Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 6 of 190
Found at i:498557 original size:229 final size:231
Alignment explanation
Indices: 498156--498609 Score: 618
Period size: 229 Copynumber: 2.0 Consensus size: 231
498146 ATCAATTAAC
* *
498156 TAAAAATATTTAAAAATTATTAGTTATTCAAAACTAATTCTTTAATAATTTACATATATATAATC
1 TAAAAATATTTAAAAATTATAAGTTATCCAAAACTAATTCTTTAATAATTTA-ATATATATAATC
* * * *
498221 TAATATATATCCTTTTATCGTATAAAATTAGTTTTCTAATAATTTTATGTTATTTATCAAATAAA
65 TAATATATATCCTTTTATCGTATAAAATTAATTTACTAATAATTATATGGTATTTATCAAATAAA
*
498286 TAAAAGATTTAAAATTACTAGTTATCCAAAATTAATTTTCTAAT-CATTT-ATATATA-AATTTA
130 TAAAAGATTAAAAATTACTAGTTATCCAAAATTAATTTTCTAATAC-TTTAATATATATAATTTA
* *
498348 AATATATA-TTTTTATCTTTTAAAATTAATCCAATAAA
194 AATATATACCTTTTACCTTTTAAAATTAATCCAATAAA
* * *
498385 TAAAAATATTTAAAAATTATAAGTTATCCAAAATTAATT-TTCTAATAATTT-GTATA-A-AATT
1 TAAAAATATTTAAAAATTATAAGTTATCCAAAACTAATTCTT-TAATAATTTAATATATATAATC
* * * *
498446 TAAATATATATCTTTTTTATCTTCTAAAATTAATTTACTAATAATTATGTGGTATTTATCAAATA
65 T-AATATATATC-CTTTTATCGTATAAAATTAATTTACTAATAATTATATGGTATTTATCAAATA
*
498511 AATAAAAGTATTAAAAATTTATTAGTTATCCAAAATTAATTTTCTAATACTTTAGATATATATAA
128 AATAAAAG-ATTAAAAA-TTACTAGTTATCCAAAATTAATTTTCTAATACTTTA-ATATATATAA
*
498576 TTTAAATATGTACCTTTTACCTTTTAAAATTAAT
190 TTTAAATATATACCTTTTACCTTTTAAAATTAAT
498610 TTTTTAATAA
Statistics
Matches: 197, Mismatches: 18, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
225 4 0.02
226 11 0.06
227 56 0.28
228 9 0.05
229 77 0.39
230 1 0.01
231 7 0.04
232 13 0.07
233 19 0.10
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (231 bp):
TAAAAATATTTAAAAATTATAAGTTATCCAAAACTAATTCTTTAATAATTTAATATATATAATCT
AATATATATCCTTTTATCGTATAAAATTAATTTACTAATAATTATATGGTATTTATCAAATAAAT
AAAAGATTAAAAATTACTAGTTATCCAAAATTAATTTTCTAATACTTTAATATATATAATTTAAA
TATATACCTTTTACCTTTTAAAATTAATCCAATAAA
Found at i:500696 original size:26 final size:25
Alignment explanation
Indices: 500642--500696 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
500632 CTCACCTAAG
*
500642 AATTTTATAAAAATTTACCATTTGA
1 AATTTTATAAAAATTTACCATTGGA
* *
500667 AATTTT-TATAAATTCTATCATTGGA
1 AATTTTATAAAAATT-TACCATTGGA
500692 TAATT
1 -AATT
500697 AATATTTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (25 bp):
AATTTTATAAAAATTTACCATTGGA
Found at i:501487 original size:83 final size:83
Alignment explanation
Indices: 501381--501604 Score: 245
Period size: 83 Copynumber: 2.7 Consensus size: 83
501371 AGACTCAATG
* * * ** * * * *
501381 ACTTTTGAGAAATAAAATACTCCTCTAAGTAGAGGCACCATAA-TTTTGGAAAGTAAATTGCTCC
1 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACTTTAGAAAAATAAATTGCTCC
* *
501445 TCTAAATAGAGGTACCATA
66 TCTAAACAGAGG-ACCACA
* *
501464 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGTACCACAACTTTAGAAAAATAAATTTCTCC
1 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACTTTAGAAAAATAAATTGCTCC
*
501529 TTTAAACAGAGGACCACA
66 TCTAAACAGAGGACCACA
* * * * *
501547 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGACAACACAA-TTTTGAAAAAATAAA
1 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACTTTAG-AAAAATAAA
501605 AAATTTCTTG
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
82 4 0.03
83 88 0.74
84 27 0.23
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (83 bp):
ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGCACCACAACTTTAGAAAAATAAATTGCTCC
TCTAAACAGAGGACCACA
Found at i:501498 original size:42 final size:42
Alignment explanation
Indices: 501381--501604 Score: 236
Period size: 42 Copynumber: 5.4 Consensus size: 42
501371 AGACTCAATG
* * * * ** * *
501381 ACTTTTGAGAAATAAAATACTCCTCTAAGTAGAGGCACCATA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACA
* * * *
501423 ATTTTGG-AAAGTAAATTGCTCCTCTAAATAGAGGTACCATA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACA
*
501464 ACTTTGGAAAAATAAAATGCTCCTCTAAACAGAGGTACCACA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACA
* * *
501506 ACTTTAGAAAAATAAATTTCTCCTTTAAACAGAGG-ACCACA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACA
* ** *
501547 ACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGACAACACA
1 ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACA
* *
501589 ATTTTGAAAAAATAAA
1 ACTTTGGAAAAATAAA
501605 AAATTTCTTG
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 70 0.45
42 86 0.55
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (42 bp):
ACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGTACCACA
Found at i:502077 original size:22 final size:25
Alignment explanation
Indices: 502051--502113 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
502041 TTCACACCTC
502051 AAAGATTCTCATTT-AAGAACTC-T
1 AAAGATTCTCATTTGAAGAACTCTT
**
502074 -AAGATTCTCATTTGAAGATTTCTT
1 AAAGATTCTCATTTGAAGAACTCTT
502098 AAAGATTCTCATTTGA
1 AAAGATTCTCATTTGA
502114 GTTCGAAGAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 13 0.37
23 6 0.17
24 1 0.03
25 15 0.43
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (25 bp):
AAAGATTCTCATTTGAAGAACTCTT
Found at i:502093 original size:14 final size:14
Alignment explanation
Indices: 502074--502113 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
502064 TAAGAACTCT
502074 AAGATTCTCATTTG
1 AAGATTCTCATTTG
*
502088 AAGATT-TC--TTA
1 AAGATTCTCATTTG
502099 AAGATTCTCATTTG
1 AAGATTCTCATTTG
502113 A
1 A
502114 GTTCGAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 6
0.72 0.07 0.21
Matches are distributed among these distances:
11 8 0.38
12 2 0.10
13 2 0.10
14 9 0.43
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (14 bp):
AAGATTCTCATTTG
Found at i:502193 original size:79 final size:79
Alignment explanation
Indices: 502102--502295 Score: 336
Period size: 79 Copynumber: 2.5 Consensus size: 79
502092 TTTCTTAAAG
502102 ATTCTCATTTGAGTTCGAAGATTCACATTTGATAAATTTTTGATTTCACACCTCAAAGATTCTCA
1 ATTCTCATTTGAGTTCGAAGATTCACATTTGATAAATTTTTGATTTCACACCTCAAAGATTCTCA
502167 TTTAAAACTAAAAA
66 TTTAAAACTAAAAA
* *
502181 ATTCTCATTTGAGTTTGAAGATTCACATTCGATAAATTTTTGATTTCACACCTCAAAGATTCTCA
1 ATTCTCATTTGAGTTCGAAGATTCACATTTGATAAATTTTTGATTTCACACCTCAAAGATTCTCA
* *
502246 TTTAAAACTCAAAG
66 TTTAAAACTAAAAA
*
502260 ATTCTCATTTGAGTTCGAAGATTCTCATTTGA-AAAT
1 ATTCTCATTTGAGTTCGAAGATTCACATTTGATAAAT
502296 GTCTTAAAGA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
78 4 0.04
79 104 0.96
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (79 bp):
ATTCTCATTTGAGTTCGAAGATTCACATTTGATAAATTTTTGATTTCACACCTCAAAGATTCTCA
TTTAAAACTAAAAA
Found at i:502256 original size:21 final size:21
Alignment explanation
Indices: 502232--502324 Score: 89
Period size: 21 Copynumber: 4.3 Consensus size: 21
502222 GATTTCACAC
502232 CTCAAAGATTCTCATTTAAAA
1 CTCAAAGATTCTCATTTAAAA
* *
502253 CTCAAAGATTCTCATTT-GAG
1 CTCAAAGATTCTCATTTAAAA
* *
502273 TTCGAAGATTCTCATTTGAAAA
1 CTCAAAGATTCTCATTT-AAAA
* *
502295 TGTCTTAAAGATTCTCATTTAAGA
1 ---CTCAAAGATTCTCATTTAAAA
502319 CTCAAA
1 CTCAAA
502325 AATTGAAAAC
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
20 16 0.29
21 22 0.39
22 1 0.02
24 3 0.05
25 14 0.25
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTAAAA
Found at i:503544 original size:31 final size:31
Alignment explanation
Indices: 503509--503579 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 31
503499 TTTTCTCTCA
503509 TTTTCATCTTTT-TATTCTTTCATTTTTT-ATT
1 TTTTCAT-TTTTCTATTCTTTC-TTTTTTCATT
*
503540 TTTTCATTTTTCTCTTCTTTCTTTTTTCA-T
1 TTTTCATTTTTCTATTCTTTCTTTTTTCATT
503570 TTTTCATTTT
1 TTTTCATTTT
503580 ATTCCTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
30 21 0.57
31 16 0.43
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTCATTTTTCTATTCTTTCTTTTTTCATT
Found at i:503579 original size:6 final size:7
Alignment explanation
Indices: 503509--503598 Score: 63
Period size: 8 Copynumber: 11.7 Consensus size: 7
503499 TTTTCTCTCA
503509 TTTTCAT
1 TTTTCAT
*
503516 CTTTTTAT
1 -TTTTCAT
503524 TCTTTCAT
1 T-TTTCAT
*
503532 TTTTTATT
1 TTTTCA-T
503540 TTTTCAT
1 TTTTCAT
*
503547 TTTTCTCT
1 TTTTC-AT
*
503555 TCTTTCTT
1 T-TTTCAT
503563 TTTTCAT
1 TTTTCAT
503570 TTTTCATT
1 TTTTCA-T
*
503578 TTATTCCT
1 TT-TTCAT
503586 TTTTCACT
1 TTTTCA-T
503594 TTTTC
1 TTTTC
503599 TTATCTTTCA
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
7 25 0.38
8 34 0.52
9 7 0.11
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTCAT
Found at i:509699 original size:27 final size:28
Alignment explanation
Indices: 509669--509722 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
509659 TTTTTCGTTG
509669 TTATAAGT-AAATAATAT-TTAATTTTTA
1 TTATAA-TAAAATAATATCTTAATTTTTA
*
509696 TTATGATAAAATAATATGCTTAATTTT
1 TTATAATAAAATAATAT-CTTAATTTT
509723 AATTGAGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 14 0.61
29 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (28 bp):
TTATAATAAAATAATATCTTAATTTTTA
Found at i:510163 original size:19 final size:19
Alignment explanation
Indices: 510124--510163 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
510114 TATTTGAATT
***
510124 AAAAAAAATTGAAATTTAA
1 AAAAAAAATTGAAAAAAAA
510143 AAAAAAAATTGAAAAAAAA
1 AAAAAAAATTGAAAAAAAA
510162 AA
1 AA
510164 GATACATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (19 bp):
AAAAAAAATTGAAAAAAAA
Found at i:510243 original size:20 final size:20
Alignment explanation
Indices: 510218--510262 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
510208 TAGTGTAACC
510218 TATATGTCTAAGTGGGAATA
1 TATATGTCTAAGTGGGAATA
510238 TATATGTCTAAGTGGGAATA
1 TATATGTCTAAGTGGGAATA
*
510258 CATAT
1 TATAT
510263 CGGAGCTAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (20 bp):
TATATGTCTAAGTGGGAATA
Found at i:510572 original size:19 final size:19
Alignment explanation
Indices: 510532--510569 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
510522 AATGATTTAA
**
510532 TATAAATTTTAATTTATAT
1 TATAAATTTTAATCGATAT
510551 TATAAA-TTTAATCGATAT
1 TATAAATTTTAATCGATAT
510569 T
1 T
510570 TATTCAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TATAAATTTTAATCGATAT
Found at i:514805 original size:27 final size:27
Alignment explanation
Indices: 514762--514822 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
514752 AGATATATCT
514762 ATTTTAAGTTTTAAAATTTT-AAATATA
1 ATTTTAAGTTTTAAAATTTTCAAATA-A
*
514789 ATTTTAA-TTTTATAAATTTTCTAATAA
1 ATTTTAAGTTTTA-AAATTTTCAAATAA
514816 ATTTTAA
1 ATTTTAA
514823 CAGAGCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.16
27 22 0.71
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
ATTTTAAGTTTTAAAATTTTCAAATAA
Found at i:515863 original size:2 final size:2
Alignment explanation
Indices: 515858--515882 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
515848 AAAAAATAGT
515858 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
515883 GCTTGTAAGG
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:516188 original size:22 final size:23
Alignment explanation
Indices: 516163--516206 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
516153 TTTAAAATAC
516163 TAAAAAATTTTACTA-TTATTTA
1 TAAAAAATTTTACTATTTATTTA
*
516185 TAAAGAATTTTACTATTTATTT
1 TAAAAAATTTTACTATTTATTT
516207 TCATAGGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
TAAAAAATTTTACTATTTATTTA
Found at i:517867 original size:168 final size:168
Alignment explanation
Indices: 517575--517913 Score: 581
Period size: 168 Copynumber: 2.0 Consensus size: 168
517565 AGGTGGGGAG
517575 ATTGTAACGCCCCAATCCCACATCAAGAAGATGTGTGGATAAGAAATGATATATATGTAGAGACT
1 ATTGTAACGCCCCAATCCCACATCAAGAAGATGTGTGGATAAGAAATGATATATATGTAGAGACT
** *
517640 TAATCCCAAACTTGTGAGGTGCCTTTTGTGGGACAAAACCGTGAGACATTCGGGTCAAAGCGGAC
66 TAATCCCAAACTTGTGAGGCACCTTTTGTGGGACAAAACCGTGAGACATTCGAGTCAAAGCGGAC
*
517705 AATACCTCGCAGGTTGGGTGCGGGTCTCCACAAAT-GT
131 AATACCTCACAGGTTGGGTGCGGGTCTCCACAAATGGT
* * *
517742 ATTGTAACGCCCTCAATCCCACATCAGGAGGATGTGTGGATAAGGAATGATATATATGTAGAGAC
1 ATTGTAACGCCC-CAATCCCACATCAAGAAGATGTGTGGATAAGAAATGATATATATGTAGAGAC
* *
517807 TTAATCCCAAACTTGTGAGGCACCTTTTGTGGGACAAAACCGTGAGACCTTCGAGTCAAAGTGGA
65 TTAATCCCAAACTTGTGAGGCACCTTTTGTGGGACAAAACCGTGAGACATTCGAGTCAAAGCGGA
517872 CAATACCTCACAGGTTGGGTGCGGGTCTCCACAAATGGT
130 CAATACCTCACAGGTTGGGTGCGGGTCTCCACAAATGGT
517911 ATT
1 ATT
517914 AGAGCGGTCA
Statistics
Matches: 161, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
167 12 0.07
168 144 0.89
169 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.24
Consensus pattern (168 bp):
ATTGTAACGCCCCAATCCCACATCAAGAAGATGTGTGGATAAGAAATGATATATATGTAGAGACT
TAATCCCAAACTTGTGAGGCACCTTTTGTGGGACAAAACCGTGAGACATTCGAGTCAAAGCGGAC
AATACCTCACAGGTTGGGTGCGGGTCTCCACAAATGGT
Found at i:518175 original size:201 final size:201
Alignment explanation
Indices: 517830--518228 Score: 717
Period size: 201 Copynumber: 2.0 Consensus size: 201
517820 TGTGAGGCAC
*
517830 CTTTTGTGGGACAAAACCGTGAGACCTTCGAGTCAAAGTGGACAATACCTCACAGGTTGGGTGCG
1 CTTTTGTGGGACAAAACCGTGAGACCTTCGAGTCAAAGCGGACAATACCTCACAGGTTGGGTGCG
*
517895 GGTCTCCACAAATGGTATTAGAGCGGTCACCAGTTCACAGTCGTGGGAGTCACTAAGTGCTACAC
66 GGTCTCCACAAATGGTATCAGAGCGGTCACCAGTTCACAGTCGTGGGAGTCACTAAGTGCTACAC
*
517960 GGTGAAGCCGTGGGAGTCACTAAGTGTTACACGATAGTCTGGTGTGATCTTGGTCCTATGGATGG
131 GGTGAAGCCGTGGGAGTCACTAAGTGTTACACGATAGTCTGGTGTGATCTTGGTCCTATGGATAG
518025 ACTTGA
196 ACTTGA
* **
518031 CTTTTGTGGGACAAAACCGTGAGACCTTCGGGTCAAAGCGGACAATACCTCGTAGGTTGGGTGCG
1 CTTTTGTGGGACAAAACCGTGAGACCTTCGAGTCAAAGCGGACAATACCTCACAGGTTGGGTGCG
* *
518096 GGTCTCCACAAATGGTATCAGAGTGGTCACCAGTTCGCAGTCGTGGGAGTCACTAAGTGCTACAC
66 GGTCTCCACAAATGGTATCAGAGCGGTCACCAGTTCACAGTCGTGGGAGTCACTAAGTGCTACAC
*
518161 GGTGGAGCCGTGGGAGTCACTAAGTGTTACACGATAGTCTGGTGTGATCTTGGTCCTATGGATAG
131 GGTGAAGCCGTGGGAGTCACTAAGTGTTACACGATAGTCTGGTGTGATCTTGGTCCTATGGATAG
518226 ACT
196 ACT
518229 CGGCTTGACA
Statistics
Matches: 189, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
201 189 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.25
Consensus pattern (201 bp):
CTTTTGTGGGACAAAACCGTGAGACCTTCGAGTCAAAGCGGACAATACCTCACAGGTTGGGTGCG
GGTCTCCACAAATGGTATCAGAGCGGTCACCAGTTCACAGTCGTGGGAGTCACTAAGTGCTACAC
GGTGAAGCCGTGGGAGTCACTAAGTGTTACACGATAGTCTGGTGTGATCTTGGTCCTATGGATAG
ACTTGA
Found at i:518696 original size:59 final size:61
Alignment explanation
Indices: 518569--518857 Score: 227
Period size: 59 Copynumber: 4.8 Consensus size: 61
518559 TTTATACAAG
* * *
518569 AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTCTTTTTTGAAAATTTTATTTTCAGA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATAC-TCCTTTTTGAAAATTTTATTTTCAAA
* * * *
518631 GAAAATTGATACTTTCAATTTTTTCTCAAAAAT-C-CCTTTTTG-AAATCTTTATTTTTAAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATACTCCTTTTTGAAAAT-TTTATTTTCAAA
* * * * * * *
518690 AAAAATTGATACTTTTAACTTTTCTTTAAAAATA-T-TTTTTTGACAATTTTACTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATACTCCTTTTTGAAAATTTTATTTTCAAA
* * * * * **
518749 AAAAATTGACATTTTCAACTTTTCCTTAAAAATGCT--TTTTTAAAAAAAAAAATTATTTTCAAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATACTCCTTTTT----GAAAATTTTATTTTCAAA
* * * * *
518812 GAAAATAGATACTTTCAACTTTTTCTGAAAAATA-T-TTTTTTGAAAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAAATACTCCTTTTTGAAAA
518858 AATATATATT
Statistics
Matches: 180, Mismatches: 37, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
58 4 0.02
59 97 0.54
60 4 0.02
61 1 0.01
62 30 0.17
63 44 0.24
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (61 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAAATACTCCTTTTTGAAAATTTTATTTTCAAA
Found at i:518789 original size:118 final size:120
Alignment explanation
Indices: 518569--518857 Score: 309
Period size: 118 Copynumber: 2.4 Consensus size: 120
518559 TTTATACAAG
*
518569 AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTCTTTTTTGAAAATTTTATTTTCAGAGAA
1 AAAAATTGATACTTTCAACTTTTCCTTAAAAATAC-TCTTTTTTGAAAATTTTACTTTCAGAGAA
* * *
518634 AATTGATACTTTCAATTTTTTCTCAAAAATCCCTTTTTGAAATCTTTATTTTTAAA
65 AATTGACACTTTCAACTTTTCCTCAAAAATCCCTTTTTGAAATCTTTATTTTTAAA
* * *
518690 AAAAATTGATACTTTTAACTTTTCTTTAAAAATA-T-TTTTTTGACAATTTTACTTTCA-AGAAA
1 AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTCTTTTTTGAAAATTTTACTTTCAGAG-AA
* * * * * *** *
518752 AATTGACATTTTCAACTTTTCCTTAAAAATGCTTTTTTAAAAAAAAAAATTATTTTCAAA
65 AATTGACACTTTCAACTTTTCCTCAAAAATCCCTTTTT----GAAATCTTTATTTTTAAA
* * * *
518812 GAAAATAGATACTTTCAACTTTTTCTGAAAAATA-T-TTTTTTGAAAA
1 AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTCTTTTTTGAAAA
518858 AATATATATT
Statistics
Matches: 140, Mismatches: 23, Indels: 9
0.81 0.13 0.05
Matches are distributed among these distances:
117 2 0.01
118 53 0.38
119 1 0.01
121 32 0.23
122 52 0.37
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (120 bp):
AAAAATTGATACTTTCAACTTTTCCTTAAAAATACTCTTTTTTGAAAATTTTACTTTCAGAGAAA
ATTGACACTTTCAACTTTTCCTCAAAAATCCCTTTTTGAAATCTTTATTTTTAAA
Found at i:518864 original size:18 final size:17
Alignment explanation
Indices: 518839--518873 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
518829 ACTTTTTCTG
*
518839 AAAAATATTTTTTTGAA
1 AAAAATATATTTTTGAA
518856 AAAATATATATTTTTGAA
1 AAAA-ATATATTTTTGAA
518874 TATTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (17 bp):
AAAAATATATTTTTGAA
Found at i:520157 original size:85 final size:84
Alignment explanation
Indices: 520046--520408 Score: 304
Period size: 85 Copynumber: 4.4 Consensus size: 84
520036 CTAAACTCTG
* * *
520046 AAATGAATAGCTTAGATTAAGCCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGAC
1 AAATGAATAACTTAGACTAAGTCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGAC
* *
520111 CTAGATTGAATCGAAGTCT
66 CTAGACTGAACCGAAGTCT
* * * * *
520130 AAAGTGAATAACTTAGAATAAGTCAAAGAAAGATCTGACATAGGTCAAAATTCGAAAACAAAATG
1 AAA-TGAATAACTTAGACTAAGTCAAAGAAGGATCTGACATAAGCCAAAA-TCCAAAACAAAATG
*
520195 ACCTGGA-TGAACCGAAGTC-
64 ACCTAGACTGAACCGAAGTCT
** *
520214 ---TG-A-AA--T-G-C-AAGCT-AAAGAAGGATCTGACATAAGTTAAAATCCAAAACGAAATGA
1 AAATGAATAACTTAGACTAAG-TCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGA
* * *
520268 TCTAGACTAAACCAAAGTCT
65 CCTAGACTGAACCGAAGTCT
* * * * * * * * * *
520288 AGAACGAATGACTTGGACTAAGACAAAAAAAGATTTGACATAAGCCAAAAACTAAAATAAAATGA
1 A-AATGAATAACTTAGACTAAGTCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGA
*
520353 CCTGGACTGAACCGAAGTCT
65 CCTAGACTGAACCGAAGTCT
* *
520373 GAAATGAATAACTTGGACTAAG-CTAAAAAAGGATCT
1 -AAATGAATAACTTAGACTAAGTC-AAAGAAGGATCT
520409 AGCATAGGTC
Statistics
Matches: 221, Mismatches: 39, Indels: 37
0.74 0.13 0.12
Matches are distributed among these distances:
72 17 0.08
73 36 0.16
74 1 0.00
75 1 0.00
76 1 0.00
78 3 0.01
79 2 0.01
80 3 0.01
82 1 0.00
83 1 0.00
84 5 0.02
85 130 0.59
86 20 0.09
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (84 bp):
AAATGAATAACTTAGACTAAGTCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGAC
CTAGACTGAACCGAAGTCT
Found at i:520364 original size:158 final size:158
Alignment explanation
Indices: 520064--520378 Score: 409
Period size: 158 Copynumber: 2.0 Consensus size: 158
520054 AGCTTAGATT
* * * *
520064 AAGCCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGACCTAGATTGAATCGAAGTC
1 AAGCCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGACCTAGACTAAACCAAAGTC
* * * * * *
520129 TAAAGTGAATAACTTAGAATAAGTCAAAGAAAGATCTGACATAGGTCAAAATTCGAAAACAAAAT
66 TAAAGCGAATAACTTAGAATAAGACAAAAAAAGATCTGACATAAGCCAAAATACGAAAACAAAAT
520194 GACCTGGATGAACCGAAGTCTGAAATGC
131 GACCTGGATGAACCGAAGTCTGAAATGC
* ** * *
520222 AAGCTAAAGAAGGATCTGACATAAGTTAAAATCCAAAACGAAATGATCTAGACTAAACCAAAGTC
1 AAGCCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGACCTAGACTAAACCAAAGTC
* * * * * *
520287 TAGAA-CGAATGACTTGGACTAAGACAAAAAAAGATTTGACATAAGCCAAAA-ACTAAAATAAAA
66 TA-AAGCGAATAACTTAGAATAAGACAAAAAAAGATCTGACATAAGCCAAAATACGAAAACAAAA
520350 TGACCTGGACTGAACCGAAGTCTGAAATG
130 TGACCTGGA-TGAACCGAAGTCTGAAATG
520379 AATAACTTGG
Statistics
Matches: 134, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
157 18 0.13
158 114 0.85
159 2 0.01
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (158 bp):
AAGCCAAAGAAGGATCTGACATAAGCCAAAATCCAAAACAAAATGACCTAGACTAAACCAAAGTC
TAAAGCGAATAACTTAGAATAAGACAAAAAAAGATCTGACATAAGCCAAAATACGAAAACAAAAT
GACCTGGATGAACCGAAGTCTGAAATGC
Found at i:532358 original size:60 final size:58
Alignment explanation
Indices: 532123--532594 Score: 471
Period size: 59 Copynumber: 7.9 Consensus size: 58
532113 GCATTTTGAC
* * *
532123 ATTTCTATTTTCAA-AGAAAATTGATATTTTTAACTTTTCCTTAAAAATACTTCTTTTTTGAAA
1 ATTT-TATTTTCAAGA-AAAATTGATACTTTCAACTTTTCC-TCAAAA-A--TCTTTTTTGAAA
* * *
532186 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATCCCTTTTTGAGA
1 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-CTTTTTTGAAA
* * ** * ** *
532245 TTTTTATTTTCAAGAAAAATTGATACTTTTAACTTTTTTTAAAAAAAGTTTTTTAGACA
1 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTT-GAAA
* ** * * ***
532304 ATTTTATTTTCAAGAAAAATTAATGTTTTCAACTTTTCTTTAAAAATGCTTTTTTTTTTA
1 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-C-TTTTTTGAAA
* * *
532364 ATTTCATTTTCAAGGAAAATTGATACTTTCAACTTTTACTCAAAAATACTTTTTTTGAAA
1 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-C-TTTTTTGAAA
* *
532424 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAG
1 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAA
* * * *
532482 TTTTTATTTTCAAGGAAAATTGATGCTTTCAACTTTTCCTCAAAAATATTTTTT-AAA
1 ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAA
* * * * * *
532539 GTTTTTATTTTTTAAGGAAAATTGATACTTTTAAATTTTCCTCAAAAATATTTTTT
1 -ATTTTA-TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTT
532595 TTTGAAAATA
Statistics
Matches: 351, Mismatches: 51, Indels: 18
0.84 0.12 0.04
Matches are distributed among these distances:
57 2 0.01
58 72 0.21
59 137 0.39
60 94 0.27
61 11 0.03
62 30 0.09
63 5 0.01
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (58 bp):
ATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTGAAA
Found at i:532394 original size:178 final size:176
Alignment explanation
Indices: 532082--532588 Score: 541
Period size: 178 Copynumber: 2.9 Consensus size: 176
532072 TTTATACAAA
* **
532082 AAAAATTTGATACTTTCAACTTTTTTT---TAAAGCATTTTGAC-ATTTCTATTTTCAA-AGAAA
1 AAAAA-TTGATACTTTCAACTTTTTTTAAAAAAAGTTTTTTGACAATTT-TATTTTCAAGA-AAA
* * ** *
532142 ATTGATATTTTTAACTTTTCCTTAAAAATACTTCTTTTTTGAAAATTTTATTTTCAAGAAAAATT
63 ATTGATGTTTTCAACTTTTCCTTAAAAAT-CTT-TTTTTT-TTAA-TTTATTTTCAAGGAAAATT
* * *
532207 GATACTTTCAACTTTTTCTCAAAAAT-CCCTTTTTGAGATTTTTATTTTCAAG
124 GATACTTTCAACTTTTACTCAAAAATACCCTTTTTGAAAATTTTATTTTCAAG
*
532259 AAAAATTGATACTTTTAACTTTTTTTAAAAAAAGTTTTTTAGACAATTTTATTTTCAAGAAAAAT
1 AAAAATTGATACTTTCAACTTTTTTTAAAAAAAGTTTTTT-GACAATTTTATTTTCAAGAAAAAT
* *
532324 TAATGTTTTCAACTTTTCTTTAAAAATGCTTTTTTTTTTAATTTCATTTTCAAGGAAAATTGATA
65 TGATGTTTTCAACTTTTCCTTAAAAAT-CTTTTTTTTTTAATTT-ATTTTCAAGGAAAATTGATA
**
532389 CTTTCAACTTTTACTCAAAAATACTTTTTTTGAAAATTTTATTTTCAAG
128 CTTTCAACTTTTACTCAAAAATACCCTTTTTGAAAATTTTATTTTCAAG
* * * * *
532438 AAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTGA-AGTTTTTATTTTCAAGGAAAA
1 AAAAATTGATACTTTCAACTTTT-TTTAAAAAAAGTTTTTTGACA-ATTTTATTTTCAAGAAAAA
* * * *
532501 TTGATGCTTTCAACTTTTCCTCAAAAATATTTTTTAAAGTTTTTA-TT-TTTT-AAGGAAAATTG
64 TTGATGTTTTCAACTTTTCCTTAAAAATCTTTTTT----TTTTAATTTATTTTCAAGGAAAATTG
* * *
532563 ATACTTTTAAATTTTCCTCAAAAATA
125 ATACTTTCAACTTTTACTCAAAAATA
532589 TTTTTTTTTG
Statistics
Matches: 284, Mismatches: 32, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
176 20 0.07
177 49 0.17
178 89 0.31
179 64 0.23
180 52 0.18
181 10 0.04
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.48
Consensus pattern (176 bp):
AAAAATTGATACTTTCAACTTTTTTTAAAAAAAGTTTTTTGACAATTTTATTTTCAAGAAAAATT
GATGTTTTCAACTTTTCCTTAAAAATCTTTTTTTTTTAATTTATTTTCAAGGAAAATTGATACTT
TCAACTTTTACTCAAAAATACCCTTTTTGAAAATTTTATTTTCAAG
Found at i:532602 original size:16 final size:17
Alignment explanation
Indices: 532583--532617 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
532573 ATTTTCCTCA
*
532583 AAAATAT-TTTTTTTTG
1 AAAATATATATTTTTTG
532599 AAAATATATATTTTTTG
1 AAAATATATATTTTTTG
532616 AA
1 AA
532618 GTTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
AAAATATATATTTTTTG
Found at i:534153 original size:2 final size:2
Alignment explanation
Indices: 534146--534199 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
534136 TGATTACTCC
534146 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
534188 TA TA TA TA TA TA
1 TA TA TA TA TA TA
534200 CACGCACACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:537639 original size:30 final size:31
Alignment explanation
Indices: 537603--537660 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
537593 AAAACACTTA
**
537603 CTTATTAATAAGGTGGTATCA-TTGATTTAT
1 CTTATTAATAAGGTAATATCATTTGATTTAT
*
537633 CTTATTAATGAGGTAATATCATTTGATT
1 CTTATTAATAAGGTAATATCATTTGATT
537661 AAATATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.47
Consensus pattern (31 bp):
CTTATTAATAAGGTAATATCATTTGATTTAT
Found at i:543189 original size:119 final size:123
Alignment explanation
Indices: 543045--543264 Score: 297
Period size: 119 Copynumber: 1.8 Consensus size: 123
543035 TTTTCCTTTC
*
543045 AAAAAAAAGAAAAAGAAATTCTAAATAGG-TCCAAATTGTGAAAAATTTAGAAA-TTT-TAA-AA
1 AAAAAAAAGAAAAAGAAATTCTAAATAGGCT-CAAATTGTGAAAAATTTAGAAAGTTTGAAAGAA
* *
543106 AATATATTTTTAAATTGACCCAAATGGTAGAA-AATTTAGAAATCCAACAAAAAACTAA
65 AAAATATTTCTAAATTGACCCAAATGGTAGAATAATTTAGAAATCCAACAAAAAACTAA
* * * * *
543164 AAAAAAAATAAAGAGAATTTTTAAATATGCTCAAATTGTGAAAAATTTAGAAAGTTTGAAAGAAA
1 AAAAAAAAGAAAAAGAAATTCTAAATAGGCTCAAATTGTGAAAAATTTAGAAAGTTTGAAAGAAA
* * *
543229 AAATATTTCTAATTTGGCCCAAATGGTGGAATAATT
66 AAATATTTCTAAATTGACCCAAATGGTAGAATAATT
543265 AGATATATTT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
119 46 0.54
120 4 0.05
121 2 0.02
122 29 0.34
123 4 0.05
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.28
Consensus pattern (123 bp):
AAAAAAAAGAAAAAGAAATTCTAAATAGGCTCAAATTGTGAAAAATTTAGAAAGTTTGAAAGAAA
AAATATTTCTAAATTGACCCAAATGGTAGAATAATTTAGAAATCCAACAAAAAACTAA
Found at i:546681 original size:21 final size:22
Alignment explanation
Indices: 546626--546674 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
546616 TGAGAAGATA
546626 GAAAA-AGCCTAAGAAAAGCTT
1 GAAAATAGCCTAAGAAAAGCTT
546647 GAAAATAGCCTAAG-AAAGCTT
1 GAAAATAGCCTAAGAAAAGCTT
546668 GAAAATA
1 GAAAATA
546675 AGTTAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (22 bp):
GAAAATAGCCTAAGAAAAGCTT
Found at i:549009 original size:60 final size:59
Alignment explanation
Indices: 548936--549591 Score: 615
Period size: 61 Copynumber: 11.0 Consensus size: 59
548926 CATGCTTTTA
* * * *
548936 TTCAAGGAAAATTGATACTTTTAACTTTTCCTTAAAAATGTTTTTCTTGAAAATTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTT-TTGAAAATTTTATT
* * * * *
548996 TTCATGAAAAATTGGTACTTCCAAC-TTTACTCAAAAATACTTTTTTGAAAATTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTTATT
* * *
549054 TTCAAGAAAAATTGATACTTTCAACTTTTCCT-TAAAA-ATGTTTTTG-AAATCCTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAAT-TTTATT
* * **
549111 TTCAAGAAAAATTATATACTTTCAACTTTTTCTCAAAAAATATATTTTTTTTAAATTTTATT
1 TTCAAGAAAAATT-GATACTTTCAACTTTTCCTC-AAAAATAT-TTTTTTGAAAATTTTATT
* *
549173 TTCAAGGAAAATTGATATTTTCAACTTTTCCTCAAAAATATTTTTTT-AAAATTTTTTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAA----TTTTATT
* **
549235 TT-TAGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTTTTTTGAAAATTTTTATT
1 TTCAAG-AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAA-TTTTATT
* * * *
549295 TTCAAGAGAAATTGATACTTTCAAATTTTTCTCAAAAATAATTTTTTTAAAAATTTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTGAAAA-TTTTATT
* * * *
549356 TTCAAAAAAAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTT--TATTTTTATGT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTTAT-T
* * * * *
549414 TTAAAG-GAAATTGATACATTCAAC-TTTCCTTCAAAAATAATGTTTTT---ATTTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCC-TCAAAAAT-ATTTTTTTGAAAATTTTATT
* ** * *
549470 TTCAAGGAAAATTGATACTTTCAAC-TTTCTCTCAAAAATATATATTTTTTTAATTTTTATG
1 TTCAAGAAAAATTGATACTTTCAACTTTTC-CTCAAAAATAT-T-TTTTTGAAAATTTTATT
* * * *
549531 TTCAA-AGGAAATTGATACATTCAAC-TTTCCTTCAAAAATATTTTTTTTCAAATTTTTATT
1 TTCAAGA-AAAATTGATACTTTCAACTTTTCC-TCAAAAATA-TTTTTTTGAAAATTTTATT
549591 T
1 T
549592 AAAAAGATCA
Statistics
Matches: 503, Mismatches: 64, Indels: 58
0.80 0.10 0.09
Matches are distributed among these distances:
56 16 0.03
57 91 0.18
58 79 0.16
59 26 0.05
60 96 0.19
61 118 0.23
62 69 0.14
63 8 0.02
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (59 bp):
TTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTTATT
Found at i:549066 original size:118 final size:116
Alignment explanation
Indices: 548936--549591 Score: 614
Period size: 118 Copynumber: 5.5 Consensus size: 116
548926 CATGCTTTTA
* * * *
548936 TTCAAGGAAAATTGATACTTTTAACTTTTCCTTAAAAATGTTTTTCTTGAAAATTTTATTTTCAT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTT-TT-AAAATTTTATTTTCAA
* * * * *
549001 GAAAAATTGGTACTTCCAACTTTACTCAAAAATACTTTTTTGAAAATTTTATT
64 GAAAAATTGATACTTTCAACTTTCCTCAAAAATAATTTTTTGTAAATTTTATT
* * *
549054 TTCAAGAAAAATTGATACTTTCAACTTTTCCTT-AAAA-ATGTTTTTGAAATCCTTATTTTCAAG
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAAAAT-TTTATTTTCAAG
* * *
549117 AAAAATTATATACTTTCAACTTTTTCTCAAAAAATATATTTTTTTTAAATTTTATT
65 AAAAATT-GATACTTTCAAC-TTTCCTC-AAAAATA-ATTTTTTGTAAATTTTATT
* * *
549173 TTCAAGGAAAATTGATATTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTTTTTTTATTTT-
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAAAA----TTTTATTTTC
* ** *
549237 TAGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTTTTTTGAAAATTTTTATT
62 AAG-AAAAATTGATACTTTCAAC-TTTCCTCAAAAATAATTTTTTGTAAA-TTTTATT
* * * *
549295 TTCAAGAGAAATTGATACTTTCAAATTTTTCTCAAAAATAATTTTTTTAAAAATTTTTATTTTCA
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAT-ATTTTTTT-AAAA-TTTTATTTTCA
* * *
549360 AAAAAAATTGATACTTTCAACTTTCCCTCAAAAAT-ATTTTTT-TTATTTTTATGT
63 AGAAAAATTGATACTTTCAACTTT-CCTCAAAAATAATTTTTTGTAAATTTTAT-T
* * * * *
549414 TTAAAG-GAAATTGATACATTCAAC-TTTCCTTCAAAAATAATGTTTTT--ATTTTTATTTTCAA
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTT-AAAAAT-ATTTTTTTAAAATTTTATTTTCAA
* * * *
549475 GGAAAATTGATACTTTCAACTTTCTCTCAAAAATATATATTTTTTTAATTTTTATG
64 GAAAAATTGATACTTTCAACTTTC-CTCAAAAATA-AT-TTTTTGTAAATTTTATT
* * *
549531 TTCAA-AGGAAATTGATACATTCAAC-TTTCCTTCAAAAATATTTTTTTTCAAATTTTTATTT
1 TTCAAGA-AAAATTGATACTTTCAACTTTTCCTT-AAAAATA-TTTTTTT-AAAATTTTATTT
549592 AAAAAGATCA
Statistics
Matches: 457, Mismatches: 51, Indels: 57
0.81 0.09 0.10
Matches are distributed among these distances:
113 1 0.00
114 46 0.10
115 20 0.04
116 15 0.03
117 25 0.05
118 121 0.26
119 53 0.12
120 13 0.03
121 68 0.15
122 48 0.11
123 28 0.06
124 18 0.04
125 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (116 bp):
TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAAAATTTTATTTTCAAGA
AAAATTGATACTTTCAACTTTCCTCAAAAATAATTTTTTGTAAATTTTATT
Found at i:549573 original size:57 final size:58
Alignment explanation
Indices: 548939--549591 Score: 468
Period size: 57 Copynumber: 10.9 Consensus size: 58
548929 GCTTTTATTC
* * *
548939 AAGGAAAATTGATACTTTTAACTTTTCCTT-AAAAAT-GTTTTTCTTGAAAATTTTATTTTCA
1 AAGG-AAATTGATACTTTCAAC-TTTCCTTCAAAAATAATTTTT-TT--AATTTTTATTTTCA
* * * * * *
549000 TGAA--AAATTGGTACTTCCAACTTTAC-TCAAAAATACTTTTTTGAAAATTTTATTTTC-
1 --AAGGAAATTGATACTTTCAACTTTCCTTCAAAAATAATTTTTT-TAATTTTTATTTTCA
* * ** **
549057 AAGAAAAATTGATACTTTCAACTTTTCCTT-AAAAAT-GTTTTTGAAATCCTTATTTTC-
1 AAG-GAAATTGATACTTTCAAC-TTTCCTTCAAAAATAATTTTTTTAATTTTTATTTTCA
* * * *
549114 AAGAAAAATTATATACTTTCAACTTT-TTCTCAAAAAATATATTTTTTTTAAATTTTATTTTC-
1 AAG-GAAATT-GATACTTTCAACTTTCCT-TC-AAAAATA-A-TTTTTTTAATTTTTATTTTCA
* *
549176 AAGGAAAATTGATATTTTCAACTTTTCC-TCAAAAAT-ATTTTTTTAAAATTTTTTTTATTTTTA
1 AAGG-AAATTGATACTTTCAAC-TTTCCTTCAAAAATAATTTTTTT--AA---TTTTTATTTTCA
* ** *
549239 GAA-AAAATTGATACTTTCAACTTTTCC-TCAAAAATGCTTTTTTGAAAATTTTTATTTTC-
1 -AAGGAAATTGATACTTTCAAC-TTTCCTTCAAAAATAATTTTTT--TAATTTTTATTTTCA
* *
549298 AAGAGAAATTGATACTTTCAAATTT-TTCTCAAAAATAATTTTTTTAAAAATTTTTATTTTCA
1 AAG-GAAATTGATACTTTCAACTTTCCT-TCAAAAATAATTTTTTT---AATTTTTATTTTCA
** * *
549360 AAAAAAATTGATACTTTCAACTTTCCCTCAAAAAT-ATTTTTTTTATTTTTATGTTT-A
1 AAGGAAATTGATACTTTCAACTTTCCTTCAAAAATAATTTTTTTAATTTTTAT-TTTCA
* *
549417 AAGGAAATTGATACATTCAACTTTCCTTCAAAAATAATGTTTTT-ATTTTTATTTTC-
1 AAGGAAATTGATACTTTCAACTTTCCTTCAAAAATAATTTTTTTAATTTTTATTTTCA
*
549473 AAGGAAAATTGATACTTTCAACTTT-CTCTCAAAAATATATATTTTTTTAATTTTTATGTTCA
1 AAGG-AAATTGATACTTTCAACTTTCCT-TC-AAAA-ATA-ATTTTTTTAATTTTTATTTTCA
* *
549535 AAGGAAATTGATACATTCAACTTTCCTTCAAAAATATTTTTTTTCAAATTTTTATTT
1 AAGGAAATTGATACTTTCAACTTTCCTTCAAAAATAATTTTTTT--AATTTTTATTT
549592 AAAAAGATCA
Statistics
Matches: 484, Mismatches: 56, Indels: 103
0.75 0.09 0.16
Matches are distributed among these distances:
55 2 0.00
56 10 0.02
57 101 0.21
58 69 0.14
59 38 0.08
60 95 0.20
61 84 0.17
62 73 0.15
63 10 0.02
64 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.06, T:0.47
Consensus pattern (58 bp):
AAGGAAATTGATACTTTCAACTTTCCTTCAAAAATAATTTTTTTAATTTTTATTTTCA
Found at i:550880 original size:86 final size:87
Alignment explanation
Indices: 550659--551830 Score: 622
Period size: 86 Copynumber: 13.9 Consensus size: 87
550649 GGAATGACTC
* * ** * * * *
550659 AAAGAAGGATTTGACATAGGTCAAAA-TCCAAAACACTATGACCT-GGACTGAACCAAAGTCTAA
1 AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAACGAAGTCTGA
* * * * * *
550722 AATGAATGATTTGGATTGACCC
66 AATGAATAACTTGGACTAAGCT
** * * * * ** * * *
550744 AAAGAAAAATTTTACATAAGTCAAAA-TCTAAGAGCAAGACAACCT-GGGTTGAAACAAAGTCTA
1 AAAGAAGGATTTGACATAAGTCAAAATTC-AAAAACAAAATGACCTAGGATTGAAACGAAGTCTG
* *
550807 AAATGAATAATTTGGACTGAGCT
65 AAATGAATAACTTGGACTAAGCT
* * *
550830 GAAGAAGGATTTGACATAAGTCAAAATTCAAAAATAAAATGACCTAGG-TTGAACCGAAGTCTGA
1 AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAACGAAGTCTGA
*
550894 AATGAATAA-TCTGGACTAAGTT
66 AATGAATAACT-TGGACTAAGCT
* * * * * * * * * * *
550916 GAAGAAAGATCTGGCATATGCCAAAATCCAAAAACAGAATGA-CTTGGATTGAATCGAAGTTTGA
1 AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAACGAAGTCTGA
* *
550980 AACGAATAA-TCTAGACTAAG-T
66 AATGAATAACT-TGGACTAAGCT
* * * * * *
551001 CAAAAAAAGATCTGGCATATGTCGAAA-TCTAAAAACAAAATGACCT-GGATTGAAATCGAAGTC
1 -AAAGAAGGATTTGACATAAGTCAAAATTC-AAAAACAAAATGACCTAGGATTGAAA-CGAAGTC
551064 T-AAA-G-------T-GA--AAGGC-
63 TGAAATGAATAACTTGGACTAA-GCT
* * * * * * * *
551077 AAAGAAGGATTTGACGTAGGTCGAAA-TCTGAAAACAAAATGA-CTTGAATAG-AACTGAAGCCT
1 AAAGAAGGATTTGACATAAGTCAAAATTC-AAAAACAAAATGACCTAGGATTGAAAC-GAAGTCT
*
551139 -AAATG----ACTTGGACTAAGTT
64 GAAATGAATAACTTGGACTAAGCT
* * * * * * * *
551158 GAAGAAAGATCT-AGCATATGTTAAAATTCAAAAATAGAATGACCTA-GATTG-AACTGAAGTTT
1 AAAGAAGGATTTGA-CATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAAC-GAAGTCT
* *
551220 GAAATAAATAACTTGGACTAAGCC
64 GAAATGAATAACTTGGACTAAGCT
* * ** * * *
551244 AAAAAAGGATCTGACATAAGTCAAAATTTGAAAACAGAATGACCT-GGATTGAACCGAAGTCAGA
1 AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAACGAAGTCTGA
*
551308 AATGAATAACTTGGACT-AGGT
66 AATGAATAACTTGGACTAAGCT
* * * * *
551329 CAAAGAAAGATCT-AGTATATA-TCAAAATCCAAAAACAAAATGA-CTTGGATTG-AACTGAAGT
1 -AAAGAAGGATTTGA-CATA-AGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAAC-GAAGT
* *
551390 TTGAAATGAATAACTTAGACTAAGCT
62 CTGAAATGAATAACTTGGACTAAGCT
* * * *
551416 GAAA-AAAGATTTTACATAAGTCGAAA-TCTAAAAACAAAATGACCTA-GA--CAAAGTCGAAGT
1 -AAAGAAGGATTTGACATAAGTCAAAATTC-AAAAACAAAATGACCTAGGATTGAAA--CGAAGT
* * * *
551476 CTGAAATAAATAATTTAGACTAAGCC
62 CTGAAATGAATAACTTGGACTAAGCT
* * * * * * * *
551502 AATA-AAGGGTCTGACATAAGTCGAAA-TCTAAAACAAAATGACAT-GGACTGAATCGAAGTTTG
1 AA-AGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAACGAAGTCTG
* *
551564 AAATAAATAACTTGGATTAAGCT
65 AAATGAATAACTTGGACTAAGCT
* * * * * * *
551587 AGAGGAGGATTTGACATAAGTCAAAATTCAAAAATAGAATAACCTA-GATTG-AACTAAAGTTTG
1 AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAAC-GAAGTCTG
*
551650 AAATGAATAACTTGGACTACGCT
65 AAATGAATAACTTGGACTAAGCT
* * * * *
551673 AAAGAAGGATTTG-GATATG-CTGAAATCCAAAAACAAAATGA-CTTGGATT-AAACTGAAGTCT
1 AAAGAAGGATTTGACATAAGTC-AAAATTCAAAAACAAAATGACCTAGGATTGAAAC-GAAGTCT
* * *
551734 GAAATGAAAAACTTAGACTAAGCC
64 GAAATGAATAACTTGGACTAAGCT
* * ** *
551758 GAAGAAGGATTTGACATAAGTCAAAATCCAAAAATGAAATGACCTA-GA-TGAAACTAAAGTCTG
1 AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAAC-GAAGTCTG
551821 AAATGAATAA
65 AAATGAATAA
551831 TCTAGACTAA
Statistics
Matches: 853, Mismatches: 174, Indels: 119
0.74 0.15 0.10
Matches are distributed among these distances:
73 1 0.00
74 13 0.02
75 42 0.05
76 1 0.00
77 2 0.00
78 2 0.00
79 2 0.00
80 2 0.00
81 41 0.05
82 8 0.01
84 4 0.00
85 174 0.20
86 529 0.62
87 32 0.04
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.23
Consensus pattern (87 bp):
AAAGAAGGATTTGACATAAGTCAAAATTCAAAAACAAAATGACCTAGGATTGAAACGAAGTCTGA
AATGAATAACTTGGACTAAGCT
Found at i:551435 original size:172 final size:171
Alignment explanation
Indices: 551144--551830 Score: 606
Period size: 171 Copynumber: 4.0 Consensus size: 171
551134 AGCCTAAATG
** * * * * * * *
551144 ACTTGGACTAAGTTGAAGAAAGATCTAGCATATGTTAAAATTCAAAAATAGAATGACCTAGATTG
1 ACTTGGACTAAGTCAAAGAAAGATCTAG-ATATATCAAAATCCAAAAACAAAATGACTTGGATTG
* * *
551209 AACTGAAGTTTGAAATAAATAACTTGGACTAAGC-CAAAAAAGGATCTGACATAAGTCAAAATTT
65 AACTGAAGTTTGAAATAAATAACTTAGACTAAGCTGAAAAAA-GATTTGACATAAGTCAAAATTT
* * *
551273 GAAAACAGAATGACCTGGATTGAACCGAAGTCAGAAATGAATA
129 AAAAACAGAATGACCTAGATTGAACCGAAGTCTGAAATGAATA
*
551316 ACTTGGACTAGGTCAAAGAAAGATCTAGTATATATCAAAATCCAAAAACAAAATGACTTGGATTG
1 ACTTGGACTAAGTCAAAGAAAGATCTAG-ATATATCAAAATCCAAAAACAAAATGACTTGGATTG
* * * *
551381 AACTGAAGTTTGAAATGAATAACTTAGACTAAGCTGAAAAAAGATTTTACATAAGTCGAAATCTA
65 AACTGAAGTTTGAAATAAATAACTTAGACTAAGCTGAAAAAAGATTTGACATAAGTCAAAATTTA
* ** * *
551446 AAAACAAAATGACCTAGA-CAAAGTCGAAGTCTGAAATAAATA
130 AAAACAGAATGACCTAGATTGAA-CCGAAGTCTGAAATGAATA
* * * * * * * * * *
551488 ATTTAGACTAAGCCAATA-AAGGGTCT-GACATAAGTCGAAAT-CTAAAACAAAATGACATGGAC
1 ACTTGGACTAAGTCAA-AGAAAGATCTAGATAT-A-TCAAAATCCAAAAACAAAATGACTTGGAT
* * ** *
551550 TGAA-TCGAAGTTTGAAATAAATAACTTGGATTAAGCT-AGAGGAGGATTTGACATAAGTCAAAA
63 TGAACT-GAAGTTTGAAATAAATAACTTAGACTAAGCTGA-AAAAAGATTTGACATAAGTCAAAA
* * * ** *
551613 TTCAAAAATAGAATAACCTAGATTGAACTAAAGTTTGAAATGAATA
126 TTTAAAAACAGAATGACCTAGATTGAACCGAAGTCTGAAATGAATA
* * * * * *
551659 ACTTGGACTACG-CTAAAGAAGGATTTGGATAT-GCTGAAATCCAAAAACAAAATGACTTGGATT
1 ACTTGGACTAAGTC-AAAGAAAGATCTAGATATATC-AAAATCCAAAAACAAAATGACTTGGATT
* * * * * *
551722 AAACTGAAGTCTGAAATGAAA-AACTTAGACTAAGCCGAAGAAGGATTTGACATAAGTCAAAATC
64 GAACTGAAGTTTGAAAT-AAATAACTTAGACTAAGCTGAAAAAAGATTTGACATAAGTCAAAATT
* * **
551786 CAAAAA-TGAAATGACCTAGA-TGAAACTAAAGTCTGAAATGAATA
128 TAAAAACAG-AATGACCTAGATTG-AACCGAAGTCTGAAATGAATA
551830 A
1 A
551831 TCTAGACTAA
Statistics
Matches: 420, Mismatches: 77, Indels: 37
0.79 0.14 0.07
Matches are distributed among these distances:
169 1 0.00
170 15 0.04
171 226 0.54
172 171 0.41
173 7 0.02
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (171 bp):
ACTTGGACTAAGTCAAAGAAAGATCTAGATATATCAAAATCCAAAAACAAAATGACTTGGATTGA
ACTGAAGTTTGAAATAAATAACTTAGACTAAGCTGAAAAAAGATTTGACATAAGTCAAAATTTAA
AAACAGAATGACCTAGATTGAACCGAAGTCTGAAATGAATA
Found at i:552730 original size:48 final size:48
Alignment explanation
Indices: 552633--552730 Score: 108
Period size: 48 Copynumber: 2.0 Consensus size: 48
552623 GAACCATCCC
* * * * *
552633 TTTTTGGAACTCAATCCGCCCTTTACGAATTTTTAATTTAAGGCTTTT
1 TTTTTAGAACTCAAACCGCCCTTTACGAATTTTCAATTTAAGCCCTTT
* * *
552681 TTTTTAGAACTCAAACTGCCCTTTAC-AGGTTTTCAATTTGAGCCCTTT
1 TTTTTAGAACTCAAACCGCCCTTTACGA-ATTTTCAATTTAAGCCCTTT
552729 TT
1 TT
552731 GTTTTTTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.45
Consensus pattern (48 bp):
TTTTTAGAACTCAAACCGCCCTTTACGAATTTTCAATTTAAGCCCTTT
Found at i:552745 original size:61 final size:62
Alignment explanation
Indices: 552676--552844 Score: 236
Period size: 62 Copynumber: 2.7 Consensus size: 62
552666 TAATTTAAGG
* *
552676 CTTTTTTTTTAGAACTCAAA-CTGCCCTTTACAGGTTTTCAATTTGAGCCCTTTT-TGTTTTTTT
1 CTTTTTTTTT-CAACTCAAATC-GCCCTTTACGGGTTTTCAATTTGAGCCCTTTTCT-TTTTTTT
* *
552739 CTTTTTTTTTCAACTCAAATCGCCCTTTATGGGTTTTCAATTTGAGCTCTTTTCTTTTTTTT
1 CTTTTTTTTTCAACTCAAATCGCCCTTTACGGGTTTTCAATTTGAGCCCTTTTCTTTTTTTT
* *
552801 GTTTTTTTTT-AACTCAAATCACCCTTTACGGGTTTTCAATTTGA
1 CTTTTTTTTTCAACTCAAATCGCCCTTTACGGGTTTTCAATTTGA
552845 TCTTTTTTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
61 32 0.33
62 53 0.55
63 12 0.12
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.53
Consensus pattern (62 bp):
CTTTTTTTTTCAACTCAAATCGCCCTTTACGGGTTTTCAATTTGAGCCCTTTTCTTTTTTTT
Found at i:563382 original size:59 final size:59
Alignment explanation
Indices: 563228--563766 Score: 359
Period size: 59 Copynumber: 9.2 Consensus size: 59
563218 AAAGTTTTTT
** * * * *
563228 TTTTATTTTCGAGAAAATTTGATAC-TT-AACTTTTCCTTAAAATTGTTTTTCTTGAGAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTT-TTGAAAA
* * * * * *
563286 TTTTATTTTCAAGGAAATTTGGTACTTCCAAC-ATTCCTCAAAAATGTTTTTTTGAAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTGAAAA
* * *
563344 TTTTATTTTTACGAAAAATTGATACTTTCAACTTTTCCTTAAAAATG--TTTTTG-ACA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTGAAAA
* * * *
563400 TCTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATGCTTTTTTGAAAG
1 T-TTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTGAAAA
* *
563460 TTTT-TGTTTTCAAGAAAAATTGATACTTTCAAC-TTTCCTTC-AACA---CTTTTT-----
1 TTTTAT-TTTT-AAGAAAAATTGATACTTTCAACTTTTCC-TCAAAAATGTTTTTTTGAAAA
* * * * *
563511 TTTTATTTTTGAGAAAAATTGATACTTTCAACTTTCCCTTAAAAATATTTTTTT---AT
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTGAAAA
* *
563567 TTTTATTTTTAAGAAAAATTGATACTTTTAACTTTTTCTCAAAAATGTTTTTTTTTTTTGAAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATG-----TTTTTTTGAAAA
* * * * * *** *
563631 TTTTTTATTTTCAA-AGGAAATTGATACTTTCAACTTTCCCTCAGAAATATTTTTTTTTTAT
1 --TTTTATTTTTAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTGAAAA
* * * * * * *
563692 TTTTA-TGTTCAGAGGAAATTGATACATTCAAC-TTTCCTTCAAAAAATTTTTTTTTTCAAAT
1 TTTTATTTTTAAGA-AAAATTGATACTTTCAACTTTTCC-TC-AAAAA-TGTTTTTTTGAAAA
*
563753 TTTTATTTTAAAGA
1 TTTTATTTTTAAGA
563767 GATCATTGAA
Statistics
Matches: 384, Mismatches: 63, Indels: 64
0.75 0.12 0.13
Matches are distributed among these distances:
50 22 0.06
51 15 0.04
52 1 0.00
54 5 0.01
56 49 0.13
57 48 0.12
58 62 0.16
59 74 0.19
60 33 0.09
61 30 0.08
62 5 0.01
64 1 0.00
65 1 0.00
66 38 0.10
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (59 bp):
TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGTTTTTTTGAAAA
Found at i:563419 original size:57 final size:56
Alignment explanation
Indices: 563175--563618 Score: 350
Period size: 58 Copynumber: 7.8 Consensus size: 56
563165 CATGCTTTTA
* * ****
563175 TTCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAGTAT-TTTAAAGTTTTTTTTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAA-AATGTTT----TTGAAATTTTATT
* * *
563235 TTCGAGAAAATTTGATAC-TT-AACTTTTCCTTAAAATTGTTTTTCTTGAGAATTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATG--TTT-TTGA-AATTTTATT
* * * * * *
563293 TTCAAGGAAATTTGGTACTTCCAAC-ATTCCTCAAAAATGTTTTTTTGAAAATTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATG--TTTTTG-AAATTTTATT
* * *
563351 TTTACGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTGACATCTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTGAAAT-TTTATT
* * *
563408 TTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATGCTTTTTTGAAAGTTTTTGTT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATG--TTTTTGAAA--TTTTATT
* * *
563468 TTCAAGAAAAATTGATACTTTCAAC-TTTCCTTCAACA-CTTTTT----TTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTGAAATTTTATT
** * * ** *
563518 TTTGAGAAAAATTGATACTTTCAACTTTCCCTTAAAAATATTTTTTTATTTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTGAAATTTTATT
* * * *
563574 TTTAAGAAAAATTGATACTTTTAACTTTTTCTCAAAAATGTTTTT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTT
563619 TTTTTTTGAA
Statistics
Matches: 315, Mismatches: 50, Indels: 42
0.77 0.12 0.10
Matches are distributed among these distances:
50 29 0.09
51 9 0.03
52 5 0.02
56 54 0.17
57 51 0.16
58 66 0.21
59 48 0.15
60 52 0.17
61 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (56 bp):
TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATGTTTTTGAAATTTTATT
Found at i:563514 original size:50 final size:54
Alignment explanation
Indices: 563344--563601 Score: 222
Period size: 57 Copynumber: 4.6 Consensus size: 54
563334 TTTTTGAAAA
* * *
563344 TTTTATTTTTACGAAAAATTGATACTTTCAACTTTTCCTTAAAA-ATGTTTTTGACAT
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTCCCTTAAAACAT-CTTTT---AT
* * ** *
563401 CTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAA-ATGCTTTTTTGAAAGT
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTCCCTTAAAACAT-C--TTTT---A-T
* * *
563461 TTTTGTTTTCAAGAAAAATTGATACTTTCAACTTT-CCTT-CAACA-CTTTT-T
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTCCCTTAAAACATCTTTTAT
* * *
563511 TTTTATTTTTGAGAAAAATTGATACTTTCAACTTTCCCTTAAAAATATTTTTTTAT
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTCCCTT-AAAACA-TCTTTTAT
*
563567 TTTTATTTTTAAGAAAAATTGATACTTTTAACTTT
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTT
563602 TTCTCAAAAA
Statistics
Matches: 171, Mismatches: 20, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
50 33 0.19
51 4 0.02
53 3 0.02
55 8 0.05
56 34 0.20
57 43 0.25
58 2 0.01
59 10 0.06
60 34 0.20
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (54 bp):
TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTCCCTTAAAACATCTTTTAT
Found at i:563742 original size:122 final size:117
Alignment explanation
Indices: 563526--563765 Score: 279
Period size: 125 Copynumber: 2.0 Consensus size: 117
563516 TTTTTGAGAA
* * *
563526 AAATTGATACTTTCAACTTTCCCTTAAAAATATTTTTTTATTTTTATTTTTAAGAAAAATTGATA
1 AAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTTATTTTTATGTTCAAGAAAAATTGATA
* * * *
563591 CTTTTAACTTTTTCTCAAAAATGTTTTTTTTTTTTGAAAATTTTTTATTTTCAAAGG
66 CATTCAACTTTCTCTCAAAAA--TATTTTTTTTTT-AAAA-TTTTTATTTT-AAAGG
* *
563648 AAATTGATACTTTCAACTTTCCCTCAGAAATATTTTTTTTTTATTTTTATGTTC-AGAGGAAATT
1 AAATTGATACTTTCAACTTTCCCTCA-AAA-A-TATTTTTTTATTTTTATGTTCAAGA-AAAATT
*
563712 GATACATTCAACTTTC-CTTCAAAAA-ATTTTTTTTTTCAAATTTTTATTTTAAAG
62 GATACATTCAACTTTCTC-TCAAAAATATTTTTTTTTTAAAATTTTTATTTTAAAG
563766 AGATCATTGA
Statistics
Matches: 103, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
119 4 0.04
120 10 0.10
121 3 0.03
122 35 0.34
123 3 0.03
124 5 0.05
125 43 0.42
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (117 bp):
AAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTTATTTTTATGTTCAAGAAAAATTGATA
CATTCAACTTTCTCTCAAAAATATTTTTTTTTTAAAATTTTTATTTTAAAGG
Found at i:563806 original size:23 final size:22
Alignment explanation
Indices: 563780--563828 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
563770 CATTGAAAAT
563780 TAAAGAATGTTTAATTAAATAAA
1 TAAAGAAT-TTTAATTAAATAAA
** * *
563803 TAAATTATTTTAATTTAATCAA
1 TAAAGAATTTTAATTAAATAAA
563825 TAAA
1 TAAA
563829 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
TAAAGAATTTTAATTAAATAAA
Found at i:571107 original size:41 final size:41
Alignment explanation
Indices: 571055--571258 Score: 257
Period size: 41 Copynumber: 5.0 Consensus size: 41
571045 ATGATTGTTG
*
571055 AGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTTTGTTTAA
1 AGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAA
** * *
571096 AAAAGCTTTTTA-TTTTCAAAGTTGTTGTGCCTCTGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAA
* * * *
571136 AGGAGCCTTTTATTTTCCAATGTTGTTGTGCCTCAGTTTAG
1 AGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAA
* * *
571177 ATGAGCCTTTTATTTTTTAAAGTTGTTATGCCTCTGTTTAA
1 AGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAA
* * *
571218 AGGAGCCTTTTATTTTTCAAAAATCGTTGAGCCTCTGTTTA
1 AGGAGCCTTTTATTTTTC-AAAGTTGTTGTGCCTCTGTTTA
571259 GAGAAGCTTT
Statistics
Matches: 137, Mismatches: 24, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
40 35 0.26
41 84 0.61
42 18 0.13
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (41 bp):
AGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAA
Found at i:571189 original size:81 final size:82
Alignment explanation
Indices: 571054--571238 Score: 255
Period size: 81 Copynumber: 2.3 Consensus size: 82
571044 CATGATTGTT
* ** *
571054 GAGGAGCCTTTTATTTTTCAAAGTTGTTGTGCCTTTGTTTAAAAAAGCTTTTTA-TTTTCAAAGT
1 GAGGAGCCTTTTATTTTCCAAAGTTGTTGTGCCTCAGTTTAAAAAAGCCTTTTATTTTTCAAAGT
*
571118 TGTTGTGCCTCTGTTTA
66 TGTTATGCCTCTGTTTA
* * ** *
571135 GAGGAGCCTTTTATTTTCCAATGTTGTTGTGCCTCAGTTTAGATGAGCCTTTTATTTTTTAAAGT
1 GAGGAGCCTTTTATTTTCCAAAGTTGTTGTGCCTCAGTTTAAAAAAGCCTTTTATTTTTCAAAGT
571200 TGTTATGCCTCTGTTTA
66 TGTTATGCCTCTGTTTA
* *
571217 AAGGAGCCTTTTATTTTTCAAA
1 GAGGAGCCTTTTATTTTCCAAA
571239 AATCGTTGAG
Statistics
Matches: 90, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
81 46 0.51
82 44 0.49
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (82 bp):
GAGGAGCCTTTTATTTTCCAAAGTTGTTGTGCCTCAGTTTAAAAAAGCCTTTTATTTTTCAAAGT
TGTTATGCCTCTGTTTA
Found at i:572758 original size:57 final size:57
Alignment explanation
Indices: 572677--572859 Score: 198
Period size: 57 Copynumber: 3.3 Consensus size: 57
572667 TATTATTTTC
* *
572677 TTTCCAAAAAAAAA-AAGA-ATTTCTAAATAAGCCCAAATGGTGAAAAATTTAGAAA
1 TTTCAAAAAAAAAATAAAATATTTCTAAATAAGCCCAAATGGTGAAAAATTTAGAAA
* *
572732 TTTCAAAAAAAAAATAAAATATTTCTAAAT-TGACCCAAATAGTGAAAAATTTAGAAA
1 TTTCAAAAAAAAAATAAAATATTTCTAAATAAG-CCCAAATGGTGAAAAATTTAGAAA
* * * * * *
572789 -TCCAAAAAAAAGAGAGAAT-TTT-TAAATAGGCCCAAATGGTGAAAAATTTAAAAA
1 TTTCAAAAAAAAAATAAAATATTTCTAAATAAGCCCAAATGGTGAAAAATTTAGAAA
* *
572843 TTTTGAAAAAGAAAATA
1 -TTTCAAAAAAAAAATA
572860 TTTCTAATTT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
54 27 0.25
55 17 0.16
56 29 0.27
57 33 0.31
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (57 bp):
TTTCAAAAAAAAAATAAAATATTTCTAAATAAGCCCAAATGGTGAAAAATTTAGAAA
Found at i:572878 original size:53 final size:54
Alignment explanation
Indices: 572679--572878 Score: 176
Period size: 54 Copynumber: 3.7 Consensus size: 54
572669 TTATTTTCTT
** * *
572679 TCCAAAAAAAA-AAAGA-ATTTCTAAATAAGCCCAAATGGTGAAAAATTTAGAAATT
1 TCCAAAAAAAAGAAA-ATATTTCTAAATTGGCCCAAATAGTGAAAAATTTA-AAA-A
* * * *
572734 TCAAAAAAAAAATAAAATATTTCTAAATTGACCCAAATAGTGAAAAATTTAGAAA
1 TC-CAAAAAAAAGAAAATATTTCTAAATTGGCCCAAATAGTGAAAAATTTAAAAA
* *
572789 TCCAAAAAAAAGAGAGAAT-TTT-TAAATAGGCCCAAATGGTGAAAAATTTAAAAA
1 TCCAAAAAAAAGA-A-AATATTTCTAAATTGGCCCAAATAGTGAAAAATTTAAAAA
**** *
572843 T-TTTGAAAAAGAAAATATTTCTAATTTGGCCCAAAT
1 TCCAAAAAAAAGAAAATATTTCTAAATTGGCCCAAAT
572879 TGTGGAATAA
Statistics
Matches: 119, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
51 3 0.03
52 4 0.03
53 20 0.17
54 38 0.32
55 8 0.07
56 14 0.12
57 32 0.27
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.26
Consensus pattern (54 bp):
TCCAAAAAAAAGAAAATATTTCTAAATTGGCCCAAATAGTGAAAAATTTAAAAA
Found at i:574334 original size:17 final size:15
Alignment explanation
Indices: 574294--574337 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
574284 AAGTAGAGCA
*
574294 TTTTGTATTTTTATT
1 TTTTTTATTTTTATT
574309 TTATTTTATTATTTCATT
1 TT-TTTTATT-TTT-ATT
574327 TTTTTTATTTT
1 TTTTTTATTTT
574338 GGAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 8 0.32
17 10 0.40
18 5 0.20
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTATTTTTATT
Found at i:579227 original size:52 final size:50
Alignment explanation
Indices: 579171--579279 Score: 119
Period size: 50 Copynumber: 2.1 Consensus size: 50
579161 AATTATTCCG
* *
579171 CCATTTGTGCCAAATTAGAAATATCTTCTCTTTTGAATTTTTAAATTCTCCA
1 CCATTTGAGCCAAATTAGAAAT-TCTT-TCTTTTGAATTTCTAAATTCTCCA
* * * * ** *
579223 CCATTTGAGCCTATTTCGAAATTCTTTTTTTTTTATTTCTAAATTCTCCT
1 CCATTTGAGCCAAATTAGAAATTCTTTCTTTTGAATTTCTAAATTCTCCA
579273 CCATTTG
1 CCATTTG
579280 GGATAATTTA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
50 26 0.54
51 4 0.08
52 18 0.38
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (50 bp):
CCATTTGAGCCAAATTAGAAATTCTTTCTTTTGAATTTCTAAATTCTCCA
Found at i:579498 original size:16 final size:16
Alignment explanation
Indices: 579479--579525 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
579469 TACTAAAGTT
579479 TTTTTTATTTTTTATA
1 TTTTTTATTTTTTATA
* *
579495 TTTTTTCTCTTTTATA
1 TTTTTTATTTTTTATA
579511 TTTTATTATTATTTT
1 TTTT-TTATT-TTTT
579526 TTTGAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 18 0.72
17 3 0.12
18 4 0.16
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTATTTTTTATA
Found at i:579794 original size:23 final size:23
Alignment explanation
Indices: 579750--579794 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
579740 CAAATACTTA
*
579750 AAATAAATAAATAACAAATAAAC
1 AAATAAATAAATAAAAAATAAAC
*
579773 AAATAGATAAA-AAAAAACTAAA
1 AAATAAATAAATAAAAAA-TAAA
579795 AACTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.16
Consensus pattern (23 bp):
AAATAAATAAATAAAAAATAAAC
Found at i:580432 original size:15 final size:14
Alignment explanation
Indices: 580405--580434 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
580395 CTTTTCTGCT
580405 TTTCTATATCTATA
1 TTTCTATATCTATA
580419 TTTCTATGATCTATA
1 TTTCTAT-ATCTATA
580434 T
1 T
580435 GTTTTCTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.27, C:0.13, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTCTATATCTATA
Found at i:580693 original size:18 final size:19
Alignment explanation
Indices: 580650--580694 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
580640 GCAGAAACCT
580650 AAAGATAAATCAACCAAAA
1 AAAGATAAATCAACCAAAA
* *
580669 TAA-ATAAAT-AATCAAAA
1 AAAGATAAATCAACCAAAA
580686 AAAGATAAA
1 AAAGATAAA
580695 GCCCAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 9 0.41
18 11 0.50
19 2 0.09
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (19 bp):
AAAGATAAATCAACCAAAA
Found at i:581094 original size:84 final size:81
Alignment explanation
Indices: 580991--581240 Score: 227
Period size: 89 Copynumber: 3.0 Consensus size: 81
580981 AAATTTTAGA
* * * **
580991 AAATAAATAAAGCTCTTCTAAATAGAGGCTTAATGACTTTTGAAAAATAAATAATAAGGCTCCTC
1 AAATAAATAAAGCTCTTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAAT-A-AA-GCTCCTC
* *
581056 TAATTAGAGGCTCAACGAT
63 TAAATAGAGACTCAACGAT
* *
581075 AAATAAAT-AAGACTTTTCTAAACAAATGCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTA
1 AAATAAATAAAG-CTCTTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTA
581139 AATAGAGACTCAACGACTTTT
65 AATAGAGACTCAACGA----T
* * * *
581160 GAAAAAATAAATAAGGCTCATGC-AACCAGAA-GCTCAACTACTTTTGAAAAATAAATAAAGCTC
1 ----AAATAAATAAAGCTC-TTCTAAACA-AAGGCTCAACAACTTTTGAAAAATAAATAAAGCTC
*
581223 CTCTAAACAGAGACTCAA
60 CTCTAAATAGAGACTCAA
581241 TGACTTTTGA
Statistics
Matches: 139, Mismatches: 15, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
81 23 0.17
82 2 0.01
83 4 0.03
84 41 0.29
85 1 0.01
89 62 0.45
90 6 0.04
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.26
Consensus pattern (81 bp):
AAATAAATAAAGCTCTTCTAAACAAAGGCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAA
ATAGAGACTCAACGAT
Found at i:581124 original size:44 final size:45
Alignment explanation
Indices: 581075--581266 Score: 202
Period size: 44 Copynumber: 4.4 Consensus size: 45
581065 GCTCAACGAT
** *
581075 AAATAAATAAGA-CTTTTCTAAACAAATG-CTCAACAACTTTTGAA
1 AAATAAATAAGAGCTCCTCTAAACAAA-GACTCAACGACTTTTGAA
* *
581119 AAATAAATAA-AGCTCCTCTAAATAGAGACTCAACGACTTTTGAAA
1 AAATAAATAAGAGCTCCTCTAAACAAAGACTCAACGACTTTTG-AA
* * *
581164 AAATAAATAAG-GCTCATGC-AACCAGAAG-CTCAACTACTTTTGAA
1 AAATAAATAAGAGCTCCT-CTAAACA-AAGACTCAACGACTTTTGAA
* *
581208 AAATAAATAA-AGCTCCTCTAAACAGAGACTCAATGACTTTTGAA
1 AAATAAATAAGAGCTCCTCTAAACAAAGACTCAACGACTTTTGAA
581252 AAATAAATAAG-GCTC
1 AAATAAATAAGAGCTC
581267 TTTCATGACT
Statistics
Matches: 123, Mismatches: 15, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
43 5 0.04
44 82 0.67
45 33 0.27
46 3 0.02
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.25
Consensus pattern (45 bp):
AAATAAATAAGAGCTCCTCTAAACAAAGACTCAACGACTTTTGAA
Found at i:581196 original size:45 final size:44
Alignment explanation
Indices: 581103--581266 Score: 215
Period size: 44 Copynumber: 3.7 Consensus size: 44
581093 TAAACAAATG
* *
581103 CTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAAATAGAGA
1 CTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGA
* * *
581147 CTCAACGACTTTTGAAAAAATAAATAAGGCTCATGC-AACCAGA-A
1 CTCAACGACTTTTG-AAAAATAAATAAAGCTCCT-CTAAACAGAGA
*
581191 GCTCAACTACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGA
1 -CTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGA
* *
581236 CTCAATGACTTTTGAAAAATAAATAAGGCTC
1 CTCAACGACTTTTGAAAAATAAATAAAGCTC
581267 TTTCATGACT
Statistics
Matches: 103, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.01
44 65 0.63
45 36 0.35
46 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (44 bp):
CTCAACGACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGA
Found at i:581203 original size:89 final size:88
Alignment explanation
Indices: 581102--581266 Score: 294
Period size: 89 Copynumber: 1.9 Consensus size: 88
581092 CTAAACAAAT
*
581102 GCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAAATAGAGACTCAACGACTTTTGAAAAAA
1 GCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAAA
581167 TAAATAAGGCTCATGCAACCAGAA
65 TAAATAAGGCTCATGCAACCAGAA
* *
581191 GCTCAACTACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAATGACTTTTGAAAAAT
1 GCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACGACTTTTGAAAAAT
581256 AAATAAGGCTC
66 AAATAAGGCTC
581267 TTTCATGACT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 17 0.23
89 56 0.77
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (88 bp):
GCTCAACAACTTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGACTCAACGACTTTTGAAAAAT
AAATAAGGCTCATGCAACCAGAA
Found at i:581650 original size:23 final size:23
Alignment explanation
Indices: 581615--581661 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
581605 AATACAATCT
* *
581615 AAATTCAAAGGTTCTCATTCAAA
1 AAATTCAAAGGTTCGCATCCAAA
* *
581638 AAATTTAAGGGTTCGCATCCAAA
1 AAATTCAAAGGTTCGCATCCAAA
581661 A
1 A
581662 TTTTAAAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (23 bp):
AAATTCAAAGGTTCGCATCCAAA
Found at i:581835 original size:14 final size:14
Alignment explanation
Indices: 581781--581839 Score: 65
Period size: 14 Copynumber: 4.6 Consensus size: 14
581771 ACTCAAAGAC
*
581781 AAAGATTCTTATTC
1 AAAGATTCTTATTT
581795 AAAGATTCTTATTT
1 AAAGATTCTTATTT
581809 AAA-A--CTT-TTT
1 AAAGATTCTTATTT
*
581819 AAAGATTCTCATTT
1 AAAGATTCTTATTT
581833 AAA-ATTC
1 AAAGATTC
581840 AAATATTCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 6 0.15
11 4 0.10
13 7 0.18
14 22 0.56
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (14 bp):
AAAGATTCTTATTT
Found at i:583042 original size:14 final size:13
Alignment explanation
Indices: 583018--583124 Score: 101
Period size: 14 Copynumber: 8.0 Consensus size: 13
583008 TGAGTTCTCC
*
583018 TTTTGCATTTTTT
1 TTTTTCATTTTTT
583031 TTCTTTCATTTTTT
1 TT-TTTCATTTTTT
*
583045 ATTTTTCATTTTAT
1 -TTTTTCATTTTTT
* *
583059 TTTTTC-TTTCTC
1 TTTTTCATTTTTT
583071 TTTTTC-TTTTTCT
1 TTTTTCATTTTT-T
*
583084 TTTCTCATTTTTCT
1 TTTTTCATTTTT-T
*
583098 TTTTTCATTTCTCT
1 TTTTTCATTT-TTT
583112 TTTTTCATTTTTT
1 TTTTTCATTTTTT
583125 CTCTATTTTT
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
12 13 0.17
13 15 0.19
14 47 0.60
15 3 0.04
ACGTcount: A:0.07, C:0.15, G:0.01, T:0.77
Consensus pattern (13 bp):
TTTTTCATTTTTT
Found at i:583049 original size:19 final size:19
Alignment explanation
Indices: 583027--583142 Score: 54
Period size: 19 Copynumber: 6.3 Consensus size: 19
583017 CTTTTGCATT
583027 TTTTTTCTTTCATTTTTTA
1 TTTTTTCTTTCATTTTTTA
583046 ----TT-TTTCA--TTTTA
1 TTTTTTCTTTCATTTTTTA
*
583058 TTTTTTCTTTC-TCTTTTTC
1 TTTTTTCTTTCAT-TTTTTA
* *
583077 TTTTTCTTTTCTCA-TTTTTC
1 TTTTT-TCTT-TCATTTTTTA
*
583097 TTTTTTCATTTCTCTTTTTTCA
1 TTTTTTC-TTTC-ATTTTTT-A
*
583119 TTTTTTCTCT-ATTTTTTA
1 TTTTTTCTTTCATTTTTTA
583137 TATTTT
1 T-TTTT
583143 AATTTTCTTT
Statistics
Matches: 74, Mismatches: 7, Indels: 32
0.65 0.06 0.28
Matches are distributed among these distances:
12 5 0.07
14 5 0.07
15 2 0.03
16 2 0.03
17 4 0.05
18 2 0.03
19 22 0.30
20 16 0.22
21 9 0.12
22 7 0.09
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTCTTTCATTTTTTA
Found at i:583072 original size:6 final size:7
Alignment explanation
Indices: 583034--583123 Score: 75
Period size: 7 Copynumber: 13.4 Consensus size: 7
583024 ATTTTTTTTC
583034 TTTCATT
1 TTTCATT
*
583041 TTTTATT
1 TTTCATT
583048 TTTCA-T
1 TTTCATT
583054 TTT-ATTT
1 TTTCA-TT
583061 TTTC-TT
1 TTTCATT
*
583067 TCTC-TT
1 TTTCATT
583073 TTTC-TT
1 TTTCATT
583079 TTTC-TT
1 TTTCATT
583085 TTCTCATT
1 TT-TCATT
*
583093 TTTCTTT
1 TTTCATT
583100 TTTCATT
1 TTTCATT
* *
583107 TCTCTTT
1 TTTCATT
583114 TTTCATT
1 TTTCATT
583121 TTT
1 TTT
583124 TCTCTATTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
5 1 0.01
6 24 0.35
7 39 0.57
8 4 0.06
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCATT
Found at i:583135 original size:40 final size:40
Alignment explanation
Indices: 583053--583167 Score: 121
Period size: 39 Copynumber: 2.9 Consensus size: 40
583043 TTATTTTTCA
* *
583053 TTTTATTTTTTC-TTTCTC-TTTTTCTTTTTCTTTTCTCAT
1 TTTTATTTTTTCATTTCTCTTTTTTCATTTT-TTCTCTCAT
*
583092 TTTTCTTTTTTCATTTCTCTTTTTTCATTTTTTCTCT-ATT
1 TTTTATTTTTTCATTTCTCTTTTTTCATTTTTTCTCTCA-T
* * **
583132 TTTTATATTTTAATTT-TCTTTTCCCATTTTTTCTCT
1 TTTTATTTTTTCATTTCTCTTTTTTCATTTTTTCTCT
583168 TACACATTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 30 0.46
40 25 0.38
41 10 0.15
ACGTcount: A:0.09, C:0.17, G:0.00, T:0.74
Consensus pattern (40 bp):
TTTTATTTTTTCATTTCTCTTTTTTCATTTTTTCTCTCAT
Found at i:583536 original size:10 final size:9
Alignment explanation
Indices: 583509--583574 Score: 62
Period size: 9 Copynumber: 7.2 Consensus size: 9
583499 GTGGCAATCA
583509 TTTTTCTTT
1 TTTTTCTTT
*
583518 TCTTTCTTT
1 TTTTTCTTT
583527 TTTTTGCTTT
1 TTTTT-CTTT
* *
583537 GTTTTGTTT
1 TTTTTCTTT
*
583546 TTTTT-TTC
1 TTTTTCTTT
*
583554 TTTTTGTTT
1 TTTTTCTTT
583563 TTTTCTCTTT
1 TTTT-TCTTT
583573 TT
1 TT
583575 ATCTTTAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
8 7 0.15
9 25 0.54
10 14 0.30
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:583571 original size:16 final size:17
Alignment explanation
Indices: 583509--583574 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 17
583499 GTGGCAATCA
* *
583509 TTTTTCTTTTCTTTCTTT
1 TTTTTCTCTT-TTTGTTT
*
583527 TTTTTGCTTTGTTTTGTTT
1 TTTTT-CTCT-TTTTGTTT
*
583546 TTTTTTTCTTTTTG-TT
1 TTTTTCTCTTTTTGTTT
583562 TTTTTCTCTTTTT
1 TTTTTCTCTTTTT
583575 ATCTTTAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
16 14 0.33
17 5 0.12
18 7 0.17
19 15 0.36
20 1 0.02
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTTCTCTTTTTGTTT
Found at i:583574 original size:17 final size:16
Alignment explanation
Indices: 583509--583574 Score: 60
Period size: 17 Copynumber: 3.8 Consensus size: 16
583499 GTGGCAATCA
*
583509 TTTTTCTTTTCTTTCTTT
1 TTTTTCTTTT-TTT-GTT
583527 TTTTTGCTTTGTTTTGTT
1 TTTTT-CTTT-TTTTGTT
*
583545 TTTTTTTTCTTTTTGTT
1 TTTTTCTT-TTTTTGTT
*
583562 TTTTTCTCTTTTT
1 TTTTTCTTTTTTT
583575 ATCTTTAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 5 0.12
17 15 0.37
18 13 0.32
19 7 0.17
20 1 0.02
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (16 bp):
TTTTTCTTTTTTTGTT
Found at i:587857 original size:23 final size:23
Alignment explanation
Indices: 587831--587874 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
587821 CGTTCTCAAA
*
587831 TTTCTCTTTCCT-TCTCTTTCTTC
1 TTTC-CTTTCCTCTCCCTTTCTTC
587854 TTTCCTTTCCTCTCCCTTTCT
1 TTTCCTTTCCTCTCCCTTTCT
587875 CTAGAGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTCCTTTCCTCTCCCTTTCTTC
Found at i:598070 original size:2 final size:2
Alignment explanation
Indices: 598063--598089 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
598053 TTAGTGTTTG
598063 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
598090 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:600812 original size:29 final size:29
Alignment explanation
Indices: 600771--600830 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
600761 AATTAAATAA
*
600771 AAATGTGACAAAATA-TTGAACAA-AAATT
1 AAATGTGACAAAA-ACTTGAAAAATAAATT
*
600799 AAATGTTGATAAAAACTTGAAAAATAAATT
1 AAATG-TGACAAAAACTTGAAAAATAAATT
600829 AA
1 AA
600831 GAATTTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 6 0.22
29 14 0.52
30 7 0.26
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (29 bp):
AAATGTGACAAAAACTTGAAAAATAAATT
Found at i:602635 original size:24 final size:20
Alignment explanation
Indices: 602592--602639 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 20
602582 TGATGATAAA
602592 ATTATAATATCATCAATTTC
1 ATTATAATATCATCAATTTC
602612 ATTATAAGTATCATATCAAATTTC
1 ATTATAA-TATC--ATC-AATTTC
602636 ATTA
1 ATTA
602640 ATCGATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.29
21 4 0.17
23 3 0.12
24 10 0.42
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTATAATATCATCAATTTC
Found at i:605661 original size:52 final size:52
Alignment explanation
Indices: 605520--605676 Score: 154
Period size: 52 Copynumber: 3.0 Consensus size: 52
605510 TGGACAAAAA
* * * *
605520 GACTTGCAAAAGAATAATTCTAAGAT-AAAGAGGATTCTTAACAGGTAAGTCT
1 GACTTACAAAAGAAAAATTCTAAGATGAAAGA-GATTCTTAATAGGTAAGTTT
* * * * *
605572 GACTTGCAAGAGAAAAATTTTAAAAGGAAAGAGATTCTTAATAGGTAAGTTT
1 GACTTACAAAAGAAAAATTCTAAGATGAAAGAGATTCTTAATAGGTAAGTTT
* * * * * **
605624 GGCTTATAAAAGAAGAATTCTAAGATGAGAGATATTCTTAATAGACAAGTTT
1 GACTTACAAAAGAAAAATTCTAAGATGAAAGAGATTCTTAATAGGTAAGTTT
605676 G
1 G
605677 TATGATTATA
Statistics
Matches: 85, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
52 80 0.94
53 5 0.06
ACGTcount: A:0.43, C:0.08, G:0.20, T:0.29
Consensus pattern (52 bp):
GACTTACAAAAGAAAAATTCTAAGATGAAAGAGATTCTTAATAGGTAAGTTT
Found at i:606243 original size:31 final size:31
Alignment explanation
Indices: 606159--606243 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
606149 AGGCTTTTAG
* *
606159 CCCAATAAATGGTATCAAAGCTGTGGTGTTC
1 CCCAACAAATGGTATCAAAGTTGTGGTGTTC
* * *
606190 CTCGACAAATGGTATCAGAGTTGTGGTGTTC
1 CCCAACAAATGGTATCAAAGTTGTGGTGTTC
*
606221 CCCAACAAGTGGTATCAAAGTTG
1 CCCAACAAATGGTATCAAAGTTG
606244 AAGGTTCGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (31 bp):
CCCAACAAATGGTATCAAAGTTGTGGTGTTC
Found at i:606284 original size:25 final size:25
Alignment explanation
Indices: 606256--606338 Score: 96
Period size: 25 Copynumber: 3.3 Consensus size: 25
606246 GGTTCGAAAC
* *
606256 GTGAGAAGAGTTAAAGATTCAAGAT
1 GTGAGAAGAGCTAAAGATTTAAGAT
* *
606281 GTGAGAAGAGCTAAAAATTTGAGAT
1 GTGAGAAGAGCTAAAGATTTAAGAT
*
606306 GTG-GAAAGAGCTAAAGGTTTAAGAT
1 GTGAG-AAGAGCTAAAGATTTAAGAT
*
606331 GTGGGAAG
1 GTGAGAAG
606339 TGCTTGGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.33, T:0.23
Consensus pattern (25 bp):
GTGAGAAGAGCTAAAGATTTAAGAT
Found at i:606631 original size:24 final size:20
Alignment explanation
Indices: 606573--606632 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
606563 TTGACTCAAA
606573 TCCCATAAGAGATTTGTTTG
1 TCCCATAAGAGATTTGTTTG
606593 TCCCATAAGAGATTTGTTTG
1 TCCCATAAGAGATTTGTTTG
* *
606613 TCCCGTAAGAGATTTATTTG
1 TCCCATAAGAGATTTGTTTG
606633 AAATTTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (20 bp):
TCCCATAAGAGATTTGTTTG
Found at i:606753 original size:52 final size:52
Alignment explanation
Indices: 606666--606768 Score: 156
Period size: 52 Copynumber: 2.0 Consensus size: 52
606656 GGACAAGAAG
* *
606666 ACTTGCAAAAGAATAATTCTAAGAGAAAGAGGATTCTTAATAGGTAAGTTTA
1 ACTTGCAAAAGAATAATTCTAAAAGAAAGAGGATTCTTAATAGGGAAGTTTA
606718 ACTTG-AAATAGAATAATTCTAAAAGGAAAGA-GATTCTTAATAGGGAAGTTT
1 ACTTGCAAA-AGAATAATTCTAAAA-GAAAGAGGATTCTTAATAGGGAAGTTT
606769 GAGAGATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
51 3 0.06
52 38 0.81
53 6 0.13
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (52 bp):
ACTTGCAAAAGAATAATTCTAAAAGAAAGAGGATTCTTAATAGGGAAGTTTA
Found at i:606793 original size:24 final size:24
Alignment explanation
Indices: 606746--606793 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
606736 CTAAAAGGAA
*
606746 AGAGATTCTTAATAGGGAAGTTTG
1 AGAGATTCTTAATAGGGAAATTTG
*
606770 AGAGATTTTTAAT-GGGCAAATTTG
1 AGAGATTCTTAATAGGG-AAATTTG
606794 TATAGTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (24 bp):
AGAGATTCTTAATAGGGAAATTTG
Found at i:607365 original size:25 final size:25
Alignment explanation
Indices: 607337--607409 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
607327 GAGCTGAAGG
*
607337 TTCAAAACGTGAGAAGAGTTAAAAA
1 TTCAAAACGTGAGAAGAGCTAAAAA
* * *
607362 TTCAATATGTGAGAAGAGCTGAAAA
1 TTCAAAACGTGAGAAGAGCTAAAAA
* * * *
607387 TTTAAGATGTGGGAAGAGCTAAA
1 TTCAAAACGTGAGAAGAGCTAAA
607410 GGTTTAAGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 40 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (25 bp):
TTCAAAACGTGAGAAGAGCTAAAAA
Found at i:607415 original size:25 final size:25
Alignment explanation
Indices: 607345--607423 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
607335 GGTTCAAAAC
* * * *
607345 GTGAGAAGAGTTAAAAATTCAATAT
1 GTGAGAAGAGCTGAAAATTTAAGAT
607370 GTGAGAAGAGCTGAAAATTTAAGAT
1 GTGAGAAGAGCTGAAAATTTAAGAT
* *
607395 GTGGGAAGAGCT-AAAGGTTTAAGAT
1 GTGAGAAGAGCTGAAA-ATTTAAGAT
607420 GTGA
1 GTGA
607424 TAAATGCATA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
24 3 0.07
25 43 0.93
ACGTcount: A:0.42, C:0.04, G:0.29, T:0.25
Consensus pattern (25 bp):
GTGAGAAGAGCTGAAAATTTAAGAT
Found at i:610629 original size:5 final size:6
Alignment explanation
Indices: 610557--610637 Score: 56
Period size: 6 Copynumber: 12.2 Consensus size: 6
610547 TATATCATAG
* *
610557 ATTTTT ATTTTTT ATTTTGA ATTTATT -TTTTT ATTTTTT CCCTTTTT
1 ATTTTT A-TTTTT ATTTT-T ATTT-TT ATTTTT A-TTTTT --ATTTTT
610604 ATATTTAAT ATTTTT ATTTTT ATTTTT ATTTTT A
1 AT-TTT--T ATTTTT ATTTTT ATTTTT ATTTTT A
610638 GAGCTAATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
5 2 0.03
6 29 0.48
7 18 0.30
8 9 0.15
9 3 0.05
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:610888 original size:30 final size:29
Alignment explanation
Indices: 610832--610888 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
610822 CCATAACAAA
*
610832 TAAAAAAAGAAAAAGAGAAGAGAAAAACT
1 TAAAAAAAGAAAAAGAGAAGACAAAAACT
610861 TAAAAAAAGAGAAAAGA-AACGACAAAAA
1 TAAAAAAAGA-AAAAGAGAA-GACAAAAA
610889 ACACAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.74, C:0.05, G:0.16, T:0.05
Consensus pattern (29 bp):
TAAAAAAAGAAAAAGAGAAGACAAAAACT
Found at i:610897 original size:31 final size:29
Alignment explanation
Indices: 610833--610898 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
610823 CATAACAAAT
* **
610833 AAAAAAAGAAAAAGAGAAGAGAAAAACTT
1 AAAAAAAGAAAAAGAGAAGAAAAAAACAC
610862 AAAAAAAGAGAAAAGA-AACGACAAAAAACAC
1 AAAAAAAGA-AAAAGAGAA-GA-AAAAAACAC
610893 AAAAAA
1 AAAAAA
610899 TAAAAAGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 11 0.35
30 8 0.26
31 12 0.39
ACGTcount: A:0.76, C:0.08, G:0.14, T:0.03
Consensus pattern (29 bp):
AAAAAAAGAAAAAGAGAAGAAAAAAACAC
Found at i:611200 original size:19 final size:18
Alignment explanation
Indices: 611178--611222 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
611168 GAAAAATTGT
611178 AAAAAAAGCAAAA-AAACA
1 AAAAAAAGCAAAAGAAA-A
611196 AAAAAAAGCAAAAGAAAA
1 AAAAAAAGCAAAAGAAAA
611214 AGAAAAAAG
1 A-AAAAAAG
611223 AATTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAGCAAAAGAAAA
Found at i:611690 original size:19 final size:20
Alignment explanation
Indices: 611657--611711 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
611647 AAATATTTTT
611657 TAAAAAAATAATAAAAGATA
1 TAAAAAAATAATAAAAGATA
* **
611677 TAAAAAAAT-TTAAACTATA
1 TAAAAAAATAATAAAAGATA
611696 TAAAATAAATAA-AAAA
1 TAAAA-AAATAATAAAA
611712 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAAAAATAATAAAAGATA
Found at i:612332 original size:17 final size:18
Alignment explanation
Indices: 612303--612338 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
612293 ATATTTTAAG
*
612303 TTATTTGTAAATTTTTGT
1 TTATTTGTAAATTATTGT
612321 TTATTT-TAAATTATTGT
1 TTATTTGTAAATTATTGT
612338 T
1 T
612339 GCTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTATTTGTAAATTATTGT
Found at i:612359 original size:21 final size:21
Alignment explanation
Indices: 612335--612376 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
612325 TTTAAATTAT
*
612335 TGTTGCTTAAATTTATTTTAA
1 TGTTGATTAAATTTATTTTAA
* *
612356 TGTTTATTATATTTATTTTAA
1 TGTTGATTAAATTTATTTTAA
612377 ATATTTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
TGTTGATTAAATTTATTTTAA
Found at i:613477 original size:27 final size:26
Alignment explanation
Indices: 613436--613507 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
613426 AAATTATAAT
613436 AAAATATTTAATATAATATTTAAATTA
1 AAAAT-TTTAATATAATATTTAAATTA
* *
613463 AAAGATTTTAATATAGTATTTGAATTA
1 AAA-ATTTTAATATAATATTTAAATTA
*
613490 TAAATTTATAAT-TAATAT
1 AAAATTT-TAATATAATAT
613508 GATATTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 9 0.23
27 28 0.72
28 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AAAATTTTAATATAATATTTAAATTA
Found at i:613633 original size:29 final size:29
Alignment explanation
Indices: 613564--613649 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 29
613554 ATAAATAATT
*
613564 TTTTAATTATCATATTAATTAATATATTTAAAA
1 TTTTAA-TATCATATTAA--AAT-TTTTTAAAA
*
613597 TTTGAATATCATATTAAAATTTTTTAAAA
1 TTTTAATATCATATTAAAATTTTTTAAAA
*
613626 TTTTAATATTATATTAAATATTTT
1 TTTTAATATCATATTAAA-ATTTT
613650 ATTATAATAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 24 0.50
30 8 0.17
32 11 0.23
33 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTTAATATCATATTAAAATTTTTTAAAA
Found at i:614311 original size:2 final size:2
Alignment explanation
Indices: 614304--614328 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
614294 TTGGGTTTGC
614304 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
614329 GTAGTAGGTA
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:617021 original size:30 final size:29
Alignment explanation
Indices: 616965--617021 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
616955 CCATAATAAA
*
616965 TAAAAAAAGAAAAAGAGAAGAGAAAAACT
1 TAAAAAAAGAAAAAGAGAAGACAAAAACT
616994 TAAAAAAAGAAAAA-AGAAACGACAAAAA
1 TAAAAAAAGAAAAAGAG-AA-GACAAAAA
617022 ACACAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.05
Consensus pattern (29 bp):
TAAAAAAAGAAAAAGAGAAGACAAAAACT
Found at i:617223 original size:3 final size:3
Alignment explanation
Indices: 617217--617245 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
617207 AAAATATTTT
617217 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
617246 TCAAATGGGC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:617337 original size:19 final size:20
Alignment explanation
Indices: 617301--617359 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
617291 TATTAAATAA
617301 AAAAGAAAAATTGTAAAAAAAAC
1 AAAAGAAAAA--G-AAAAAAAAC
*
617324 AAAA-AAACAA-AAAAAAAGC
1 AAAAGAAA-AAGAAAAAAAAC
617343 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
617360 GAATTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
19 14 0.44
20 9 0.28
22 3 0.09
23 6 0.19
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAGAAAAAAAAC
Found at i:617360 original size:19 final size:19
Alignment explanation
Indices: 617315--617360 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
617305 GAAAAATTGT
617315 AAAAAAAA-CAAAAAAACA
1 AAAAAAAAGCAAAAAAACA
617333 AAAAAAAAGCAAAAGAAA-A
1 AAAAAAAAGCAAAA-AAACA
*
617352 AGAAAAAAG
1 AAAAAAAAG
617361 AATTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 14 0.56
20 3 0.12
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGCAAAAAAACA
Found at i:618480 original size:17 final size:18
Alignment explanation
Indices: 618451--618486 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
618441 ATATTTTAAG
*
618451 TTATTTGTAAATTTTTGT
1 TTATTTGTAAATTATTGT
618469 TTATTT-TAAATTATTGT
1 TTATTTGTAAATTATTGT
618486 T
1 T
618487 GCTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTATTTGTAAATTATTGT
Found at i:618507 original size:21 final size:21
Alignment explanation
Indices: 618483--618524 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
618473 TTTAAATTAT
*
618483 TGTTGCTTAAATTTATTTTAA
1 TGTTGATTAAATTTATTTTAA
* *
618504 TGTTTATTATATTTATTTTAA
1 TGTTGATTAAATTTATTTTAA
618525 ATATTTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
TGTTGATTAAATTTATTTTAA
Found at i:619622 original size:27 final size:26
Alignment explanation
Indices: 619581--619652 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
619571 AAATTATAAT
619581 AAAATATTTAATATAATATTTAAATTA
1 AAAAT-TTTAATATAATATTTAAATTA
* *
619608 AAAGATTTTAATATAGTATTTGAATTA
1 AAA-ATTTTAATATAATATTTAAATTA
*
619635 TAAATTTATAAT-TAATAT
1 AAAATTT-TAATATAATAT
619653 GATATTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 9 0.23
27 28 0.72
28 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
AAAATTTTAATATAATATTTAAATTA
Found at i:619778 original size:29 final size:29
Alignment explanation
Indices: 619709--619794 Score: 100
Period size: 29 Copynumber: 2.8 Consensus size: 29
619699 ATAAATAATT
*
619709 TTTTAATTATCATATTAATTAATATATTTAAAA
1 TTTTAA-TATCATATTAA--AAT-TTTTTAAAA
*
619742 TTTGAATATCATATTAAAATTTTTTAAAA
1 TTTTAATATCATATTAAAATTTTTTAAAA
*
619771 TTTTAATATTATATTAAATATTTT
1 TTTTAATATCATATTAAA-ATTTT
619795 ATTATAATAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 24 0.50
30 8 0.17
32 11 0.23
33 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTTAATATCATATTAAAATTTTTTAAAA
Found at i:620456 original size:2 final size:2
Alignment explanation
Indices: 620449--620473 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
620439 TTGGGTTTGC
620449 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
620474 GTAGTAGGTA
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:623167 original size:30 final size:29
Alignment explanation
Indices: 623111--623167 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
623101 CCATAATAAA
*
623111 TAAAAAAAGAAAAAGAGAAGAGAAAAACT
1 TAAAAAAAGAAAAAGAGAAGACAAAAACT
623140 TAAAAAAAGAAAAA-AGAAACGACAAAAA
1 TAAAAAAAGAAAAAGAG-AA-GACAAAAA
623168 ACACAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.05
Consensus pattern (29 bp):
TAAAAAAAGAAAAAGAGAAGACAAAAACT
Found at i:623370 original size:3 final size:3
Alignment explanation
Indices: 623362--623390 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
623352 AAAATATTTT
623362 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
623391 TCAAATGGGC
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:623482 original size:19 final size:20
Alignment explanation
Indices: 623446--623504 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
623436 TATTAAATAA
623446 AAAAGAAAAATTGTAAAAAAAAC
1 AAAAGAAAAA--G-AAAAAAAAC
*
623469 AAAA-AAACAA-AAAAAAAGC
1 AAAAGAAA-AAGAAAAAAAAC
623488 AAAAGAAAAAGAAAAAA
1 AAAAGAAAAAGAAAAAA
623505 GAATTAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
19 14 0.44
20 9 0.28
22 3 0.09
23 6 0.19
ACGTcount: A:0.81, C:0.05, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAGAAAAAAAAC
Found at i:623505 original size:19 final size:19
Alignment explanation
Indices: 623460--623505 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
623450 GAAAAATTGT
623460 AAAAAAAA-CAAAAAAACA
1 AAAAAAAAGCAAAAAAACA
623478 AAAAAAAAGCAAAAGAAA-A
1 AAAAAAAAGCAAAA-AAACA
*
623497 AGAAAAAAG
1 AAAAAAAAG
623506 AATTAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 8 0.32
19 14 0.56
20 3 0.12
ACGTcount: A:0.85, C:0.07, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGCAAAAAAACA
Found at i:623942 original size:24 final size:23
Alignment explanation
Indices: 623898--623960 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
623888 CAAAAGATAA
623898 TAAAAGAT-ATAAAAAGCTTTTCT
1 TAAAA-ATAATAAAAAGCTTTTCT
** *
623921 TAAAATATAATAAAAATTTTTTTT
1 TAAAA-ATAATAAAAAGCTTTTCT
*
623945 TAAAAATAATTAAAAG
1 TAAAAATAATAAAAAG
623961 TATAAAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 16 0.48
24 17 0.52
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (23 bp):
TAAAAATAATAAAAAGCTTTTCT
Found at i:623980 original size:16 final size:17
Alignment explanation
Indices: 623947--623994 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
623937 TTTTTTTTTA
*
623947 AAAATAATTAAAAGTAT
1 AAAATAATTAAAACTAT
*
623964 AAAA-AATTTAAACTAT
1 AAAATAATTAAAACTAT
623980 ATAAATACATTAAAA
1 A-AAATA-ATTAAAA
623995 ATTAATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
16 11 0.44
17 7 0.28
18 1 0.04
19 6 0.24
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATAATTAAAACTAT
Found at i:624609 original size:17 final size:18
Alignment explanation
Indices: 624580--624615 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
624570 ATATTTTAAG
*
624580 TTATTTGTAAATTTTTGT
1 TTATTTGTAAATTATTGT
624598 TTATTT-TAAATTATTGT
1 TTATTTGTAAATTATTGT
624615 T
1 T
624616 GCTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTATTTGTAAATTATTGT
Found at i:624636 original size:21 final size:21
Alignment explanation
Indices: 624612--624653 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
624602 TTTAAATTAT
*
624612 TGTTGCTTAAATTTATTTTAA
1 TGTTGATTAAATTTATTTTAA
* *
624633 TGTTTATTATATTTATTTTAA
1 TGTTGATTAAATTTATTTTAA
624654 ATATTTATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (21 bp):
TGTTGATTAAATTTATTTTAA
Found at i:625938 original size:29 final size:30
Alignment explanation
Indices: 625901--625969 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
625891 AATTAATATA
*
625901 TTTATAATTTAAATATAATGTTAAA-ATTT
1 TTTATAATTTAAATATAATATTAAATATTT
* * *
625930 TTTAAAATTTTAATATTATATTAAATATTT
1 TTTATAATTTAAATATAATATTAAATATTT
625960 TATTATAATT
1 T-TTATAATT
625970 CAAGATTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 21 0.64
30 5 0.15
31 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
TTTATAATTTAAATATAATATTAAATATTT
Found at i:626017 original size:54 final size:54
Alignment explanation
Indices: 625955--626066 Score: 206
Period size: 54 Copynumber: 2.1 Consensus size: 54
625945 TTATATTAAA
* *
625955 TATTTTATTATAATTCAAGATTATTGAGATCATTGACTTTAGAATAGGGGATAT
1 TATTTTATTATAATTCAAGATTATTGAGATCATTGACTTTAGAATAGGAGATAC
626009 TATTTTATTATAATTCAAGATTATTGAGATCATTGACTTTAGAATAGGAGATAC
1 TATTTTATTATAATTCAAGATTATTGAGATCATTGACTTTAGAATAGGAGATAC
626063 TATT
1 TATT
626067 ACTAGCTAGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.15, T:0.43
Consensus pattern (54 bp):
TATTTTATTATAATTCAAGATTATTGAGATCATTGACTTTAGAATAGGAGATAC
Found at i:633120 original size:13 final size:14
Alignment explanation
Indices: 633088--633120 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
633078 TTAAAACAAA
633088 TTAAATAAAATCAT
1 TTAAATAAAATCAT
633102 TT-AATAAAAT-AT
1 TTAAATAAAATCAT
633114 TTAAATA
1 TTAAATA
633121 TCAAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 12 0.67
14 2 0.11
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAATAAAATCAT
Found at i:633446 original size:111 final size:114
Alignment explanation
Indices: 633314--633529 Score: 296
Period size: 113 Copynumber: 1.9 Consensus size: 114
633304 AAAATTAAAA
* * ** *
633314 GGAATAAAATCAAATCAATTAATTGGATT-AAAAGTTAAAAACAGCCTACTC-CAGACA-TCTGA
1 GGAATAAAATAAAATAAATTAATTGGATTAAAAAGCAAAAAACACCCTACTCTCAGACATTC-GA
633376 GGCATTCATACCTATCCTGCCCATCTTACTC-ATTATTTTATTAATTAAT
65 GGCATTCATACCTATCCTGCCCATCTTACTCGATTATTTTATTAATTAAT
* *
633425 GGAATTAAATAAAATAAATTAATTGGATTAAAAAGCAAAAAACACCCTACTCTGAGACATTCGAG
1 GGAATAAAATAAAATAAATTAATTGGATTAAAAAGCAAAAAACACCCTACTCTCAGACATTCGAG
** *
633490 GCATTCATTTCTATCCTGCGCATCTTACTCGTATTATTTT
66 GCATTCATACCTATCCTGCCCATCTTACTCG-ATTATTTT
633530 TTATTACTTG
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
111 26 0.29
112 19 0.21
113 35 0.39
114 2 0.02
115 8 0.09
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (114 bp):
GGAATAAAATAAAATAAATTAATTGGATTAAAAAGCAAAAAACACCCTACTCTCAGACATTCGAG
GCATTCATACCTATCCTGCCCATCTTACTCGATTATTTTATTAATTAAT
Found at i:633603 original size:23 final size:24
Alignment explanation
Indices: 633571--633618 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
633561 TGGCTCTATT
* *
633571 TTATATAAAATATT-ATATTTATA
1 TTATACAAAATATTAAAATTTATA
633594 TTATACAAAATATTAAAATTTATA
1 TTATACAAAATATTAAAATTTATA
633618 T
1 T
633619 GTTTATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
TTATACAAAATATTAAAATTTATA
Found at i:633644 original size:32 final size:30
Alignment explanation
Indices: 633567--633655 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 30
633557 ATGATGGCTC
633567 TATTTTATATAAAATATTATA-TTTATATTA
1 TATTTTATATAAAAT-TTATATTTTATATTA
****
633597 TACAAAATATTAAAATTTATATGTTTATATTA
1 TATTTTATA-TAAAATTTATAT-TTTATATTA
* *
633629 TATTTTATATAAAAATTATATATTATA
1 TATTTTATATAAAATTTATATTTTATA
633656 ATTTATGAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
30 15 0.33
31 17 0.37
32 14 0.30
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (30 bp):
TATTTTATATAAAATTTATATTTTATATTA
Found at i:633667 original size:23 final size:25
Alignment explanation
Indices: 633622--633667 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
633612 TTTATATGTT
*
633622 TATATTATATTTTATATAAAAATTA
1 TATATTATATATTATATAAAAATTA
*
633647 TATATTATA-ATT-TATGAAAAT
1 TATATTATATATTATATAAAAAT
633668 ATAAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 2 0.11
25 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
TATATTATATATTATATAAAAATTA
Found at i:633695 original size:62 final size:62
Alignment explanation
Indices: 633567--633702 Score: 145
Period size: 62 Copynumber: 2.2 Consensus size: 62
633557 ATGATGGCTC
* * ***
633567 TATTTTATATAAAATATTATATTTATATTATACAAAATATTAAAATTTATATGTTTATATTA
1 TATTTTATATAAAATATTATATTTATATTATACAAAATATAAAAATATATAAAATTATATTA
* * *
633629 TATTTTATATAAAA-ATTATATATTATAATT-TATGAAAATATAAAAATATA-AAAATTATTTTT
1 TATTTTATATAAAATATTATAT-TTAT-ATTATA-CAAAATATAAAAATATATAAAATTATATTA
633691 TATTTTAT-TAAA
1 TATTTTATATAAA
633703 TTAATATCTA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
61 11 0.17
62 35 0.56
63 17 0.27
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (62 bp):
TATTTTATATAAAATATTATATTTATATTATACAAAATATAAAAATATATAAAATTATATTA
Found at i:633735 original size:16 final size:16
Alignment explanation
Indices: 633716--633758 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
633706 ATATCTAATT
633716 ATTATTA-ATATTTTAA
1 ATTATTATAT-TTTTAA
*
633732 ATTATTTTATTTTTAA
1 ATTATTATATTTTTAA
633748 ATTATT-TATTT
1 ATTATTATATTT
633759 ATATCATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 18 0.72
17 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTATTATATTTTTAA
Found at i:634715 original size:15 final size:17
Alignment explanation
Indices: 634677--634715 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
634667 TTACTTTTTC
634677 TAATTTTTTATATTTAA
1 TAATTTTTTATATTTAA
634694 TAA-TTTTT-TATTTAA
1 TAATTTTTTATATTTAA
634709 -AATTTTT
1 TAATTTTT
634716 AAAAGTGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 2 0.10
15 11 0.52
16 5 0.24
17 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TAATTTTTTATATTTAA
Found at i:635630 original size:23 final size:24
Alignment explanation
Indices: 635603--635649 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
635593 CAGTGATCTA
* *
635603 TTTTCTCTT-TTTTTTTTCTTTTT
1 TTTTCTCTTAATTTTTTTATTTTT
635626 TTTTCTCTTAATTTTTTTATTTTT
1 TTTTCTCTTAATTTTTTTATTTTT
635650 AATTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTCTCTTAATTTTTTTATTTTT
Found at i:637608 original size:13 final size:13
Alignment explanation
Indices: 637590--637628 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
637580 GATAAAAGCT
637590 TAAATGAAATTGA
1 TAAATGAAATTGA
*
637603 TAAATG-AATAAGA
1 TAAATGAAAT-TGA
637616 TAAATGAAATTGA
1 TAAATGAAATTGA
637629 ATGCAGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 3 0.14
13 16 0.73
14 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (13 bp):
TAAATGAAATTGA
Found at i:637925 original size:30 final size:30
Alignment explanation
Indices: 637891--637956 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
637881 ATTTCAAATC
* *
637891 AATTAAATTCTTAAATATATATTTTTACTT
1 AATTAAATTCTTAAATATATATTTTCACCT
*
637921 AATTAAATTTTTAAATATATATTTTCACCT
1 AATTAAATTCTTAAATATATATTTTCACCT
637951 AATTAA
1 AATTAA
637957 GTACTCGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTAAATTCTTAAATATATATTTTCACCT
Found at i:638911 original size:2 final size:2
Alignment explanation
Indices: 638906--638946 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
638896 AACTAACTTT
638906 TA TA 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 TA TA T
638947 TCTTTCTTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:639398 original size:20 final size:20
Alignment explanation
Indices: 639373--639429 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
639363 TTTTTCAGAA
*
639373 AAGGGATCGATCCCCTACA-T
1 AAGGGATCGATCCCCTA-AGC
*
639393 AAGGGATCGATCACCTAAGGC
1 AAGGGATCGATCCCCTAA-GC
639414 AAGGGATCGATCCCCT
1 AAGGGATCGATCCCCT
639430 CTTAAAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.03
20 16 0.50
21 15 0.47
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (20 bp):
AAGGGATCGATCCCCTAAGC
Done.