATAAATATAAAATATTA
Found at i:6870031 original size:15 final size:15
Alignment explanation
Indices: 6869974--6870032 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
6869964 TGTTATTTTC
* *
6869974 CCTGTAATCACATTG
1 CCTGCAATCACATTA
* *
6869989 CTTACAATCACATTA
1 CCTGCAATCACATTA
* *
6870004 CTTGCAATTACATTA
1 CCTGCAATCACATTA
*
6870019 CCTGTAATCACATT
1 CCTGCAATCACATT
6870033 GCATTGTAAT
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (15 bp):
CCTGCAATCACATTA
Found at i:6881486 original size:2 final size:2
Alignment explanation
Indices: 6881479--6881503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6881469 CAAAGACTAC
6881479 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
6881504 GTGTGTGTGT
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:6892977 original size:7 final size:7
Alignment explanation
Indices: 6892965--6892989 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6892955 AATGGTGTGG
6892965 GAGGATT
1 GAGGATT
6892972 GAGGATT
1 GAGGATT
6892979 GAGGATT
1 GAGGATT
6892986 GAGG
1 GAGG
6892990 GGGTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (7 bp):
GAGGATT
Found at i:6914762 original size:35 final size:37
Alignment explanation
Indices: 6914711--6914782 Score: 94
Period size: 35 Copynumber: 2.0 Consensus size: 37
6914701 CTACCAAGAT
*
6914711 TTTCTTTTCTGTTTCCTAATTCTTTGCTATTTTGAAA
1 TTTCTTTTCTGTTTCCTAATTCTTTGCTACTTTGAAA
* * *
6914748 TTTC-TTT-TGTTTCCTTATTTTTTGCTGCTTTGAAA
1 TTTCTTTTCTGTTTCCTAATTCTTTGCTACTTTGAAA
6914783 ACTGGAGAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 24 0.77
36 3 0.10
37 4 0.13
ACGTcount: A:0.14, C:0.15, G:0.10, T:0.61
Consensus pattern (37 bp):
TTTCTTTTCTGTTTCCTAATTCTTTGCTACTTTGAAA
Found at i:6925298 original size:21 final size:21
Alignment explanation
Indices: 6925268--6925310 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
6925258 TTTGCCTAGC
*
6925268 CCTTCCGGCAAGACAGACCGA
1 CCTTCAGGCAAGACAGACCGA
6925289 CCTTCAGGCAAGACAGACCGA
1 CCTTCAGGCAAGACAGACCGA
6925310 C
1 C
6925311 TCAGGACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.23, T:0.09
Consensus pattern (21 bp):
CCTTCAGGCAAGACAGACCGA
Found at i:6932058 original size:2 final size:2
Alignment explanation
Indices: 6932051--6932081 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
6932041 CATATCAATT
*
6932051 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6932082 TAATTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6950905 original size:79 final size:79
Alignment explanation
Indices: 6950763--6950919 Score: 208
Period size: 79 Copynumber: 2.0 Consensus size: 79
6950753 ACCCGATTTC
* *
6950763 GGCAACGTCCTCATTGTCGTCGACCACCCTATCTACCCTGGTCCGTTAGGGCGCTTGGCGTGAGT
1 GGCAACGTCCTCATTGTCGTCGACCACCCTATCTACCCCGATCCGTTAGGGCGCTTGGCGTGAGT
* *
6950828 CGGTTGAGGTCCAA
66 CAGATGAGGTCCAA
* * * * * *
6950842 GGCAACGTCCTCATTG-CAGTTGACCACCCTATCTACCCCGATCTGTTGGGGTGTTTGGTGTGAG
1 GGCAACGTCCTCATTGTC-GTCGACCACCCTATCTACCCCGATCCGTTAGGGCGCTTGGCGTGAG
6950906 TCAGATGAGGTCCA
65 TCAGATGAGGTCCA
6950920 GTTGGACATG
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
78 1 0.01
79 66 0.99
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.27
Consensus pattern (79 bp):
GGCAACGTCCTCATTGTCGTCGACCACCCTATCTACCCCGATCCGTTAGGGCGCTTGGCGTGAGT
CAGATGAGGTCCAA
Found at i:6951030 original size:23 final size:21
Alignment explanation
Indices: 6950981--6951031 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
6950971 ACGCCTATTA
6950981 GGGTGTGTAACATGCCTGTTG
1 GGGTGTGTAACATGCCTGTTG
6951002 GGGTGTGTAACATGCCTGTTG
1 GGGTGTGTAACATGCCTGTTG
6951023 GGGTGTGTA
1 GGGTGTGTA
6951032 GCACACCCGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.12, G:0.41, T:0.33
Consensus pattern (21 bp):
GGGTGTGTAACATGCCTGTTG
Found at i:6951525 original size:20 final size:20
Alignment explanation
Indices: 6951500--6951538 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
6951490 GGTCAAGTGT
6951500 TTTATTAAATAATA-ATAATA
1 TTTATT-AATAATATATAATA
6951520 TTTATTAATAATATATAAT
1 TTTATTAATAATATATAAT
6951539 GGGCAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTATTAATAATATATAATA
Found at i:6960935 original size:15 final size:15
Alignment explanation
Indices: 6960917--6960957 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
6960907 GTAATTACAG
*
6960917 GTAATGTGTTTGCAA
1 GTAATGTGATTGCAA
6960932 GTAATGTGATTGCAA
1 GTAATGTGATTGCAA
*
6960947 GCAATGTGATT
1 GTAATGTGATT
6960958 ACAGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.37
Consensus pattern (15 bp):
GTAATGTGATTGCAA
Found at i:6961178 original size:27 final size:25
Alignment explanation
Indices: 6961132--6961334 Score: 83
Period size: 27 Copynumber: 7.6 Consensus size: 25
6961122 TATTATATTA
*
6961132 ATTTTTATATAATATCATTTCTTAAATAT
1 ATTTTTA-AT-ATATTATTT-TT-AATAT
6961161 ATTTTTAATATATTATTTATT--T-T
1 ATTTTTAATATATTATTT-TTAATAT
* * * *
6961184 ATTTATTATTATAATATTTTATATTTT
1 ATTT-TTAATATATTATTTT-TAATAT
*
6961211 ATTTTTTAAT-TATTTATATTTTATTATT
1 A-TTTTTAATATA-TTAT-TTTTAATA-T
*
6961239 AATTTTTATATAATATCATTTCTTAAATAT
1 -ATTTTTA-AT-ATATTATTT-TT-AATAT
* * *
6961269 ATTTTTAATATCATTATTTATATTTT
1 ATTTTTAATAT-ATTATTTTTAATAT
* * *
6961295 ATTTATTATTATAATA-TTTTATATTT
1 ATTT-TTAATATATTATTTTTA-ATAT
6961321 ATTTTTAATATATT
1 ATTTTTAATATATT
6961335 TATATTTTTA
Statistics
Matches: 137, Mismatches: 19, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
23 6 0.04
24 14 0.10
25 12 0.09
26 20 0.15
27 32 0.23
28 23 0.17
29 19 0.14
30 6 0.04
31 5 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTTTAATATATTATTTTTAATAT
Found at i:6961208 original size:15 final size:14
Alignment explanation
Indices: 6961119--6961792 Score: 156
Period size: 15 Copynumber: 49.6 Consensus size: 14
6961109 AAGTTTAATA
*
6961119 ATATATTATATTA-
1 ATATTTTATATTAT
*
6961132 AT-TTTTATATAAT
1 ATATTTTATATTAT
*
6961145 ATCATTTCT-TA-AAT
1 AT-ATTT-TATATTAT
6961159 ATATTTT-TA--AT
1 ATATTTTATATTAT
6961170 ATATTATT-TATT-T
1 ATATT-TTATATTAT
6961183 -TA-TTTATTATTAT
1 ATATTTTA-TATTAT
*
6961196 AATATTTTATATTTT
1 -ATATTTTATATTAT
*
6961211 ATTTTTTA-ATTATTT
1 ATATTTTATATTA--T
6961226 ATATTTTATTATTA-
1 ATATTTTA-TATTAT
*
6961240 AT-TTTTATATAAT
1 ATATTTTATATTAT
*
6961253 ATCATTTCT-TA-AAT
1 AT-ATTT-TATATTAT
*
6961267 ATATTTT-TAATAT
1 ATATTTTATATTAT
6961280 CAT-TATTTATATT-T
1 -ATAT-TTTATATTAT
6961294 -TA-TTTATTATTAT
1 ATATTTTA-TATTAT
6961307 AATATTTTATATT-T
1 -ATATTTTATATTAT
*
6961321 AT-TTTTAATATATTT
1 ATATTTT-ATAT-TAT
6961336 ATATTTT-TATTAT
1 ATATTTTATATTAT
*
6961349 -TAATTTTTATATAAT
1 AT-A-TTTTATATTAT
* *
6961364 CATCTTCTTA-A-AAT
1 -ATATT-TTATATTAT
6961378 ATATTTTA-ATGTCAT
1 ATATTTTATAT-T-AT
*
6961393 ATATTTTATTTTA-
1 ATATTTTATATTAT
6961406 AT-TTATTATA-TA-
1 ATATT-TTATATTAT
*
6961418 ATATTTAATATT-T
1 ATATTTTATATTAT
6961431 ATTATTTTA-ATATATT
1 A-TATTTTATAT-TA-T
6961447 ATATTTT-TATTAT
1 ATATTTTATATTAT
6961460 -TAATTTTATATAATAT
1 AT-ATTTTATAT--TAT
*
6961476 CATATTTT-TA-AAT
1 -ATATTTTATATTAT
* *
6961489 -TATTTAAATATCAT
1 ATATTT-TATATTAT
6961503 ATATTTTAT-TTAT
1 ATATTTTATATTAT
*
6961516 -TA--TTATATAAT
1 ATATTTTATATTAT
*
6961527 A-ATTTATATATTTT
1 ATATTT-TATATTAT
6961541 AT-TTTTA-ATATAT
1 ATATTTTATAT-TAT
* *
6961554 TTATATTATATTAT
1 ATATTTTATATTAT
6961568 -TAATTTTATA-TAT
1 AT-ATTTTATATTAT
6961581 ATCATTCTTA-A--AT
1 AT-ATT-TTATATTAT
6961594 ATATTTTA-ATGTCAT
1 ATATTTTATAT-T-AT
6961609 ATATTTTAT-TT-T
1 ATATTTTATATTAT
6961621 ATATTATTATA--A-
1 ATATT-TTATATTAT
6961633 ATATTTTATATT-T
1 ATATTTTATATTAT
6961646 -TATTTT-TA--AT
1 ATATTTTATATTAT
6961656 ATA-TTTATATT-T
1 ATATTTTATATTAT
* *
6961668 ATATATTAATTTTAT
1 ATAT-TTTATATTAT
* *
6961683 ATAATATCATATTAAAT
1 AT-ATTTTATATT--AT
6961700 ATATTTTA-ATGTCAT
1 ATATTTTATAT-T-AT
*
6961715 ATATTTTATTTTTAT
1 ATATTTTA-TATTAT
* *
6961730 TTATTATTATAATTTT
1 ATATT-TTAT-ATTAT
6961746 ATATATTT-TATTAT
1 ATAT-TTTATATTAT
6961760 -TATTTTA-A-TAT
1 ATATTTTATATTAT
*
6961771 -TTTTTTATATTAT
1 ATATTTTATATTAT
6961784 ATATTTTAT
1 ATATTTTAT
6961793 TTTAATTTGT
Statistics
Matches: 506, Mismatches: 47, Indels: 215
0.66 0.06 0.28
Matches are distributed among these distances:
10 10 0.02
11 45 0.09
12 86 0.17
13 90 0.18
14 101 0.20
15 113 0.22
16 44 0.09
17 16 0.03
18 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATATTTTATATTAT
Found at i:6961246 original size:42 final size:40
Alignment explanation
Indices: 6961181--6961363 Score: 135
Period size: 42 Copynumber: 4.4 Consensus size: 40
6961171 TATTATTTAT
6961181 TTTATTTATTATTATAATATTTTATAT-TTTATTTTTTAATTA
1 TTTATTT-TTATTATAAT-TTTTATATATTTATTTTTT-ATTA
* * *
6961223 TTTATATTTTATTATTAATTTTTATATAATATCATTTCTTA-AA
1 TTTAT-TTTTATTA-TAATTTTTATAT-AT-TTATTTTTTATTA
* * * *
6961266 TATATTTTTAATATCATTATTTATAT-TTTATTTATTATTA
1 TTTATTTTTATTATAATT-TTTATATATTTATTTTTTATTA
*
6961306 TAATATTTTATATT-T-ATTTTTAATATATTTATATTTTTATTA
1 T-TTATTTT-TATTATAATTTTT-ATATATTTAT-TTTTTATTA
*
6961348 TTAATTTTTA-TATAAT
1 TTTATTTTTATTATAAT
6961364 CATCTTCTTA
Statistics
Matches: 114, Mismatches: 13, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
39 12 0.11
40 13 0.11
41 24 0.21
42 45 0.39
43 11 0.10
44 2 0.02
45 7 0.06
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (40 bp):
TTTATTTTTATTATAATTTTTATATATTTATTTTTTATTA
Found at i:6961248 original size:108 final size:109
Alignment explanation
Indices: 6961119--6961757 Score: 840
Period size: 108 Copynumber: 5.9 Consensus size: 109
6961109 AAGTTTAATA
*
6961119 ATATATTA-TATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATAT-AT-TA-TTTA
1 ATATTTTATTATTAA-TTTTATATAATATCATTTCTTAAATATA-TTTTAATATCATATATTTTA
6961180 TTTTATTTATTATTATAATATTTTATATTTTATTTTTTAAT-TATTT
64 TTTTATTTATTATTATAATATTTTATATTTTA-TTTTTAATATATTT
6961226 ATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCAT-TATTTAT
1 ATATTTTATTATTAA-TTTTATATAATATCATTTCTTAAATATA-TTTTAATATCATATATTT-T
6961290 ATTTTATTTATTATTATAATATTTTATA-TTTATTTTTAATATATTT
63 ATTTTATTTATTATTATAATATTTTATATTTTATTTTTAATATATTT
*
6961336 ATATTTTTATTATTAATTTT-TAT-ATAATCATCTTCTTAAAATATATTTTAATGTCATATATTT
1 ATA-TTTTATTATTAATTTTATATAAT-ATCAT-TTCTT-AAATATATTTTAATATCATATATTT
*
6961399 TATTTTAATTTATTA-TATAATATTTAATA-TTTATTATTTTAATATA-TT
62 TATTTT-ATTTATTATTATAATATTTTATATTTTA-T-TTTTAATATATTT
* *
6961447 ATATTTTTATTATTAATTTTATATAATATCATATTTTTAAAT-TATTTAAATATCATATATTTTA
1 ATA-TTTTATTATTAATTTTATATAATATCAT-TTCTTAAATATATTTTAATATCATATATTTTA
6961511 -TTTA-TTATTA-TATAATAATTTATATATTTTATTTTTAATATATTT
64 TTTTATTTATTATTATAAT-ATTT-TATATTTTATTTTTAATATATTT
* *
6961556 ATATTATATTATTAATTTTATAT-ATATCA-TTCTTAAATATATTTTAATGTCATATATTTTATT
1 ATATTTTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTAATATCATATATTTTATT
6961619 TTA--TATTATTATAAATATTTTATATTTTATTTTTAATATATTT
66 TTATTTATTATTAT-AATATTTTATATTTTATTTTTAATATATTT
* *
6961662 ATA-TTTATATATTAATTTTATATAATATCA--TATTAAATATATTTTAATGTCATATATTTTAT
1 ATATTTTAT-TATTAATTTTATATAATATCATTTCTTAAATATATTTTAATATCATATATTTTA-
6961724 TTTTATTTATTATTATAAT-TTTATATATTTTATT
64 TTTTATTTATTATTATAATATTT-TATATTTTATT
6961758 ATTATTTTAA
Statistics
Matches: 489, Mismatches: 14, Indels: 57
0.87 0.03 0.10
Matches are distributed among these distances:
105 12 0.02
106 95 0.19
107 50 0.10
108 98 0.20
109 41 0.08
110 81 0.17
111 88 0.18
112 22 0.04
113 2 0.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (109 bp):
ATATTTTATTATTAATTTTATATAATATCATTTCTTAAATATATTTTAATATCATATATTTTATT
TTATTTATTATTATAATATTTTATATTTTATTTTTAATATATTT
Found at i:6961346 original size:27 final size:26
Alignment explanation
Indices: 6961160--6961695 Score: 152
Period size: 29 Copynumber: 19.8 Consensus size: 26
6961150 TTCTTAAATA
*
6961160 TATTTTTAATATATTATTTATTTTATT
1 TATTTTTAATATATTATAT-TTTTATT
*
6961187 TATTATTATAATATTTTATA-TTTTA--
1 TATT-TT-TAATATATTATATTTTTATT
6961212 T-TTTTTAAT-TATTTATATTTTATTATT
1 TATTTTTAATATA-TTATA-TTT-TTATT
* * *
6961239 AATTTTT-ATATAATATCATTTCTTAAATA
1 TATTTTTAATATATTAT-ATTT-TT--ATT
6961268 TATTTTTAATATCATTATTTATATTTTATT
1 TATTTTTAATAT-ATTA--TAT-TTTTATT
* *
6961298 TATTATT-ATA-A-TAT-TTTATATT
1 TATTTTTAATATATTATATTTTTATT
6961320 TATTTTTAATATATTTATATTTTTATTAT
1 TATTTTTAATATA-TTATATTTTTA-T-T
* * * **
6961349 TAATTTTT-ATATAATCATCTTCTTAAAA
1 T-ATTTTTAATAT-ATTATATT-TTTATT
*
6961377 TATATTTTAATGTCA-TATA-TTTTATT
1 TAT-TTTTAATAT-ATTATATTTTTATT
* * * *
6961403 T-TAATTTATTATATAATATTTAATATT
1 TAT-TTTTAATATATTATATTT-TTATT
6961430 TATTATTTTAATATATTATATTTTTATTAT
1 TA-T-TTTTAATATATTATATTTTTA-T-T
* *
6961460 TAATTTTATATAATATCATATTTTTA--
1 TATTTTTA-AT-ATATTATATTTTTATT
* *
6961486 AATTATTTAA-ATATCATATATTTTATT
1 TATT-TTTAATATATTATAT-TTTTATT
* *
6961513 TATTATT-ATATAATA-ATTTATATATTT
1 TATTTTTAATATATTATATTT-T-TA-TT
6961540 TATTTTTAATATATTTATATTATATTA-T
1 TATTTTTAATATA-TTATATT-T-TTATT
* * **
6961568 TAATTTT-ATATA-TATCATTCTTAAA
1 TATTTTTAATATATTAT-ATTTTTATT
*
6961593 TATATTTTAATGTCA-TATA-TTTTATT
1 TAT-TTTTAATAT-ATTATATTTTTATT
* * *
6961619 T-TATATTATTATA-AATATTTTATATTT
1 TAT-TTTTAATATATTATATTTT-TA-TT
*
6961646 TATTTTTAATATATTTATATTTATATAT
1 TATTTTTAATATA-TTATATTTTTAT-T
* *
6961674 TAATTTTATATAATATCATATT
1 TATTTTTA-AT-ATATTATATT
6961696 AAATATATTT
Statistics
Matches: 381, Mismatches: 63, Indels: 128
0.67 0.11 0.22
Matches are distributed among these distances:
21 1 0.00
22 21 0.06
23 6 0.02
24 25 0.07
25 40 0.10
26 36 0.09
27 69 0.18
28 52 0.14
29 72 0.19
30 46 0.12
31 6 0.02
32 4 0.01
33 3 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTTTTAATATATTATATTTTTATT
Found at i:6961481 original size:24 final size:24
Alignment explanation
Indices: 6961454--6961504 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
6961444 ATTATATTTT
6961454 TATTATT-AATT-TTATATAATATCA
1 TATTATTAAATTATT-TA-AATATCA
*
6961478 TATTTTTAAATTATTTAAATATCA
1 TATTATTAAATTATTTAAATATCA
6961502 TAT
1 TAT
6961505 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 16 0.67
25 6 0.25
26 2 0.08
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTATTAAATTATTTAAATATCA
Found at i:6961491 original size:32 final size:27
Alignment explanation
Indices: 6961170--6961770 Score: 174
Period size: 27 Copynumber: 21.9 Consensus size: 27
6961160 TATTTTTAAT
* *
6961170 ATATTATTTATT-TTA-TTTATTATTATA
1 ATATT-TTTATTATTATTTTAATA-TATC
6961197 ATATTTTATATT-TTATTTTTTAAT-TAT-
1 ATATTTT-TATTATTA--TTTTAATATATC
*
6961224 TTATATTTTATTATTAATTTTTATATAATATC
1 ATAT-TTTTATTATT-A-TTTTA-AT-ATATC
* * *
6961256 AT-TTCTTA-AATATATTTTTA-ATATC
1 ATATTTTTATTAT-TATTTTAATATATC
* * *
6961281 ATTATTTATATT-TTA-TTTATTATTATA
1 A-TATTTTTATTATTATTTTAATA-TATC
*
6961308 ATA-TTTTA-TATTTATTTTTAATATATTT
1 ATATTTTTATTA-TTA-TTTTAATATA-TC
*
6961336 ATATTTTTATTATTAATTTTTATATAATC
1 ATATTTTTATTATT-ATTTTAATAT-ATC
* * ** *
6961365 ATCTTCTTAAAATATATTTT-A-ATGTC
1 ATATTTTTATTAT-TATTTTAATATATC
* * *
6961391 ATATATTTTATT-TTAATTTATTATATA
1 ATAT-TTTTATTATTATTTTAATATATC
* *
6961418 ATATTTAATATTTATTATTTTAATATATT
1 ATATTT-TTA-TTATTATTTTAATATATC
6961447 ATATTTTTATTATTAATTTTATATAATATC
1 ATATTTTTATTATT-ATTTTA-AT-ATATC
*
6961477 ATATTTTTA-AATTA-TTTAA-ATATC
1 ATATTTTTATTATTATTTTAATATATC
*
6961501 ATATATTTTATTTATTATTAT-ATA-AT-
1 ATAT-TTTTA-TTATTATTTTAATATATC
6961527 A-ATTTATATATT-TTATTTTTAATATAT-
1 ATATTT-T-TATTATTA-TTTTAATATATC
* *
6961554 TTATATTATATTATTAATTTTATATATATC
1 ATAT-TTTTATTATT-ATTTTA-ATATATC
* * * *
6961584 AT-TCTTAAATA-TATTTT-A-ATGTC
1 ATATTTTTATTATTATTTTAATATATC
* * *
6961607 ATATATTTTATT-TTATATTATTATA-A
1 ATAT-TTTTATTATTATTTTAATATATC
6961633 ATATTTTATATT-TTATTTTTAATATAT-
1 ATATTTT-TATTATTA-TTTTAATATATC
* *
6961660 TTATATTTATATATTAATTTTATATAATATC
1 ATATTTTTAT-TATT-ATTTTA-AT-ATATC
* * * * *
6961691 ATATTAAATATATT-TTAATGTCATATATT
1 ATATT---TTTATTATTATTTTAATATATC
* * *
6961720 TTATTTTTATTTATTATTATAAT-T-TT
1 ATATTTTTA-TTATTATTTTAATATATC
6961746 ATATATTTTATTATTATTTTAATAT
1 ATAT-TTTTATTATTATTTTAATAT
6961771 TTTTTTATAT
Statistics
Matches: 428, Mismatches: 73, Indels: 146
0.66 0.11 0.23
Matches are distributed among these distances:
23 6 0.01
24 17 0.04
25 43 0.10
26 65 0.15
27 94 0.22
28 70 0.16
29 80 0.19
30 35 0.08
31 10 0.02
32 3 0.01
33 1 0.00
34 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
ATATTTTTATTATTATTTTAATATATC
Found at i:6961591 original size:21 final size:19
Alignment explanation
Indices: 6961169--6961689 Score: 63
Period size: 20 Copynumber: 27.3 Consensus size: 19
6961159 ATATTTTTAA
*
6961169 TATATTATTTATTTTAT-T
1 TATATTATTAATTTTATAT
*
6961187 TATTATTATAATATTTTATAT
1 TA-TATTATTA-ATTTTATAT
* *
6961208 TTTATTTTTTAATTATTTATAT
1 TATA-TTATTAA-T-TTTATAT
*
6961230 TTTATTATTAATTTTTATAT
1 TATATTATTAA-TTTTATAT
* * * *
6961250 AATATCATT--TCTTA-AA
1 TATATTATTAATTTTATAT
*
6961266 TATATTTTTAA---TATCAT
1 TATATTATTAATTTTAT-AT
6961283 TAT-TTA-T-ATTTTAT-T
1 TATATTATTAATTTTATAT
*
6961298 TATTATTATAATATTTTATAT
1 TA-TATTATTA-ATTTTATAT
*
6961319 T-TATTTTTAATATATTTATATT
1 TATATTATT-A-AT-TTTATA-T
*
6961341 TTTATTATTAATTTT-TA-
1 TATATTATTAATTTTATAT
* * * *
6961358 TATAATCATCT--TCTTAAAA
1 TAT-ATTAT-TAATTTTATAT
*
6961377 TATATT-TTAATGTCATATAT
1 TATATTATTAAT-T-TTATAT
*
6961397 TTTATT-TTAA-TTTAT-T
1 TATATTATTAATTTTATAT
* *
6961413 ATATAATATTTAATATT-TAT
1 -TATATTA-TTAATTTTATAT
* * *
6961433 TATTTTAAT-ATATTATATT
1 TATATTATTAATTTTATA-T
*
6961452 TTTATTATTAATTTTATAT
1 TATATTATTAATTTTATAT
* * * *
6961471 AATATCA-TATTTTTAAAT
1 TATATTATTAATTTTATAT
6961489 TAT-TTA--AA---TATCA-
1 TATATTATTAATTTTAT-AT
6961502 TATATT-TT-A-TTTATTAT
1 TATATTATTAATTTTA-TAT
*
6961519 TATA-TAATAATTTATATAT
1 TATATTATTAATTT-TATAT
* *
6961538 TTTATTTTTAATATATTTATAT
1 TATATTATT-A-AT-TTTATAT
6961560 TATATTATTAATTTTATAT
1 TATATTATTAATTTTATAT
* * * *
6961579 ATATCATTCTTAAATATATTT
1 -TAT-ATTATTAATTTTATAT
*
6961600 TA-ATGTCA-TATATTTTATTT
1 TATAT-T-ATTA-ATTTTATAT
6961620 TATATTATTATAAATATTTTATAT
1 TATATTA-T-T--A-ATTTTATAT
* *
6961644 TTTATTTTTAATATATTTATAT
1 TATATTATT-A-AT-TTTATAT
6961666 T-TATATATTAATTTTATAT
1 TATAT-TATTAATTTTATAT
*
6961685 AATAT
1 TATAT
6961690 CATATTAAAT
Statistics
Matches: 366, Mismatches: 68, Indels: 136
0.64 0.12 0.24
Matches are distributed among these distances:
13 5 0.01
14 5 0.01
15 6 0.02
16 17 0.05
17 40 0.11
18 28 0.08
19 65 0.18
20 85 0.23
21 50 0.14
22 41 0.11
23 9 0.02
24 15 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTATTAATTTTATAT
Found at i:6961641 original size:24 final size:24
Alignment explanation
Indices: 6961607--6961685 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 24
6961597 TTTTAATGTC
6961607 ATATATTTTATTTTATATTATTATA
1 ATATATTTTATTTTATATTATT-TA
6961632 A-ATATTTTATATTT-TATT-TTTA
1 ATATATTTTAT-TTTATATTATTTA
*
6961654 ATATATTTATATTTATATATTAATTTT
1 ATATATTT-TATTT-TATATT-ATTTA
6961681 ATATA
1 ATATA
6961686 ATATCATATT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
22 3 0.07
23 10 0.22
24 17 0.37
25 8 0.17
27 8 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATATATTTTATTTTATATTATTTA
Found at i:6961643 original size:46 final size:47
Alignment explanation
Indices: 6961592--6961755 Score: 136
Period size: 48 Copynumber: 3.2 Consensus size: 47
6961582 TCATTCTTAA
6961592 ATATATTTTAATGTCATATATTTTATTTTATATTATTATAAATATTT
1 ATATATTTTAATGTCATATATTTTATTTTATATTATTATAAATATTT
* * *
6961639 -TATATTTTATTTTTAATATATTTATATTTATATATTAATTTTATATAATATCATATT
1 ATATATTTTA-ATGTCATATATTT-TATTT-TATATT-A---T-TATAA-AT-AT-TT
6961696 AAATATATTTTAATGTCATATATTTTATTTT-TATTTATTATTATAAT-TTT
1 --ATATATTTTAATGTCATATATTTTATTTTATA-TTATTA-TA-AATATTT
6961746 ATATATTTTA
1 ATATATTTTA
6961756 TTATTATTTT
Statistics
Matches: 94, Mismatches: 6, Indels: 33
0.71 0.05 0.25
Matches are distributed among these distances:
46 9 0.10
47 10 0.11
48 15 0.16
49 6 0.06
50 3 0.03
51 1 0.01
52 2 0.02
53 6 0.06
54 6 0.06
55 2 0.02
56 5 0.05
57 5 0.05
58 5 0.05
59 10 0.11
60 9 0.10
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (47 bp):
ATATATTTTAATGTCATATATTTTATTTTATATTATTATAAATATTT
Found at i:6961755 original size:23 final size:22
Alignment explanation
Indices: 6961729--6961792 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
6961719 TTTATTTTTA
6961729 TTTATTATTATAATTTTATATAT
1 TTTATTATTATAATTTTATAT-T
*
6961752 TTTATTATTAT--TTTAATATT
1 TTTATTATTATAATTTTATATT
*
6961772 TTTTTATATTATATATTTTAT
1 TTTAT-TATTATA-ATTTTAT
6961793 TTTAATTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 5 0.15
21 13 0.38
23 11 0.32
24 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTATTATTATAATTTTATATT
Found at i:6961774 original size:29 final size:28
Alignment explanation
Indices: 6961713--6961889 Score: 96
Period size: 29 Copynumber: 6.1 Consensus size: 28
6961703 TTTTAATGTC
*
6961713 ATATATTTTATTTTTATTTATTATTATAATTTT
1 ATATATTTTA-TTTTA-TT-TTA--ATATTTTT
6961746 ATATATTTTATTATTATTTTAATATTTTT
1 ATATATTTTATT-TTATTTTAATATTTTT
*
6961775 TTATATTATATATTTTATTTTAAT-TTGTTT
1 ATATATT-T-TATTTTATTTTAATATT-TTT
* * * * *
6961805 ACCTATA-TATATATAAATGT-A-ATTTTT
1 A--TATATTTTATTTTATTTTAATATTTTT
* *
6961832 -GATATTTTATTTTATTTTAATTTTTATT
1 ATATATTTTATTTTATTTTAATATTT-TT
* *
6961860 CT-TATATATATTTTATTTTAATATTTTT
1 ATATAT-TTTATTTTATTTTAATATTTTT
6961888 AT
1 AT
6961890 TTTAATTATA
Statistics
Matches: 112, Mismatches: 19, Indels: 31
0.69 0.12 0.19
Matches are distributed among these distances:
24 3 0.03
25 8 0.07
26 1 0.01
27 6 0.05
28 11 0.10
29 40 0.36
30 14 0.12
31 8 0.07
32 8 0.07
33 13 0.12
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (28 bp):
ATATATTTTATTTTATTTTAATATTTTT
Found at i:6961775 original size:21 final size:20
Alignment explanation
Indices: 6961724--6961783 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 20
6961714 TATATTTTAT
* *
6961724 TTTTATTTATTATTATA--A
1 TTTTATATATTTTTATATTA
6961742 TTTTATATA-TTTTATTATTA
1 TTTTATATATTTTTA-TATTA
*
6961762 TTTTAATATTTTTTTATATTA
1 TTTT-ATATATTTTTATATTA
6961783 T
1 T
6961784 ATATTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 4 0.12
18 10 0.29
20 5 0.15
21 10 0.29
22 5 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATATATTTTTATATTA
Found at i:6961781 original size:86 final size:80
Alignment explanation
Indices: 6961308--6961791 Score: 213
Period size: 84 Copynumber: 5.9 Consensus size: 80
6961298 TATTATTATA
* * *
6961308 ATATTTTATA-TTTATTTTTAATATATTTATATTTTTATTATTAATTTTTATATAATCATCTTCT
1 ATATTTTATATTTTATTTTTAATATATTTATATTTATA-TATTAA-TTTTATATAAT-ATCATAT
6961372 TAAAATATATTTTAATGTCAT
63 T---ATATATTTTAATGTCAT
* * *
6961393 ATATTTTAT-TTTAATTTATTATATAATATTTA-A--TATTTATT-ATTTTA-AT-ATATTATAT
1 ATATTTTATATTTTATTT-TTA-AT-ATATTTATATTTATATATTAATTTTATATAATATCATAT
* * *
6961451 T-TTTATTATTAATTTTAT
63 TATATATT-TTAATGTCAT
* * *
6961469 ATAATATCATATTTTTAAATTATTTAA-ATATCATATATTT-TAT-TT-ATTATTATATAATA--
1 AT-ATTTTATA-TTTT--ATT-TTTAATATAT-TTATATTTATATATTAATT-TTATATAATATC
* * *
6961528 AT-TTATATATTTTATTTTTA-
59 ATATTATATATTTTAATGTCAT
* * * * * * * *
6961548 ATATATTTATATTATATTATT-A-AT-TTTATATATATCATTCTTAAATATATTTTAATGTCATA
1 ATAT-TTTATATTTTATTTTTAATATATTTATATTTAT-A-TATTAATTTTA-TATAATATCATA
* * *
6961610 -TATTTTATTTTATATTATTAT
62 TTA-TATATTTTA-A-TGTCAT
6961631 AAATATTTTATATTTTATTTTTAATATATTTATATTTATATATTAATTTTATATAATATCATATT
1 --ATATTTTATATTTTATTTTTAATATATTTATATTTATATATTAATTTTATATAATATCATATT
6961696 AAATATATTTTAATGTCAT
64 --ATATATTTTAATGTCAT
* * ** * *
6961715 ATATTTTAT-TTTTATTTATTATTATAATTTTATATATTTTATTATT-ATTTTAATATTTTTTTA
1 ATATTTTATATTTTATTT-TTAATAT-A-TTTATAT-TTATA-TATTAATTTT-ATATAATATCA
6961778 TATTATATATTTTA
60 TATTATATATTTTA
6961792 TTTTAATTTG
Statistics
Matches: 306, Mismatches: 46, Indels: 95
0.68 0.10 0.21
Matches are distributed among these distances:
72 6 0.02
73 2 0.01
74 4 0.01
75 8 0.03
76 17 0.06
77 12 0.04
78 9 0.03
79 20 0.07
80 27 0.09
81 28 0.09
82 28 0.09
83 5 0.02
84 49 0.16
85 41 0.13
86 29 0.09
87 14 0.05
88 7 0.02
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (80 bp):
ATATTTTATATTTTATTTTTAATATATTTATATTTATATATTAATTTTATATAATATCATATTAT
ATATTTTAATGTCAT
Found at i:6961864 original size:6 final size:5
Alignment explanation
Indices: 6961834--6961893 Score: 50
Period size: 5 Copynumber: 11.4 Consensus size: 5
6961824 TAATTTTTGA
* * *
6961834 TATTT TATTT TATTT TAATTTT TATTCT TATATA TATTT TATTT TAATA
1 TATTT TATTT TATTT T-A-TTT TATT-T TAT-TT TATTT TATTT TATTT
6961883 T-TTT TATTT TA
1 TATTT TATTT TA
6961894 ATTATAATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
4 2 0.05
5 28 0.64
6 9 0.20
7 5 0.11
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
TATTT
Found at i:6961873 original size:17 final size:14
Alignment explanation
Indices: 6961841--6961895 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
6961831 TGATATTTTA
6961841 TTTTATTTT-A-AT
1 TTTTATTTTAATAT
6961853 TTTTATTCTTATATAT
1 TTTTATT-TTA-ATAT
6961869 ATTTTATTTTAATAT
1 -TTTTATTTTAATAT
6961884 TTTTATTTTAAT
1 TTTTATTTTAAT
6961896 TATAATATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.18
13 2 0.05
14 12 0.32
15 5 0.13
16 5 0.13
17 7 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTATTTTAATAT
Found at i:6961886 original size:56 final size:58
Alignment explanation
Indices: 6961754--6961887 Score: 143
Period size: 54 Copynumber: 2.3 Consensus size: 58
6961744 TTATATATTT
*
6961754 TATTATTATTTTAATATTTTTTTATATTATATATTTTATTTTAATTTGTTTACCTATATA
1 TATT-TTATTTTAATA-TTTTTGATATTATATATTTTATTTTAATTTGTTTACCTATATA
* * * * * *
6961814 TATATAAATGT-A-ATTTTTGATATT-T-TATTTTATTTTAATTT-TTATTCTTATATA
1 TATTTTATTTTAATATTTTTGATATTATATATTTTATTTTAATTTGTT-TACCTATATA
6961868 TATTTTATTTTAATATTTTT
1 TATTTTATTTTAATATTTTT
6961888 ATTTTAATTA
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
53 2 0.03
54 31 0.52
55 2 0.03
56 16 0.27
57 1 0.02
58 1 0.02
59 4 0.07
60 3 0.05
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (58 bp):
TATTTTATTTTAATATTTTTGATATTATATATTTTATTTTAATTTGTTTACCTATATA
Found at i:6962941 original size:20 final size:20
Alignment explanation
Indices: 6962912--6962951 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6962902 TTTAATCATG
6962912 TTAATCATATAAATCGTGTA
1 TTAATCATATAAATCGTGTA
* *
6962932 TTAATTATATCAATCGTGTA
1 TTAATCATATAAATCGTGTA
6962952 AATAGGTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (20 bp):
TTAATCATATAAATCGTGTA
Found at i:6970511 original size:33 final size:34
Alignment explanation
Indices: 6970473--6970557 Score: 120
Period size: 34 Copynumber: 2.5 Consensus size: 34
6970463 TATATTACTT
* *
6970473 AATATGATAATCACGAATGCTTTGC-AAAAAATA
1 AATATGATAATCACGAATGCCTTGCAAAAAAAAA
*
6970506 TATATGATAATCAC-AGATGCCTTGCAAAAAAAAA
1 AATATGATAATCACGA-ATGCCTTGCAAAAAAAAA
6970540 AATATGATAATCACGAAT
1 AATATGATAATCACGAAT
6970558 ACTCTTAGAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
32 1 0.02
33 21 0.47
34 22 0.49
35 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (34 bp):
AATATGATAATCACGAATGCCTTGCAAAAAAAAA
Found at i:6971568 original size:21 final size:21
Alignment explanation
Indices: 6971505--6971568 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
6971495 GATTTTAGGG
6971505 TTTTA-AAGTTTGATGAATCGA
1 TTTTAGAA-TTTGATGAATCGA
** * *
6971526 TTCCAG-ATTTTATTAATCGA
1 TTTTAGAATTTGATGAATCGA
*
6971546 TTTTAGAATTTGATGAATTGA
1 TTTTAGAATTTGATGAATCGA
6971567 TT
1 TT
6971569 CTAAGATTTT
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (21 bp):
TTTTAGAATTTGATGAATCGA
Found at i:6971577 original size:21 final size:21
Alignment explanation
Indices: 6971513--6971577 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
6971503 GGTTTTAAAG
*
6971513 TTTGATGAATCGATTC-CAGA
1 TTTGATGAATCGATTCTAAGA
* * *
6971533 TTTTATTAATCGATT-TTAGAA
1 TTTGATGAATCGATTCTAAG-A
*
6971554 TTTGATGAATTGATTCTAAGA
1 TTTGATGAATCGATTCTAAGA
6971575 TTT
1 TTT
6971578 TGAATGCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 15 0.43
21 17 0.49
22 3 0.09
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (21 bp):
TTTGATGAATCGATTCTAAGA
Done.