Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008746.1 Hibiscus syriacus cultivar Beakdansim tig00111835_pilon, 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: 2013901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:454849 original size:21 final size:21
Alignment explanation
Indices: 454808--454870 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
454798 AATCATATTG
454808 CCCAGGGGGTACAGATT-CCC
1 CCCAGGGGGTACAGATTCCCC
454828 CCCAGGGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
454849 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
454870 C
1 C
454871 TGTCTAACGG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:455264 original size:32 final size:34
Alignment explanation
Indices: 455197--455266 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
455187 TTTTGTAAAG
*
455197 GGGAAAGGTTCTAGTTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
455231 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
455263 GGGA
1 GGGA
455267 GTTGTAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 12 0.34
33 1 0.03
34 22 0.63
ACGTcount: A:0.30, C:0.14, G:0.31, T:0.24
Consensus pattern (34 bp):
GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
Found at i:457619 original size:20 final size:20
Alignment explanation
Indices: 457594--457675 Score: 128
Period size: 20 Copynumber: 4.1 Consensus size: 20
457584 AATCATATTG
457594 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
457614 CCCAGGGGGTACTGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
457634 CCAAGGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
457654 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
457674 CC
1 CC
457676 TGTCTAACGG
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.15
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:461099 original size:32 final size:30
Alignment explanation
Indices: 461040--461099 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
461030 TTAAACTTAT
* **
461040 ATTTTGATATAATAAATATTTGTAAAATTG
1 ATTTTGACATAATAAATATTTCAAAAATTG
461070 ATTTTAGACATAATCAAATATTTCAAAAAT
1 ATTTT-GACATAAT-AAATATTTCAAAAAT
461100 AATTAAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.20
31 7 0.28
32 13 0.52
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (30 bp):
ATTTTGACATAATAAATATTTCAAAAATTG
Found at i:466140 original size:19 final size:19
Alignment explanation
Indices: 466123--466168 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
466113 TGAAAAGATT
466123 TAATAAAATAAAATAGATAA
1 TAAT-AAATAAAATAGATAA
* *
466143 TAATAAATAAAATGGAAAA
1 TAATAAATAAAATAGATAA
466162 TAATAAA
1 TAATAAA
466169 ATAATAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.24
Consensus pattern (19 bp):
TAATAAATAAAATAGATAA
Found at i:466180 original size:12 final size:11
Alignment explanation
Indices: 466123--466184 Score: 53
Period size: 10 Copynumber: 6.0 Consensus size: 11
466113 TGAAAAGATT
466123 TAATAAAATAA
1 TAATAAAATAA
*
466134 -AAT-AGATAA
1 TAATAAAATAA
466143 TAAT-AAATAA
1 TAATAAAATAA
**
466153 -AATGGAA-AA
1 TAATAAAATAA
466162 TAATAAAATAA
1 TAATAAAATAA
466173 TAAGTAAAATAA
1 TAA-TAAAATAA
466185 AAAAGATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
9 10 0.24
10 18 0.44
11 5 0.12
12 8 0.20
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.24
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:466181 original size:20 final size:19
Alignment explanation
Indices: 466123--466188 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
466113 TGAAAAGATT
466123 TAATAAAATAAAA-TAGATAA
1 TAATAAAATAAAAGTA-A-AA
*
466143 TAAT-AAATAAAATGGAAAA
1 TAATAAAATAAAA-GTAAAA
466162 TAATAAAATAATAAGTAAAA
1 TAATAAAATAA-AAGTAAAA
466182 TAA-AAAA
1 TAATAAAA
466189 GATTTTTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 18 0.45
20 19 0.47
21 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (19 bp):
TAATAAAATAAAAGTAAAA
Found at i:466246 original size:17 final size:18
Alignment explanation
Indices: 466210--466251 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
466200 GTTGTTTTTA
466210 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
* *
466228 AAATAAAATA-AATAATT
1 AAATAAAAGATAAGAATT
466245 AAATAAA
1 AAATAAA
466252 TAATCTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:466250 original size:12 final size:13
Alignment explanation
Indices: 466233--466262 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
466223 GAATTAAATA
466233 AAATAAATAAT-T
1 AAATAAATAATCT
466245 AAATAAATAATCT
1 AAATAAATAATCT
466258 AAATA
1 AAATA
466263 TATAGAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATAATCT
Found at i:466885 original size:112 final size:113
Alignment explanation
Indices: 466668--466892 Score: 344
Period size: 112 Copynumber: 2.0 Consensus size: 113
466658 TGAAAGACAA
466668 TTAGCTAAGCATGACCAAAGTCATACTTAGCATAATTGAAAAAGCATGCAAAAAATAGAGAGAAA
1 TTAGCTAAGCATGACCAAAGTCATACTTAGCATAATTGAAAAAGCATGCAAAAAATAGAGAGAAA
* * *
466733 TATAGAGTGAAAAAGAAGATTTTATTCTCAAATGACAGAGATATGTTT
66 GATAGAGAGAAAAAGAAGAATTTATTCTCAAATGACAGAGATATGTTT
* **
466781 TTAGCTAAGCATGGCCAAAGTCATACTTAGCATAATTG-AAAAGCATGTGAAAAATAGAGAGAAA
1 TTAGCTAAGCATGACCAAAGTCATACTTAGCATAATTGAAAAAGCATGCAAAAAATAGAGAGAAA
* * * * *
466845 GCTTGAGAGAAGAAGAAGAATTTATTCTCAGATGAGAGAGATATGTTT
66 GATAGAGAGAAAAAGAAGAATTTATTCTCAAATGACAGAGATATGTTT
466893 CTAGGTTTAC
Statistics
Matches: 101, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
112 64 0.63
113 37 0.37
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.25
Consensus pattern (113 bp):
TTAGCTAAGCATGACCAAAGTCATACTTAGCATAATTGAAAAAGCATGCAAAAAATAGAGAGAAA
GATAGAGAGAAAAAGAAGAATTTATTCTCAAATGACAGAGATATGTTT
Found at i:468463 original size:47 final size:47
Alignment explanation
Indices: 468412--468707 Score: 472
Period size: 47 Copynumber: 6.3 Consensus size: 47
468402 CCATTTATAT
*
468412 ATTTTAATTTATGGCATCCTTTCATGGCTTAATGCATCATTTCATGC
1 ATTTTAATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
468459 ATTTTCAA-TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTT-AATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
468506 ATTTTCAA-TTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTT-AATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
468553 ATTTTTAA-TTATGGCATTCTTTCATGCCTTAATGTATCATTTCATGC
1 A-TTTTAATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
*
468600 ATTTTAATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTTAATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* *
468647 ATTTTAATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTTAATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
468694 ATTTTAATTTATGG
1 ATTTTAATTTATGG
468708 AATCGATTTA
Statistics
Matches: 235, Mismatches: 11, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
46 6 0.03
47 223 0.95
48 6 0.03
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (47 bp):
ATTTTAATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:469880 original size:3 final size:3
Alignment explanation
Indices: 469872--469908 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
469862 ACACCAACAT
469872 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
469909 TGTAGAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:473201 original size:25 final size:28
Alignment explanation
Indices: 473154--473204 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
473144 TGAGACCATG
*
473154 AATTCCAAATATGAGAAATTGATTTCTA
1 AATTCCAAAAATGAGAAATTGATTTCTA
473182 AATT-CAAAAATGA-AAA-TGATTTC
1 AATTCCAAAAATGAGAAATTGATTTC
473205 CTTTTGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 3 0.14
27 8 0.36
28 4 0.18
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (28 bp):
AATTCCAAAAATGAGAAATTGATTTCTA
Found at i:474605 original size:20 final size:22
Alignment explanation
Indices: 474580--474619 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
474570 TGTTGTATAT
474580 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
474600 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
474620 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:474776 original size:21 final size:20
Alignment explanation
Indices: 474732--474805 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
474722 GCAGGCTTTG
*
474732 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
**
474752 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CAGGA
**
474773 TGCATCGATGCACATAAGGA
1 TGCATCGATGCACAGCAGGA
474793 TGCATCGATGCAC
1 TGCATCGATGCAC
474806 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:474872 original size:22 final size:23
Alignment explanation
Indices: 474840--474882 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
474830 ATGGATGCAT
474840 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
474863 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
474883 GCAGGGATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:474895 original size:21 final size:20
Alignment explanation
Indices: 474826--474924 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
474816 CGGTGTTTTA
* *
474826 GTGCATGGATGCATTGCATG
1 GTGCATGGATGCACTGCAGG
*
474846 GTGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
474868 GTGCATGGATGCACTGCAGG
1 GTGCATGGATGCACTGCAGG
474888 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
474910 GTGCATGGATGCACT
1 GTGCATGGATGCACT
474925 TTGACACCCT
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 31 0.44
22 17 0.24
23 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.23
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:475987 original size:20 final size:20
Alignment explanation
Indices: 475961--476026 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
475951 ATGTGTTTAG
*
475961 AAGTTTTGATACTTTCA-CA
1 AAGTTTTGAAACTTTCATCA
475980 ATAGTTTTGAAACTTTCATCA
1 A-AGTTTTGAAACTTTCATCA
**
476001 AAGTTTCAAAACTTTCATCA
1 AAGTTTTGAAACTTTCATCA
476021 AAGTTT
1 AAGTTT
476027 CAAAACTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.02
20 38 0.90
21 3 0.07
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (20 bp):
AAGTTTTGAAACTTTCATCA
Found at i:476027 original size:20 final size:20
Alignment explanation
Indices: 475971--476034 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
475961 AAGTTTTGAT
**
475971 ACTTTCA-CAATAGTTTTGAA
1 ACTTTCATCAA-AGTTTCAAA
475991 ACTTTCATCAAAGTTTCAAA
1 ACTTTCATCAAAGTTTCAAA
476011 ACTTTCATCAAAGTTTCAAA
1 ACTTTCATCAAAGTTTCAAA
476031 ACTT
1 ACTT
476035 CATGTGTGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 38 0.93
21 3 0.07
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (20 bp):
ACTTTCATCAAAGTTTCAAA
Found at i:484198 original size:18 final size:18
Alignment explanation
Indices: 484175--484218 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
484165 TTAGGTGGTT
*
484175 GATACATTGGTGGCGGAG
1 GATACATTGGTGGCAGAG
484193 GATACATTGGTGGCAGAG
1 GATACATTGGTGGCAGAG
484211 GATACATT
1 GATACATT
484219 TGAGGTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.36, T:0.25
Consensus pattern (18 bp):
GATACATTGGTGGCAGAG
Found at i:488573 original size:21 final size:21
Alignment explanation
Indices: 488546--488605 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
488536 CGTCCGAGTT
*
488546 ACCCGCGACGGCCGTAATAGC
1 ACCCGCGACGGCCGCAATAGC
** *
488567 GTCCGCGACAGCCGCAATAGC
1 ACCCGCGACGGCCGCAATAGC
*
488588 ACCCGCGACGGCTGCAAT
1 ACCCGCGACGGCCGCAAT
488606 CACGGTAAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.38, G:0.28, T:0.10
Consensus pattern (21 bp):
ACCCGCGACGGCCGCAATAGC
Found at i:498260 original size:23 final size:23
Alignment explanation
Indices: 498227--498283 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
498217 TTTATATGGG
498227 ACTTCGGTGCAATTCTACGCGAC
1 ACTTCGGTGCAATTCTACGCGAC
* * *
498250 ACTTCGATGCAATTCTACGTGGC
1 ACTTCGGTGCAATTCTACGCGAC
498273 ACTTCGGTGCA
1 ACTTCGGTGCA
498284 TTTATATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (23 bp):
ACTTCGGTGCAATTCTACGCGAC
Found at i:503321 original size:13 final size:14
Alignment explanation
Indices: 503303--503331 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
503293 TATATAAGAC
503303 GATAT-AATTATAA
1 GATATAAATTATAA
503316 GATATAAATTATAA
1 GATATAAATTATAA
503330 GA
1 GA
503332 ATATTGATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (14 bp):
GATATAAATTATAA
Found at i:514651 original size:2 final size:2
Alignment explanation
Indices: 514644--514677 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
514634 ATAGAAAATA
*
514644 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
514678 GGTCGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:524507 original size:20 final size:20
Alignment explanation
Indices: 524484--524533 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
524474 TTGTTCATGT
524484 AGTATCGATAATGTAAGAAC
1 AGTATCGATAATGTAAGAAC
524504 AGTATCGATAATGTAAGAAC
1 AGTATCGATAATGTAAGAAC
524524 AGTATCGATA
1 AGTATCGATA
524534 CTACTACCCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.10, G:0.20, T:0.26
Consensus pattern (20 bp):
AGTATCGATAATGTAAGAAC
Found at i:526421 original size:20 final size:20
Alignment explanation
Indices: 526396--526435 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
526386 GATTACCTCA
*
526396 TTCTTCTTATTTTTCTTCTT
1 TTCTTCATATTTTTCTTCTT
*
526416 TTCTTCATCTTTTTCTTCTT
1 TTCTTCATATTTTTCTTCTT
526436 CCTTTATCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTCATATTTTTCTTCTT
Found at i:530118 original size:20 final size:20
Alignment explanation
Indices: 530090--530127 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
530080 ATGCTTACCC
*
530090 CTTCTTCTTGTTT-TTCTTTT
1 CTTCATCTT-TTTCTTCTTTT
530110 CTTCATCTTTTTCTTCTT
1 CTTCATCTTTTTCTTCTT
530128 CCTTTACCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (20 bp):
CTTCATCTTTTTCTTCTTTT
Found at i:530840 original size:173 final size:168
Alignment explanation
Indices: 530404--530752 Score: 473
Period size: 173 Copynumber: 2.0 Consensus size: 168
530394 TTGATTTTGG
* * * **
530404 TTTCCCTCAATAAATTGATTCATTCATGAGTGACTTGTAGCTTGTCTCAAATCTACTTGGCATTA
1 TTTCCATCAATAAATGGATTCATTAATGAGTGACTTCAAGC-T-TCTCAAATC-ACTTGGCATTA
**
530469 GAACAAGAGGAGTCTCTTCCATATTCATACGTGCTTAATGCACAAATAGAATGTTTCAAAGCCTT
63 GAACAAGA-GAG-CTAATCCATATTCATACGTGCTTAATGCACAAATAGAATGTTTCAAAGCCTT
530534 TGCATTGAGTTGGAACTTCTTCTTCTCTCCATCACTTCAATCA
126 TGCATTGAGTTGGAACTTCTTCTTCTCTCCATCACTTCAATCA
* * * **
530577 TTTCCCTCAATAAATTGATTCATTCATGAGTGACTTGTAGCTTGTCTCAAATCTACTTGGCATTA
1 TTTCCATCAATAAATGGATTCATTAATGAGTGACTTCAAGC-T-TCTCAAATC-ACTTGGCATTA
**
530642 GAACAAGAGGAGTCTCTTCCATATTCATACGTGCTTAATGCACAAAATAGAATGTTTCAAAGCCT
63 GAACAAGA-GAG-CTAATCCATATTCATACGTGCTTAATGCAC-AAATAGAATGTTTCAAAGCCT
530707 TTGCATTGAGTTGGAACTTCTTCTTCTCTCCATCACTTCAATCA
125 TTGCATTGAGTTGGAACTTCTTCTTCTCTCCATCACTTCAATCA
530751 TT
1 TT
530753 CATCTCATCG
Statistics
Matches: 175, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
173 108 0.62
174 67 0.38
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (168 bp):
TTTCCATCAATAAATGGATTCATTAATGAGTGACTTCAAGCTTCTCAAATCACTTGGCATTAGAA
CAAGAGAGCTAATCCATATTCATACGTGCTTAATGCACAAATAGAATGTTTCAAAGCCTTTGCAT
TGAGTTGGAACTTCTTCTTCTCTCCATCACTTCAATCA
Found at i:533265 original size:20 final size:20
Alignment explanation
Indices: 533240--533285 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
533230 ACTCTATGCA
533240 CTAAACCTTAAATTAAAACT
1 CTAAACCTTAAATTAAAACT
533260 CTAAACCTTAAATTAAAACT
1 CTAAACCTTAAATTAAAACT
533280 CTAAAC
1 CTAAAC
533286 AATAGTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (20 bp):
CTAAACCTTAAATTAAAACT
Found at i:533747 original size:21 final size:21
Alignment explanation
Indices: 533698--533737 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
533688 ATACCCCTAA
*
533698 CTTAAACCCTAAATTATAAAT
1 CTTAAACCCTAAATCATAAAT
533719 CTTAAACCCTAAATCATAA
1 CTTAAACCCTAAATCATAA
533738 CCTCTAAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (21 bp):
CTTAAACCCTAAATCATAAAT
Found at i:538482 original size:13 final size:12
Alignment explanation
Indices: 538447--538509 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
538437 AATAAACTAT
538447 TTATAATTAATA
1 TTATAATTAATA
538459 TTAAAATAATTATATA
1 TT---ATAATTA-ATA
538475 TTATAATTAATA
1 TTATAATTAATA
*
538487 TTA-ATATTAA-C
1 TTATA-ATTAATA
538498 TTAT-ATTAATA
1 TTATAATTAATA
538509 T
1 T
538510 AATCTAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
10 5 0.12
11 5 0.12
12 13 0.31
13 7 0.17
15 7 0.17
16 5 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
TTATAATTAATA
Found at i:538502 original size:28 final size:27
Alignment explanation
Indices: 538427--538505 Score: 92
Period size: 28 Copynumber: 3.0 Consensus size: 27
538417 ATTCCTATAA
*
538427 AATTTATATTAATA-AAC-TAT-TTAT
1 AATTAATATTAATATAACTTATATTAT
* *
538451 AATTAATATTAAAATAATTATATATTAT
1 AATTAATATTAATATAACT-TATATTAT
538479 AATTAATATTAATATTAACTTATATTA
1 AATTAATATTAATA-TAACTTATATTA
538506 ATATAATCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
24 12 0.27
25 2 0.04
27 3 0.07
28 24 0.53
29 4 0.09
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTAATATTAATATAACTTATATTAT
Found at i:538505 original size:16 final size:16
Alignment explanation
Indices: 538447--538509 Score: 65
Period size: 16 Copynumber: 3.8 Consensus size: 16
538437 AATAAACTAT
538447 TTATAATTAATATTAAA
1 TTAT-ATTAATATTAAA
*
538464 ATA-ATTATATATTATAA
1 TTATATTA-ATATTA-AA
*
538481 TTAATATTAATATTAAC
1 TT-ATATTAATATTAAA
538498 TTATATTAATAT
1 TTATATTAATAT
538510 AATCTAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 4 0.10
16 16 0.41
17 8 0.21
18 7 0.18
19 4 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATATTAATATTAAA
Found at i:538699 original size:51 final size:51
Alignment explanation
Indices: 538642--538796 Score: 134
Period size: 51 Copynumber: 2.9 Consensus size: 51
538632 TTTCAATTAA
*
538642 TATATATGTTTATATTAATAAATTAATATATAGTTTATATATACTATATAG
1 TATATATGTTTATATTAATAAATTAATATATAGTTTATATATACTATATAC
* * * * * * *
538693 TTTATATATACTA-ATGAACTATA-TAATATATAGTTTGTATATACCATATAC
1 TATATATGT-TTATATTAA-TAAATTAATATATAGTTTATATATACTATATAC
*
538744 TATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTA
1 TATATATGTT-TATAT--TAAT-AA--AT-TAATATATAGTTTATATATACTA
538797 ATGAACTGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
51 44 0.57
52 7 0.09
53 1 0.01
54 3 0.04
56 1 0.01
58 21 0.27
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (51 bp):
TATATATGTTTATATTAATAAATTAATATATAGTTTATATATACTATATAC
Found at i:538723 original size:33 final size:33
Alignment explanation
Indices: 538679--538923 Score: 317
Period size: 33 Copynumber: 7.5 Consensus size: 33
538669 ATATAGTTTA
*
538679 TATATACTATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
538712 TATATAATATATAGTTTGTATATAC-------C
1 TATATAATATATAGTTTATATATACTAATGAAC
* *
538738 -ATATACTATATAGGTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
538770 TATATAATATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
538803 TGTATAATATATAGTTTATATATACTAATGAAC
1 TATATAATATATAGTTTATATATACTAATGAAC
*
538836 TATATATAATGTATAGTTTATATATACTAATGAAC
1 --TATATAATATATAGTTTATATATACTAATGAAC
* *
538871 TATATATAATGTATAGTTTATATATACTAATAAAC
1 --TATATAATATATAGTTTATATATACTAATGAAC
*
538906 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
538924 GGGTTTTTAT
Statistics
Matches: 191, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
25 21 0.11
26 1 0.01
32 1 0.01
33 103 0.54
35 65 0.34
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (33 bp):
TATATAATATATAGTTTATATATACTAATGAAC
Found at i:538756 original size:58 final size:60
Alignment explanation
Indices: 538679--538923 Score: 253
Period size: 68 Copynumber: 3.9 Consensus size: 60
538669 ATATAGTTTA
*
538679 TATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTGTATATAC-C
1 TATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACAC
*
538738 -ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAA
1 TATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC------A
538802 C
60 C
* * *
538803 TGTATAATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACTAATG
1 TATATACTATATAGTTTATATATACTAATGAAC--TATATAATATATAGTTTATATATAC-----
538868 AAC
59 -AC
* *
538871 TATATA-TAATGTATAGTTTATATATACTAATAAACTATATAATGTATAGTTTA
1 TATATACT-A--TATAGTTTATATATACTAATGAACTATATAATATATAGTTTA
538924 GGGTTTTTAT
Statistics
Matches: 165, Mismatches: 8, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
58 55 0.33
65 1 0.01
66 29 0.18
67 1 0.01
68 56 0.34
70 23 0.14
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (60 bp):
TATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACAC
Found at i:538862 original size:68 final size:67
Alignment explanation
Indices: 538738--538923 Score: 284
Period size: 68 Copynumber: 2.7 Consensus size: 67
538728 TGTATATACC
* * *
538738 ATATACTATATAGGTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAAC
1 ATATAATATATAGTTTATATATACTAATGAACTATATAATGTATAGTTTATATATACTAATGAAC
538803 -T
66 AT
*
538804 GTATAATATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACTAATGA
1 ATATAATATATAGTTTATATATACTAATGAAC--TATATAATGTATAGTTTATATATACTAATGA
538869 ACTAT
64 AC-AT
* *
538874 ATATAATGTATAGTTTATATATACTAATAAACTATATAATGTATAGTTTA
1 ATATAATATATAGTTTATATATACTAATGAACTATATAATGTATAGTTTA
538924 GGGTTTTTAT
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
66 29 0.27
68 50 0.46
70 30 0.28
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (67 bp):
ATATAATATATAGTTTATATATACTAATGAACTATATAATGTATAGTTTATATATACTAATGAAC
AT
Found at i:538970 original size:2 final size:2
Alignment explanation
Indices: 538953--539133 Score: 71
Period size: 2 Copynumber: 84.0 Consensus size: 2
538943 ATATGTAAAT
* *
538953 TA TA CTA TA TA GTA TA TA TA GTT TA TA TA TA TA -A TA TA TA GTT
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
*
538996 TA TA TA TA TA -A TA TA TA GTA TA TGA -A TA TA AA CTA TA GTA TA
1 TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA TA -TA TA -TA TA
** * * * * *
539038 TA TA TA GG TCA TA TG CA AA CTA TA TA GTA TA TA AA TA TA AA CTA
1 TA TA TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
539082 TA GTA TA TA TA TA TA TA TA GA TCA TA TG TA AA CTA TA TA GTT TA
1 TA -TA TA TA TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA -TA TA
539126 TA TA TA TA
1 TA TA TA TA
539134 GTTCATATGT
Statistics
Matches: 133, Mismatches: 27, Indels: 38
0.67 0.14 0.19
Matches are distributed among these distances:
1 3 0.02
2 107 0.80
3 23 0.17
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (2 bp):
TA
Found at i:538979 original size:11 final size:11
Alignment explanation
Indices: 538929--539003 Score: 59
Period size: 11 Copynumber: 6.9 Consensus size: 11
538919 GTTTAGGGTT
538929 TTTATATATAG
1 TTTATATATAG
* * *
538940 TTCATATGTAAA
1 TTTATATAT-AG
538952 TTATACTATATAG
1 TT-TA-TATATAG
538965 --TATATATAG
1 TTTATATATAG
538974 TTTATATATA-
1 TTTATATATAG
*
538984 -TAATATATAG
1 TTTATATATAG
538994 TTTATATATA
1 TTTATATATA
539004 TAATATATAG
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
9 15 0.31
10 2 0.04
11 23 0.47
12 3 0.06
13 2 0.04
14 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (11 bp):
TTTATATATAG
Found at i:538983 original size:20 final size:20
Alignment explanation
Indices: 538953--539133 Score: 120
Period size: 20 Copynumber: 8.6 Consensus size: 20
538943 ATATGTAAAT
538953 TATACTATATAGT-ATATATAG
1 TATA-TATATA-TAATATATAG
*
538974 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
*
538994 TTTATATATATAATATATAG
1 TATATATATATAATATATAG
539014 TATATGA-ATATAA-ACTATAG
1 TATAT-ATATATAATA-TATAG
* * *
539034 TATATATATAGGTCATATGCAAAC
1 TATATATATA--TAATAT--ATAG
* *
539058 TATATAGTATATAAATATAAAC
1 TATATA-TATAT-AATATATAG
539080 TATAGTATATATATATATATAG
1 TATA-TATATATA-ATATATAG
*
539102 -ATCATATGTA-AACTATATAG
1 TAT-ATATATATAA-TATATAG
*
539122 TTTATATATATA
1 TATATATATATA
539134 GTTCATATGT
Statistics
Matches: 132, Mismatches: 11, Indels: 34
0.75 0.06 0.19
Matches are distributed among these distances:
19 4 0.03
20 71 0.54
21 14 0.11
22 23 0.17
23 4 0.03
24 12 0.09
25 4 0.03
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (20 bp):
TATATATATATAATATATAG
Found at i:539095 original size:33 final size:33
Alignment explanation
Indices: 539058--539298 Score: 96
Period size: 33 Copynumber: 6.6 Consensus size: 33
539048 ATATGCAAAC
539058 TATATAGTATATAAATATAAACTATAGTATATA
1 TATATAGTATATAAATATAAACTATAGTATATA
* * *
539091 TATATA-TATAGATCATATGTAAACTATATAGTTTATA
1 TATATAGTAT--AT-AAATATAAAC--TATAGTATATA
*
539128 TATATAGTTCATATGTAAATATTAACTATAGTTTATATGTA
1 TATATAG-T-ATA--TAAATATAAACTATAG--TATA--TA
* *
539169 AACTATAGTTCATATATAAATATCAACCT-TAGTATATACA
1 TA-TATAG----TATATAAATAT-AAACTATAGTATAT--A
* *
539209 TATTTATA-TATATAGTTCATATGTAAACTATAGT-TCACA
1 TA--TATAGTATATA----A-ATATAAACTATAGTAT-ATA
*
539248 TATATAGTATATAAATATAAACTATAGTTTATA
1 TATATAGTATATAAATATAAACTATAGTATATA
*
539281 TAAATAGTATA-AAATATA
1 TATATAGTATATAAATATA
539299 GTATATAAAT
Statistics
Matches: 158, Mismatches: 19, Indels: 63
0.66 0.08 0.26
Matches are distributed among these distances:
32 10 0.06
33 31 0.20
34 4 0.03
35 8 0.05
36 6 0.04
37 25 0.16
38 8 0.05
39 14 0.09
40 15 0.09
41 15 0.09
42 15 0.09
43 3 0.02
44 3 0.02
45 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (33 bp):
TATATAGTATATAAATATAAACTATAGTATATA
Found at i:539158 original size:57 final size:57
Alignment explanation
Indices: 538931--539240 Score: 175
Period size: 57 Copynumber: 5.5 Consensus size: 57
538921 TTAGGGTTTT
* * * * * * *
538931 TATATATAGTTCATATGTAAA-T-TATACTATATAGTATATATAGTTTA-TATATATA
1 TATATATAGATCATATGTAAACTATATAGTATATA-AATATAAACTATAGTAAATATA
* * * *
538986 -ATATATAGTTTATATATATAA-TATATAGTATATGAATATAAACTATAG------TA
1 TATATATAGATCATATGTA-AACTATATAGTATATAAATATAAACTATAGTAAATATA
* * *
539036 TATATATAGGTCATATGCAAACTATATAGTATATAAATATAAACTATAGTATATATA
1 TATATATAGATCATATGTAAACTATATAGTATATAAATATAAACTATAGTAAATATA
* * **
539093 TATATATAGATCATATGTAAACTATATAGTTTATATATAT-AGTTCATATGTAAATAT-
1 TATATATAGATCATATGTAAACTATATAGTATATAAATATAAACT-ATA-GTAAATATA
* * *
539150 TA-ACTATAGTTTATATGTAAACTATAGTTCA-TATATAAATATCAACCT-TAGTATATACATAT
1 TATA-TATAGATCATATGTAAACTATA--T-AGTATATAAATAT-AAACTATAG--TA-A-ATA-
539212 TTA
56 -TA
*
539215 TATATATAGTTCATATGTAAACTATA
1 TATATATAGATCATATGTAAACTATA
539241 GTTCACATAT
Statistics
Matches: 201, Mismatches: 27, Indels: 44
0.74 0.10 0.16
Matches are distributed among these distances:
50 4 0.02
51 40 0.20
54 16 0.08
55 12 0.06
56 12 0.06
57 63 0.31
58 8 0.04
59 12 0.06
60 3 0.01
61 3 0.01
62 3 0.01
64 1 0.00
65 23 0.11
66 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (57 bp):
TATATATAGATCATATGTAAACTATATAGTATATAAATATAAACTATAGTAAATATA
Found at i:539174 original size:18 final size:18
Alignment explanation
Indices: 539146--539188 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
539136 TCATATGTAA
* *
539146 ATATTAACTATAGTTTAT
1 ATATAAACTATAGTTCAT
*
539164 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTTCAT
539182 ATATAAA
1 ATATAAA
539189 TATCAACCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (18 bp):
ATATAAACTATAGTTCAT
Found at i:539273 original size:20 final size:20
Alignment explanation
Indices: 539249--539322 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
539239 TAGTTCACAT
539249 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
539269 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
539294 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
539314 TTATAGTAT
1 ATATAGTAT
539323 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:539298 original size:25 final size:23
Alignment explanation
Indices: 539249--539309 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
539239 TAGTTCACAT
539249 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
539269 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
539294 ATATAGTATATAAATA
1 ATATAGTATATAAATA
539310 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:539301 original size:12 final size:13
Alignment explanation
Indices: 539262--539311 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
539252 TAGTATATAA
539262 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
539276 TTATATAA-ATAGT
1 ATATA-AATATAGT
539289 ATA-AAATATAGT
1 ATATAAATATAGT
539301 ATATAAATATA
1 ATATAAATATA
539312 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:539423 original size:22 final size:23
Alignment explanation
Indices: 539381--539447 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 23
539371 CCCTAAACCA
*
539381 TATATATATATATATATATAAAC
1 TATATATTTATATATATATAAAC
*
539404 TATATAGTTTATAT-TA-ATAAAT
1 TATATA-TTTATATATATATAAAC
*
539426 TATATAATTTATACAATATATA
1 TATAT-ATTTATA-TATATATA
539448 TTATTTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 16 0.44
23 9 0.25
24 8 0.22
25 3 0.08
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (23 bp):
TATATATTTATATATATATAAAC
Found at i:539610 original size:27 final size:28
Alignment explanation
Indices: 539547--539613 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
539537 TAGTTCATAT
* *
539547 ATAAACTATATAGTATTATAGTTTATAC
1 ATAAAATATATAGTATTATACTTTATAC
***
539575 ATGGTATATATAGT-TTATACTTTATAC
1 ATAAAATATATAGTATTATACTTTATAC
539602 ATAAAATATATA
1 ATAAAATATATA
539614 TAAACTATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
27 21 0.68
28 10 0.32
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (28 bp):
ATAAAATATATAGTATTATACTTTATAC
Found at i:539614 original size:2 final size:2
Alignment explanation
Indices: 539607--539691 Score: 59
Period size: 2 Copynumber: 42.0 Consensus size: 2
539597 TATACATAAA
* * *
539607 AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT ACT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * *
539649 TT AT AT AT AA ACT AT AT A- AT TT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
539690 AT
1 AT
539692 TAGTTGTTTT
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
1 3 0.05
2 57 0.89
3 4 0.06
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:539631 original size:20 final size:20
Alignment explanation
Indices: 539608--539678 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 20
539598 ATACATAAAA
*
539608 TATATATAAACTATATAGTT
1 TATATATAAACTATATAATT
*
539628 TATATATATAA-TACATATACTT
1 TATATATA-AACT--ATATAATT
539650 TATATATAAACTATATAATT
1 TATATATAAACTATATAATT
539670 TATAATATA
1 TAT-ATATA
539679 TATATATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
20 19 0.43
21 9 0.20
22 16 0.36
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (20 bp):
TATATATAAACTATATAATT
Found at i:539664 original size:42 final size:44
Alignment explanation
Indices: 539608--539690 Score: 134
Period size: 42 Copynumber: 1.9 Consensus size: 44
539598 ATACATAAAA
*
539608 TATATATAAACTATATAGTTTAT-ATATATA-ATACATATACTT
1 TATATATAAACTATATAATTTATAATATATATATACATATACTT
*
539650 TATATATAAACTATATAATTTATAATATATATATATATATA
1 TATATATAAACTATATAATTTATAATATATATATACATATA
539691 TTAGTTGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 22 0.59
43 7 0.19
44 8 0.22
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (44 bp):
TATATATAAACTATATAATTTATAATATATATATACATATACTT
Found at i:539684 original size:20 final size:20
Alignment explanation
Indices: 539619--539686 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
539609 ATATATAAAC
*
539619 TATATAGTTTATATATATAATA
1 TATATAATTTATA-ATAT-ATA
* * *
539641 CATATACTTTAT-ATATAAA
1 TATATAATTTATAATATATA
539660 CTATATAATTTATAATATATA
1 -TATATAATTTATAATATATA
539681 TATATA
1 TATATA
539687 TATATTAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 20 0.53
21 6 0.16
22 10 0.26
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (20 bp):
TATATAATTTATAATATATA
Found at i:540442 original size:217 final size:217
Alignment explanation
Indices: 539716--540743 Score: 1592
Period size: 217 Copynumber: 4.8 Consensus size: 217
539706 TTTTTTCTCA
* * * *
539716 ACTTATTACTTATTTCTA-TTTATTAATTGGTCCATAACTTTTTTAAATGAGTATAATTTAGTA-
1 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAAC-TTTTTAAATGGGTATAATTTAGTAC
*
539779 TATTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCCT--T---T-TGT
65 T-TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGT
* * * *
539838 TTTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAGTTT
129 GTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAATTAGTCCTCCAAATTT
* *
539903 TATCTGCACCTGAAATTGACCCAT
194 TATTTGCATCTGAAATTGACCCAT
*
539927 ACTTATTACTT-ATT-TATATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTA-
1 ACTTATTACTTAATTCTAT-TTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC
* * *
539989 TTTTTT-TAATAATTTCAACCTCAAAATTTAAAATTATTTTGATTTGATCCCT--T---T-TGTG
65 TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTG
* * * *
540047 TTTTTTAATATATTTAATTTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
130 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAATTAGTCCTCCAAATTTT
540112 ATTTGCATCTGAAATTGACCCAT
195 ATTTGCATCTGAAATTGACCCAT
* * *
540135 ACTTATTACTTATTTCTA-TTTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTACT
1 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
*
540199 TTTTTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
66 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
*
540264 TGTTTAATTTATTTAAATTTTTATTTGTAATTTAATATTTGTTCAAATTAGTCCTCCAAATTTTA
131 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAATTAGTCCTCCAAATTTTA
*
540329 TTTGCATCTGAAATTGATCCAT
196 TTTGCATCTGAAATTGACCCAT
540351 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
1 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
540416 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
66 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
* *
540481 TGTTTAATTTATTTAAATTTTTATTTTTAATTTAATATTTGTTCAAATTAGTCCTCCAAATTTTA
131 TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAATTAGTCCTCCAAATTTTA
* * *
540546 TTTGCATATGAAATTGATCAAT
196 TTTGCATCTGAAATTGACCCAT
540568 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
1 ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
*
540633 TTTTTGTATTAATTTCAAACTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
66 TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
*
540698 TGTTTAATTTATTT-AATTTTTCTTTTGTAATTTCATATTTGTTCAA
131 TGTTTAATTTATTTAAATTTTT-ATTTGTAATTTCATATTTGTTCAA
540744 TTTAATTCTT
Statistics
Matches: 767, Mismatches: 36, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
208 186 0.24
209 15 0.02
210 70 0.09
211 28 0.04
212 1 0.00
215 1 0.00
216 110 0.14
217 356 0.46
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.50
Consensus pattern (217 bp):
ACTTATTACTTAATTCTATTTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
TTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGT
TGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAAATTAGTCCTCCAAATTTTA
TTTGCATCTGAAATTGACCCAT
Found at i:543274 original size:73 final size:73
Alignment explanation
Indices: 543150--543297 Score: 278
Period size: 73 Copynumber: 2.0 Consensus size: 73
543140 TTTACGTTAC
*
543150 TCTATGTTTACATCATCATGTCAGACTAGCATGAATTATGACCATGCTATTTAAGGTACTGTGTA
1 TCTATGTTTACAACATCATGTCAGACTAGCATGAATTATGACCATGCTATTTAAGGTACTGTGTA
543215 TGATATGT
66 TGATATGT
*
543223 TCTATGTTTACAACATCATGTCAGACTAGCATGAATTATGACCATGGTATTTAAGGTACTGTGTA
1 TCTATGTTTACAACATCATGTCAGACTAGCATGAATTATGACCATGCTATTTAAGGTACTGTGTA
543288 TGATATGT
66 TGATATGT
543296 TC
1 TC
543298 GCAAGACACC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (73 bp):
TCTATGTTTACAACATCATGTCAGACTAGCATGAATTATGACCATGCTATTTAAGGTACTGTGTA
TGATATGT
Found at i:549443 original size:3 final size:3
Alignment explanation
Indices: 549435--549516 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
549425 TTTTACTTAA
** *
549435 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
* *
549480 ATT A-T ATAT ATT A-T ATT ATT ATT A-A ATA ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
549517 TACAAACAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
2 7 0.11
3 53 0.82
4 5 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:549495 original size:25 final size:22
Alignment explanation
Indices: 549435--549516 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
549425 TTTTACTTAA
549435 ATTATTATTAAA-ATTATTATT
1 ATTATTATTAAATATTATTATT
549456 ATTATTATTAAATATTATTATT
1 ATTATTATTAAATATTATTATT
549478 A-TATTA-T--ATA-TATTA-T
1 ATTATTATTAAATATTATTATT
549494 ATTATTATTAAATAATTATTATT
1 ATTATTATTAAAT-ATTATTATT
549517 TACAAACAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.04
17 10 0.19
18 4 0.08
20 3 0.06
21 18 0.34
22 15 0.28
23 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTATTATTAAATATTATTATT
Found at i:550886 original size:3 final size:3
Alignment explanation
Indices: 550878--550918 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
550868 TTATTTACAA
* *
550878 TAT TAT TAT TAT TTT TATT TAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
550919 TATATAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:550921 original size:19 final size:19
Alignment explanation
Indices: 550878--550915 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
550868 TTATTTACAA
550878 TATTATTATTATTTTTATT
1 TATTATTATTATTTTTATT
550897 TATTATTATTATTTTTATT
1 TATTATTATTATTTTTATT
550916 ATTTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTATTATTATTTTTATT
Found at i:551241 original size:27 final size:27
Alignment explanation
Indices: 551209--551263 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
551199 ATATTTCTAA
551209 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATA-TTTATTTCATAAATAT
* *
551236 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
551263 A
1 A
551264 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:551796 original size:23 final size:26
Alignment explanation
Indices: 551738--551801 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
551728 ATTTCTTTTC
* *
551738 TTTTAAATT-TTTTATTACTTATTAT
1 TTTTATATTATTTTATTACATATTAT
551763 TTTTATATTATTTTATTA-ATATT-T
1 TTTTATATTATTTTATTACATATTAT
551787 TTTTAT-TTATTTTAT
1 TTTTATATTATTTTAT
551802 GAAGGTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 9 0.25
24 7 0.19
25 12 0.33
26 8 0.22
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTATATTATTTTATTACATATTAT
Found at i:554138 original size:21 final size:21
Alignment explanation
Indices: 554114--554153 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
554104 CTTTTCATAC
554114 ATGCATTTACATTTTGTATCT
1 ATGCATTTACATTTTGTATCT
*
554135 ATGCATTTCCATTTTGTAT
1 ATGCATTTACATTTTGTAT
554154 TCTTACTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.53
Consensus pattern (21 bp):
ATGCATTTACATTTTGTATCT
Found at i:558492 original size:114 final size:114
Alignment explanation
Indices: 558281--558494 Score: 329
Period size: 114 Copynumber: 1.9 Consensus size: 114
558271 CTCGTAGTAG
* * *
558281 AAATAAGGAGGCCCAATAGCATTTTCTAGAAGTGTTCTTTGAGTTATCTAATCTGGTTCGGTAGG
1 AAATAAGGAGCCCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTAATCTGGTTCGGTAGG
* *
558346 AACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGCTCATAGCAA
66 AACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCATAGCAA
* *
558395 AAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTCGGTAGG
1 AAATAAGGAGCCCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTAATCTGGTTCGGTAGG
* * * *
558460 AATCCCAGAACCAATCATTAGAATTGACAGATGAA
66 AACCCCAAAACCAATCATTAGAATTAAAAGATGAA
558495 CTGCATAATC
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 89 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (114 bp):
AAATAAGGAGCCCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTAATCTGGTTCGGTAGG
AACCCCAAAACCAATCATTAGAATTAAAAGATGAATTTGCTCATAGCAA
Found at i:560614 original size:54 final size:54
Alignment explanation
Indices: 560529--560686 Score: 191
Period size: 54 Copynumber: 3.0 Consensus size: 54
560519 TAATTGAGAA
*
560529 ATCTGAGCAGAAGCCACA-GAAAAGGATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGAGCAGAAGCCACATG-AAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
560583 ATCTGAGCAGAAGCTACATGAAAGGAAGAATGTGTTTTCAAATGTTTTAC-ATC
1 ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * * *
560636 -TC-GA-CGGAAACCACATGAAAAGATGAATGTATTGTCAAATGTTTTACGAAC
1 ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
560687 CAGTGATTAT
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
50 36 0.40
51 4 0.04
52 2 0.02
53 2 0.02
54 44 0.49
55 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (54 bp):
ATCTGAGCAGAAGCCACATGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:561083 original size:22 final size:22
Alignment explanation
Indices: 561054--561108 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
561044 ATCTACAATC
561054 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
** *
561076 TTTGAAGATAATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
561098 TTCAAAGATGA
1 TTCAAAGATGA
561109 AAGCTTTATG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:561898 original size:164 final size:164
Alignment explanation
Indices: 561623--561943 Score: 534
Period size: 164 Copynumber: 2.0 Consensus size: 164
561613 AAAATGAACA
* * *
561623 TTATCTTGAGATTGGGGCATGTTACCTAATCGATATGTTATTTCGAAAAATAATGAGAAAACGAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCGAAAAATAATGAGAAAACGAT
** * * *
561688 TTCCATAGTTTCTCATTTTACCTTTTCTAAAATGAAGTTGTTGAAAAGTAAGAAAACGATTTTCT
66 TTCCATAGTTTCTCATTCAACCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
*
561753 TAGTTTTTTACTTAGTAAACTATTTCCAACAGCC
131 TAGTTTCTTACTTAGTAAACTATTTCCAACAGCC
*
561787 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTTGAAAAATAATGAGAAAACGAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCGAAAAATAATGAGAAAACGAT
*
561852 TTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
66 TTCCATAGTTTCTCATTCAACCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
*
561917 TAGTTTCTTATTTAGTAAACTATTTCC
131 TAGTTTCTTACTTAGTAAACTATTTCC
561944 CACATCTGTA
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
164 145 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (164 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCGAAAAATAATGAGAAAACGAT
TTCCATAGTTTCTCATTCAACCTTTTCTAAAATGAAATTATTGAAAAGTAAGAAAACGATTTTCA
TAGTTTCTTACTTAGTAAACTATTTCCAACAGCC
Found at i:562133 original size:76 final size:76
Alignment explanation
Indices: 561946--562653 Score: 1230
Period size: 76 Copynumber: 9.4 Consensus size: 76
561936 CTATTTCCCA
* * *
561946 CATCTGTAAGTCATGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
562011 AGCCTTAGGGT
66 AGCCTTAGGGT
562022 CATC------TCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
562081 AGCCTTAGGGT
66 AGCCTTAGGGT
*
562092 TATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
562157 AACCTTAGGGT
66 AGCCTTAGGGT
*
562168 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
562233 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
562244 CATTTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
562309 AACCTTAGGGT
66 AGCCTTAGGGT
562320 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
562385 AGCCTTAGGGT
66 AGCCTTAGGGT
*
562396 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
562461 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
562472 CATCTGTAAGTCTTGCAGTGCATGATGTTTCCAAAAAGCTTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
562537 AACCTTAGGGT
66 AGCCTTAGGGT
562548 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
562613 AACCTTAGGGT
66 AGCCTTAGGGT
*
562624 CATCTGTAAGTCCTGCAGTGCATGAGGTTT
1 CATCTGTAAGTCCTGCAGTGCATGATGTTT
562654 TTAAGACCTC
Statistics
Matches: 601, Mismatches: 25, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
70 66 0.11
76 535 0.89
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:562815 original size:3 final size:3
Alignment explanation
Indices: 562807--562888 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
562797 TTTTACTTAA
** *
562807 ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AAAT ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
* *
562852 ATT A-T ATAT ATT -TT ATT ATT ATT A-A ATA ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
562889 TACAAACAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
2 7 0.11
3 53 0.82
4 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:562847 original size:22 final size:22
Alignment explanation
Indices: 562807--562888 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
562797 TTTTACTTAA
562807 ATTATTATTAAA-ATTATTATT
1 ATTATTATTAAATATTATTATT
562828 ATTATTATTAAATATTATTATT
1 ATTATTATTAAATATTATTATT
562850 A-TATTA-T--ATA-TATT-TT
1 ATTATTATTAAATATTATTATT
562866 ATTATTATTAAATAATTATTATT
1 ATTATTATTAAAT-ATTATTATT
562889 TACAAACAGG
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.06
17 9 0.17
18 4 0.08
20 3 0.06
21 18 0.34
22 14 0.26
23 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTATTATTAAATATTATTATT
Found at i:564265 original size:3 final size:3
Alignment explanation
Indices: 564257--564287 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
564247 TTATTTACAA
*
564257 TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
564288 TATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:564311 original size:18 final size:16
Alignment explanation
Indices: 564288--564322 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
564278 TTTTATTATT
564288 TATATA-AATAAATATA
1 TATATATAATAAATA-A
564304 TATATATAATAAATAA
1 TATATATAATAAATAA
564320 TAT
1 TAT
564323 TTGTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TATATATAATAAATAA
Found at i:564599 original size:27 final size:27
Alignment explanation
Indices: 564569--564623 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
564559 ATATTTCTAA
564569 ATAAATAAATATTTTATTT-ATAAATAT
1 ATAAATAAATA-TTTATTTCATAAATAT
* *
564596 ATAAATTAATATTTATTTCATAATTAT
1 ATAAATAAATATTTATTTCATAAATAT
564623 A
1 A
564624 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.28
27 18 0.72
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATAAATAAATATTTATTTCATAAATAT
Found at i:566757 original size:16 final size:16
Alignment explanation
Indices: 566737--566841 Score: 77
Period size: 16 Copynumber: 6.6 Consensus size: 16
566727 AAATTTAACG
*
566737 GAACCAAAATTAATCA
1 GAACCAAAATTAACCA
* * *
566753 AAACCGAAATTAACCT
1 GAACCAAAATTAACCA
* *
566769 GAATCAAAATTAACCC
1 GAACCAAAATTAACCA
*
566785 GAACCAAAATTAACCC
1 GAACCAAAATTAACCA
* ** *
566801 GAACCGAAAGCAACCC
1 GAACCAAAATTAACCA
* *
566817 GAATCTAAATTAA-CA
1 GAACCAAAATTAACCA
566832 TGAACCAAAA
1 -GAACCAAAA
566842 GAAACCTGAT
Statistics
Matches: 69, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
15 1 0.01
16 68 0.99
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.15
Consensus pattern (16 bp):
GAACCAAAATTAACCA
Found at i:566789 original size:48 final size:48
Alignment explanation
Indices: 566737--566841 Score: 129
Period size: 48 Copynumber: 2.2 Consensus size: 48
566727 AAATTTAACG
* ** * *
566737 GAACCAAAATTAATCAAAACCGAAATTAACCTGAATCAAAATTAACCC
1 GAACCAAAATTAACCAAAACCGAAAGCAACCCGAATCAAAATTAACAC
** * *
566785 GAACCAAAATTAACCCGAACCGAAAGCAACCCGAATCTAAATTAACAT
1 GAACCAAAATTAACCAAAACCGAAAGCAACCCGAATCAAAATTAACAC
566833 GAACCAAAA
1 GAACCAAAA
566842 GAAACCTGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.51, C:0.25, G:0.09, T:0.15
Consensus pattern (48 bp):
GAACCAAAATTAACCAAAACCGAAAGCAACCCGAATCAAAATTAACAC
Found at i:566795 original size:32 final size:32
Alignment explanation
Indices: 566754--566847 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
566744 AATTAATCAA
* * **
566754 AACCGAAATTAACCTGAATCAAAATTAACCCG
1 AACCAAAATTAACCTGAACCAAAAGCAACCCG
* *
566786 AACCAAAATTAACCCGAACCGAAAGCAACCCG
1 AACCAAAATTAACCTGAACCAAAAGCAACCCG
* * * *
566818 AATCTAAATTAACATGAACCAAAAGAAACC
1 AACCAAAATTAACCTGAACCAAAAGCAACC
566848 TGATCCGAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.50, C:0.27, G:0.10, T:0.14
Consensus pattern (32 bp):
AACCAAAATTAACCTGAACCAAAAGCAACCCG
Found at i:566856 original size:48 final size:48
Alignment explanation
Indices: 566754--566861 Score: 126
Period size: 48 Copynumber: 2.2 Consensus size: 48
566744 AATTAATCAA
** * * **
566754 AACCGAAATTAACCTGAATCAAAATTAACCCGAACCAAAATTAACCCG
1 AACCGAAAGCAACCCGAATCAAAATTAACACGAACCAAAAGAAACCCG
* * *
566802 AACCGAAAGCAACCCGAATCTAAATTAACATGAACCAAAAGAAACCTG
1 AACCGAAAGCAACCCGAATCAAAATTAACACGAACCAAAAGAAACCCG
*
566850 ATCCGAAAGCAA
1 AACCGAAAGCAA
566862 TCTGAACCGA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.49, C:0.26, G:0.11, T:0.14
Consensus pattern (48 bp):
AACCGAAAGCAACCCGAATCAAAATTAACACGAACCAAAAGAAACCCG
Found at i:566878 original size:48 final size:48
Alignment explanation
Indices: 566775--566878 Score: 109
Period size: 48 Copynumber: 2.2 Consensus size: 48
566765 ACCTGAATCA
** ** * *
566775 AAATTAACCCGAACCAAAATTAACCCGAACCGAAAGCAACCCGAATCT
1 AAATTAACATGAACCAAAAGAAACCCGAACCGAAAGCAACCCGAACCG
* * * *
566823 AAATTAACATGAACCAAAAGAAACCTGATCCGAAAGCAATCTGAACCG
1 AAATTAACATGAACCAAAAGAAACCCGAACCGAAAGCAACCCGAACCG
*
566871 AATTTAAC
1 AAATTAAC
566879 CCGACCCGAA
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.47, C:0.26, G:0.12, T:0.15
Consensus pattern (48 bp):
AAATTAACATGAACCAAAAGAAACCCGAACCGAAAGCAACCCGAACCG
Found at i:566986 original size:18 final size:19
Alignment explanation
Indices: 566947--567002 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
566937 TAATAGATTA
*
566947 ATTTA-AATAAAATTGATA-
1 ATTTATAATAAAA-TAATAG
*
566965 ATTTATAA-AAAATATTAG
1 ATTTATAATAAAATAATAG
566983 ATTTATAATAAAATAATAG
1 ATTTATAATAAAATAATAG
567002 A
1 A
567003 AAGTTTAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.09
18 17 0.53
19 12 0.38
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (19 bp):
ATTTATAATAAAATAATAG
Found at i:566997 original size:19 final size:18
Alignment explanation
Indices: 566965--567002 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
566955 AAAATTGATA
*
566965 ATTTATAAAAAATATTAG
1 ATTTATAAAAAATAATAG
566983 ATTTATAATAAAATAATAG
1 ATTTATAA-AAAATAATAG
567002 A
1 A
567003 AAGTTTAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (18 bp):
ATTTATAAAAAATAATAG
Found at i:573888 original size:22 final size:22
Alignment explanation
Indices: 573863--573914 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
573853 GAAAACTGGT
*
573863 TGGTCAACGTAAAATATTTTCC
1 TGGTCAACGTAAAATATTTTCA
573885 TGGTCAACGTAAAATATTTTCA
1 TGGTCAACGTAAAATATTTTCA
*
573907 TAGTCAAC
1 TGGTCAAC
573915 AAAATTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
TGGTCAACGTAAAATATTTTCA
Found at i:574128 original size:26 final size:24
Alignment explanation
Indices: 574066--574128 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
574056 CATTTTAATC
574066 AAAATAT-TAATTATTAAAATGTTT
1 AAAATATAT-ATTATTAAAATGTTT
*
574090 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATGTT-T
574113 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
574129 ATTTTTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATGTTT
Found at i:574144 original size:29 final size:29
Alignment explanation
Indices: 574094--574202 Score: 90
Period size: 29 Copynumber: 3.9 Consensus size: 29
574084 ATGTTTAAAA
*
574094 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTT-TT-ATA-TTATAATAATATAATAT
*
574126 TATATTTTTATATTATAATAAAAT-A-AT
1 TATATTTTTATATTATAATAATATAATAT
*
574153 CA-A---TTATATTATAATAATATAAGATAT
1 TATATTTTTATATTATAATAATAT-A-ATAT
574180 TATATTTTTAT-TT-TAATAATATA
1 TATATTTTTATATTATAATAATATA
574203 TAATAAATTA
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
23 16 0.25
26 2 0.03
27 6 0.09
28 3 0.05
29 19 0.30
30 5 0.08
31 6 0.09
32 7 0.11
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (29 bp):
TATATTTTTATATTATAATAATATAATAT
Found at i:574197 original size:52 final size:53
Alignment explanation
Indices: 574112--574312 Score: 152
Period size: 54 Copynumber: 3.8 Consensus size: 53
574102 TTAATATTTC
* *
574112 TAATAATATAATATTATATTTTTATATTATAATAA-A-ATAATCAATTATATTA
1 TAATAATATAATATTATATTTTTATATTATAATAATATATAATAAATTAT-TAA
574164 TAATAATATAAGATATTATATTTTTAT-TT-TAATAATATATAATAAATTATTAA
1 TAATAATAT-A-ATATTATATTTTTATATTATAATAATATATAATAAATTATTAA
* * * * * *
574217 TAATATTTATATTTTTTTATTAATTTCATA-GA-AATAATAT-TATTAAATTATTAA
1 TAATA-ATATAATATTATATT--TTT-ATATTATAATAATATATAATAAATTATTAA
* * *
574271 TAATGA-ATAATATTAT-TTTATAT-TTAATATTAATATTATAAT
1 TAATAATATAATATTATATTTTTATATT-ATAATAATA-TATAAT
574313 TTAATAATAT
Statistics
Matches: 117, Mismatches: 17, Indels: 30
0.71 0.10 0.18
Matches are distributed among these distances:
48 2 0.02
49 3 0.03
50 6 0.05
51 3 0.03
52 32 0.27
53 12 0.10
54 49 0.42
55 10 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (53 bp):
TAATAATATAATATTATATTTTTATATTATAATAATATATAATAAATTATTAA
Found at i:574330 original size:19 final size:18
Alignment explanation
Indices: 574278--574330 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
574268 TAATAATGAA
574278 TAATATTATTTTAT-ATT
1 TAATATTATTTTATAATT
*
574295 TAATATTAATATTATAATT
1 TAATATT-ATTTTATAATT
*
574314 TAATAATATTTTCATAA
1 TAATATTATTTT-ATAA
574331 AGATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 13 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TAATATTATTTTATAATT
Found at i:574434 original size:31 final size:29
Alignment explanation
Indices: 574409--574488 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 29
574399 ATATAATTTA
574409 TAATATTTTTATTTCAATAAAATATACCAATAT
1 TAATATTTTTA-TT-AATAAAATATA--AATAT
*
574442 TAATATTTTTATTAATAAAATTATAAA-AA
1 TAATATTTTTATTAATAAAA-TATAAATAT
*
574471 TAATA-TTTTAATAATAAA
1 TAATATTTTTATTAATAAA
574489 TAAATTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
28 12 0.27
29 6 0.14
30 2 0.05
31 7 0.16
32 6 0.14
33 11 0.25
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATTTTTATTAATAAAATATAAATAT
Found at i:574665 original size:15 final size:15
Alignment explanation
Indices: 574642--574671 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
574632 TCGTAAAACA
574642 TTTTCTAGAAAATGT
1 TTTTCTAGAAAATGT
*
574657 TTTTTTAGAAAATGT
1 TTTTCTAGAAAATGT
574672 AATTCATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (15 bp):
TTTTCTAGAAAATGT
Found at i:575047 original size:19 final size:19
Alignment explanation
Indices: 575023--575066 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
575013 TCAACAAAAC
575023 TATAAAACATTAAT-TAAAT
1 TATAAAA-ATTAATATAAAT
*
575042 TATAAAAATTAGTATAAAT
1 TATAAAAATTAATATAAAT
575061 TATAAA
1 TATAAA
575067 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
TATAAAAATTAATATAAAT
Found at i:577859 original size:42 final size:42
Alignment explanation
Indices: 577810--577889 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
577800 GGGTATATAT
577810 ATTTAAATTAAATATATAAAATATT-ATA-TATATATATATTTA
1 ATTTAAATTAAAT-TA-AAAATATTAATATTATATATATATTTA
**
577852 ATTTAAATTAAATTAAATTTATTAATATTATATATATA
1 ATTTAAATTAAATTAAAAATATTAATATTATATATATA
577890 ATAATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 6 0.18
41 5 0.15
42 23 0.68
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (42 bp):
ATTTAAATTAAATTAAAAATATTAATATTATATATATATTTA
Found at i:578041 original size:30 final size:33
Alignment explanation
Indices: 577973--578048 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 33
577963 CTCCATCCTT
**
577973 GTCCCCGTTTAGCATAAACAATTTTTTTCCATCCC
1 GTCCCCGTTTAGCATAAAC-AGGTTTTTCCA-CCC
578008 GTCCCCGTTTAGCATAAAC-GGTTTTT-C-CCC
1 GTCCCCGTTTAGCATAAACAGGTTTTTCCACCC
578038 GTCCCCGTTTA
1 GTCCCCGTTTA
578049 ATTCGATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
30 14 0.36
32 1 0.03
33 5 0.13
35 19 0.49
ACGTcount: A:0.18, C:0.33, G:0.13, T:0.36
Consensus pattern (33 bp):
GTCCCCGTTTAGCATAAACAGGTTTTTCCACCC
Found at i:588342 original size:22 final size:23
Alignment explanation
Indices: 588316--588364 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
588306 ATTTATGATT
*
588316 AAATT-TATCATTTTATATAATA
1 AAATTATATCATTTTATATAAAA
588338 AAATTACTATCATTTTATATAAAA
1 AAATTA-TATCATTTTATATAAAA
588362 AAA
1 AAA
588365 ACAGAAACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 5 0.21
24 19 0.79
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATTATATCATTTTATATAAAA
Found at i:595610 original size:15 final size:15
Alignment explanation
Indices: 595590--595620 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
595580 TACAATGTAA
595590 CTGGTAAAAATATAC
1 CTGGTAAAAATATAC
595605 CTGGTAAAAATATAC
1 CTGGTAAAAATATAC
595620 C
1 C
595621 GGTTTTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (15 bp):
CTGGTAAAAATATAC
Found at i:596009 original size:196 final size:196
Alignment explanation
Indices: 595598--596246 Score: 694
Period size: 179 Copynumber: 3.4 Consensus size: 196
595588 AACTGGTAAA
* * * * *
595598 AATAT-ACCTGGTAAAAATATACCGGTTTTATGAGAGAATAGGTAAACATAATGTATCGATACTT
1 AATATAACCT-GTAGAAATATACCGGTTTAATTAGAAAATAGGTAAACATAATGTATCGACACTT
* *
595662 TCTAAATTGTATCGATACTTTTTGTCCAAAATGACTGCCAAACGAGGTGCACGCATAAAGTGTCG
65 TCTAAATTGTATCGATACTTTTAGTCCAAAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCG
*
595727 ATACATTTATTGTAAGTATCGAACCCAAAAACATCGAAACCGATAATTATAATATAATAAGTAAA
130 ATACATTTA---TAAGTATCGAACCCAAAAACATCGAAACCGATAATTAAAATATAATAAGTAAA
595792 TTTAC
192 TTTAC
** * * *
595797 AATGCAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTTAACATAATGTATCGACATTTT
1 AATATAACCTGTAGAAATATACCGGTTTAATTAGAAAATAGGTAAACATAATGTATCGACACTTT
* * * * *
595862 TTAAATTTGTGTCGATACTTTTAGTCCAGAATGAATGCCCAATGAGGTGCACGCATAAAGTGTCG
66 CTAAA-TTGTATCGATACTTTTAGTCCAAAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCG
* * * *
595927 ATACATTTA-AAGTATGGATCCCAAAAACATCGAAACCGATAATTAAAATGTAATAGGTAAATTT
130 ATACATTTATAAGTATCGAACCCAAAAACATCGAAACCGATAATTAAAATATAATAAGTAAATTT
595991 AC
195 AC
* * *
595993 AATATAACCTGTAGAAATATACCGGTTTAATTAGAAAATATGTCAACATAATGTATCGATAC-TT
1 AATATAACCTGTAGAAATATACCGGTTTAATTAGAAAATAGGTAAACATAATGTATCGACACTTT
* * * *
596057 -T---TTGT-TC-AGAC---T-G-----AATG---GCC-AACTAGGTGTACGTATAAAGTGTCGA
66 CTAAATTGTATCGATACTTTTAGTCCAAAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGA
* * * * * * *
596103 TACATTTATAATAAGTATCGATCTCAAAAATATCGAAGCCGATAATTATAATGTAATAGGTAAAT
131 TACA-TT-T-ATAAGTATCGAACCCAAAAACATCGAAACCGATAATTAAAATATAATAAGTAAAT
596168 TTAC
193 TTAC
* * * *
596172 AATGTAACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTATCGATACCTT
1 AATATAACCTGTAGAAATATACCGGTTTAATTAGAAAATAGGTAAACATAATGTATCGACA-CTT
*
596237 TTTAAATTGT
65 TCTAAATTGT
596247 GTCGGAACCG
Statistics
Matches: 396, Mismatches: 42, Indels: 38
0.83 0.09 0.08
Matches are distributed among these distances:
175 26 0.07
176 5 0.01
177 1 0.00
178 1 0.00
179 114 0.29
180 1 0.00
181 2 0.01
182 1 0.00
184 1 0.00
185 5 0.01
188 3 0.01
189 2 0.01
190 4 0.01
194 1 0.00
195 2 0.01
196 107 0.27
199 55 0.14
200 65 0.16
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (196 bp):
AATATAACCTGTAGAAATATACCGGTTTAATTAGAAAATAGGTAAACATAATGTATCGACACTTT
CTAAATTGTATCGATACTTTTAGTCCAAAATGAATGCCAAACGAGGTGCACGCATAAAGTGTCGA
TACATTTATAAGTATCGAACCCAAAAACATCGAAACCGATAATTAAAATATAATAAGTAAATTTA
C
Found at i:596842 original size:8 final size:8
Alignment explanation
Indices: 596829--596864 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
596819 AAATAGTATA
596829 AATAAAAT
1 AATAAAAT
596837 AATAAAAT
1 AATAAAAT
596845 AATAAAAT
1 AATAAAAT
596853 ATATAAATAT
1 A-ATAAA-AT
596863 AA
1 AA
596865 AAATGTATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 17 0.65
9 6 0.23
10 3 0.12
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAAAAT
Found at i:596867 original size:16 final size:15
Alignment explanation
Indices: 596819--596868 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
596809 AAAAACAAAT
596819 AAATAGTATAAATAAA
1 AAATA-TATAAATAAA
*
596835 ATA-ATA-AAATAATA
1 AAATATATAAATAA-A
596849 AAATATATAAATATAA
1 AAATATATAAATA-AA
596865 AAAT
1 AAAT
596869 GTATGTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 6 0.21
14 5 0.18
15 4 0.14
16 12 0.43
17 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATATATAAATAAA
Found at i:596982 original size:12 final size:12
Alignment explanation
Indices: 596965--597054 Score: 51
Period size: 12 Copynumber: 6.9 Consensus size: 12
596955 ACAATATACC
596965 ATAATAATAAT-A
1 ATAATAA-AATAA
596977 ATAATAAAATAA
1 ATAATAAAATAA
*
596989 ATAATAAAACGTAGT
1 ATAATAAAA--TA-A
*
597004 ATATTAAATAATAA
1 ATAAT-AA-AATAA
597018 A-AAGT-AAATAA
1 ATAA-TAAAATAA
597029 ATAAATAAAATTAAA
1 AT-AATAAAA-T-AA
597044 ATAATAAAATA
1 ATAATAAAATA
597055 GGAATTGACC
Statistics
Matches: 62, Mismatches: 4, Indels: 24
0.69 0.04 0.27
Matches are distributed among these distances:
11 9 0.15
12 20 0.32
13 7 0.11
14 12 0.19
15 10 0.16
16 2 0.03
17 2 0.03
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (12 bp):
ATAATAAAATAA
Found at i:597023 original size:19 final size:19
Alignment explanation
Indices: 596983--597038 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
596973 AATAATAATA
596983 AAATAAATAATAAAACGTAGT
1 AAATAAATAATAAAAC--AGT
*
597004 ATATTAAATAATAAAA-AGT
1 A-AATAAATAATAAAACAGT
597023 AAATAAATAAATAAAA
1 AAATAAAT-AATAAAA
597039 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 6 0.19
19 11 0.35
21 1 0.03
22 13 0.42
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAATAAATAATAAAACAGT
Found at i:597043 original size:18 final size:18
Alignment explanation
Indices: 596970--597038 Score: 59
Period size: 18 Copynumber: 3.6 Consensus size: 18
596960 ATACCATAAT
*
596970 AATAATAATAA-TAAAATA
1 AATAATAAAAAGT-AAATA
*
596988 AATAATAAAACGTAGTATATTA
1 AATAATAAAA---AGTA-AATA
597010 AATAATAAAAAGTAAATA
1 AATAATAAAAAGTAAATA
597028 AATAAATAAAA
1 AAT-AATAAAA
597039 TTAAAATAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
18 15 0.36
19 11 0.26
21 2 0.05
22 14 0.33
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (18 bp):
AATAATAAAAAGTAAATA
Found at i:598724 original size:67 final size:67
Alignment explanation
Indices: 598516--598730 Score: 209
Period size: 69 Copynumber: 3.1 Consensus size: 67
598506 GATGATGCTC
** * * ** **
598516 CAAGAGAAGTTGTCTCAAAAGAGACAAAATCCGTTTCAAGGGAAACGATCTCAAAGATATTTGTT
1 CAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAATAATCTCAAAGAT-TTTG-T
598581 GTTT
64 GTTT
* * * * *
598585 CATGAGAAACGGTCTCAAG-GTAAACAAAGTTCTGTTTTAAGGGAAATAAAT-TCAAAAAATTTT
1 CAAGAGAAACTGTCTCAAGAG-AAACAAAATT-TGTTTCAAGGGAAAT-AATCTC-AAAGATTTT
598648 GTGTTT
62 GTGTTT
* * * *
598654 CAAGAAAAACTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAATAATCTCAAAGGTTTTGTGT
1 CAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAATAATCTCAAAGATTTTGTGT
598719 TT
66 TT
598721 CAAGAGAAAC
1 CAAGAGAAAC
598731 ATTTTCAAAG
Statistics
Matches: 117, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
67 25 0.21
68 16 0.14
69 50 0.43
70 19 0.16
71 7 0.06
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (67 bp):
CAAGAGAAACTGTCTCAAGAGAAACAAAATTTGTTTCAAGGGAAATAATCTCAAAGATTTTGTGT
TT
Found at i:598757 original size:37 final size:34
Alignment explanation
Indices: 598685--598811 Score: 129
Period size: 31 Copynumber: 3.7 Consensus size: 34
598675 ATACAAAATT
* * *
598685 TGTTTCAAGAGAAATAATCTCAAAGG---TTTTG
1 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTG
598716 TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTTTG
1 TGTTTCAAGAGAAACATTTTCAAAGG--TTTT-TTTG
*
598753 TGTTTCAAGA-AAA-ATTGTTTTAAAGGTTTTTTTG
1 TGTTTCAAGAGAAACA-T-TTTCAAAGGTTTTTTTG
*
598787 TGTTTCAAGAGAAACAATTTCAAAG
1 TGTTTCAAGAGAAACATTTTCAAAG
598812 ATTGGTGCTT
Statistics
Matches: 80, Mismatches: 6, Indels: 17
0.78 0.06 0.17
Matches are distributed among these distances:
31 23 0.29
34 21 0.26
35 8 0.10
36 6 0.08
37 22 0.28
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (34 bp):
TGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTG
Found at i:598839 original size:15 final size:15
Alignment explanation
Indices: 598821--598877 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
598811 GATTGGTGCT
598821 TCAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
* *
598836 TCAAGAGAGACAATTTGTT
1 TC-A-AGAGA-AA-CTGTC
*
598855 TTAAGAGAAACTGTC
1 TCAAGAGAAACTGTC
598870 TCAAGAGA
1 TCAAGAGA
598878 GACAAAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 12 0.38
16 3 0.09
17 10 0.31
18 3 0.09
19 4 0.12
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (15 bp):
TCAAGAGAAACTGTC
Found at i:598931 original size:37 final size:35
Alignment explanation
Indices: 598826--598931 Score: 117
Period size: 37 Copynumber: 2.9 Consensus size: 35
598816 GTGCTTCAAG
* *
598826 AGAAACTGTCTCAAGAGAGACAATTTGTTT-TAAG
1 AGAAACTGTCTCAAGAGAGACAATTTGTTTCAAAC
*
598860 AGAAACTGTCTCAAGAGAGACAAAACTTAG-TTCAAAC
1 AGAAACTGTCTCAAGAGAGAC--AA-TTTGTTTCAAAC
*
598897 AGAAACTGTCTCAAGGGAGACGAAGTTTGTTTCAA
1 AGAAACTGTCTCAAGAGAGAC-AA-TTTGTTTCAA
598932 GGAAAACAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
34 21 0.35
36 9 0.15
37 30 0.50
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.25
Consensus pattern (35 bp):
AGAAACTGTCTCAAGAGAGACAATTTGTTTCAAAC
Found at i:598979 original size:102 final size:102
Alignment explanation
Indices: 598849--599141 Score: 342
Period size: 102 Copynumber: 2.9 Consensus size: 102
598839 AGAGAGACAA
598849 TTTGTTTTAA-GAGAAACTGTCTCAAGAGAGACAAAACTT-AGTTCAAACAGAAACTGTCTCAAG
1 TTTGTTTTAAGGA-AAACTGTCTCAAGAGAGACAAAACTTAAGTTCAAA-AGAAACTGTCTCAAG
** * * *
598912 GGAGACGAAGTTTGTTTCAAGGAAAACAAATTCAAAGAT
64 AAAGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGAT
* * * * *
598951 TTTGTTTCAAGGAAAATTGTCTCAAGAGAGATAAAACTTAATTTCAAAAGAAACTGTCTCGAGAA
1 TTTGTTTTAAGGAAAACTGTCTCAAGAGAGACAAAACTTAAGTTCAAAAGAAACTGTCTCAAGAA
*
599016 AGACAAAATTTGTTTAAAGGAAAACAAATTTAAAGAT
66 AGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGAT
* * * * * *
599053 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA-TT-TGATCCAAGGAAAACTGTCTTAAGA
1 TTTGTTTTAAGGAAAACTGTCTCAAGAGAGACAAAACTTAAGTTCAAAAG-AAACTGTCTCAAGA
* * *
599116 GAGACAAAATTTATTTTAAGAGAAAA
65 AAGACAAAATTTGTTTAAAG-GAAAA
599142 TGTCACAAGA
Statistics
Matches: 162, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
100 5 0.03
101 31 0.19
102 117 0.72
103 9 0.06
ACGTcount: A:0.43, C:0.11, G:0.18, T:0.27
Consensus pattern (102 bp):
TTTGTTTTAAGGAAAACTGTCTCAAGAGAGACAAAACTTAAGTTCAAAAGAAACTGTCTCAAGAA
AGACAAAATTTGTTTAAAGGAAAACAAATTCAAAGAT
Found at i:599170 original size:37 final size:37
Alignment explanation
Indices: 599051--599206 Score: 192
Period size: 36 Copynumber: 4.3 Consensus size: 37
599041 AAATTTAAAG
* *
599051 ATTTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAA
1 ATTTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAA
* ** *
599088 A-TTTGATCCAAG-GAAAACTGTCTTAAGAGAGACAAA
1 ATTTTGTTTTAAGAGAAAA-TGTCTCAAGAGAGACAAA
* *
599124 A-TTTATTTTAAGAGAAAATGTCACAAGAGAGACAAA
1 ATTTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAA
* *
599160 ATTTTGTTTTACGAGAAATTGTCTCAAGAGAGACAAA
1 ATTTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAA
599197 ATTTTGTTTT
1 ATTTTGTTTT
599207 GAGTGAAACT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
35 4 0.04
36 50 0.50
37 47 0.47
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (37 bp):
ATTTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAA
Found at i:600754 original size:95 final size:96
Alignment explanation
Indices: 600586--600775 Score: 260
Period size: 95 Copynumber: 2.0 Consensus size: 96
600576 ATATGTAAAT
* * **
600586 ACCTTTATCAGGTTAACTGAATCTTATCCATAAAGTTGGGGCATTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
*
600651 ACAGCTCAAGCTTTA-T-TATATAATATAATC
66 ACAACTCAAGCTTTATTGTATATAA-ATAATC
** * *
600681 ACCTTTATCAGGCTAGTTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-ATCTAGAGG
1 ACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCT-TAGAGG
600745 GACAACTCAAGCTTTATTGTATATAAATAAT
65 GACAACTCAAGCTTTATTGTATATAAATAAT
600776 ATTATAATGT
Statistics
Matches: 83, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
94 1 0.01
95 69 0.83
96 6 0.07
97 7 0.08
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (96 bp):
ACCTTTATCAGGCTAACTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATATAAATAATC
Found at i:604876 original size:13 final size:13
Alignment explanation
Indices: 604860--604906 Score: 53
Period size: 12 Copynumber: 3.7 Consensus size: 13
604850 CAATAAAAAC
*
604860 AAATAAATAGTAT
1 AAATAAATAATAT
604873 AAATAAAATAATA-
1 AAAT-AAATAATAT
604886 AAATAAA-AATAT
1 AAATAAATAATAT
*
604898 ATATAAATA
1 AAATAAATA
604907 TAAAAAACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 4 0.14
12 9 0.31
13 9 0.31
14 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:606358 original size:20 final size:20
Alignment explanation
Indices: 606313--606358 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
606303 GTTTATATAA
*
606313 AGTATCTATACTTTTTGTAT
1 AGTATCGATACTTTTTGTAT
*
606333 ATGTATCGATACTTTTTGTCT
1 A-GTATCGATACTTTTTGTAT
606354 AGTAT
1 AGTAT
606359 GCTTCTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAT
Found at i:608647 original size:35 final size:34
Alignment explanation
Indices: 608563--608693 Score: 133
Period size: 35 Copynumber: 3.7 Consensus size: 34
608553 TTTGAAAACA
*
608563 TTTGAAAATGTATATAATATAGTTTTAAAAATATTT
1 TTTGAAAATGTATAT-ATATAGTTTTAAAAACA-TT
*
608599 TTTGAAAA-CTATATATATAGTTTT-AAAACATT
1 TTTGAAAATGTATATATATAGTTTTAAAAACATT
* *
608631 TTAGAAAATAG-ATATATATAGTTTTTAAAATCATT
1 TTTGAAAAT-GTATATATATAG-TTTTAAAAACATT
*
608666 TTTGAAAACTTATATAATATATAGTTTT
1 TTTGAAAA--TGTAT-ATATATAGTTTT
608694 GAATTTTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
32 9 0.11
33 15 0.19
34 14 0.17
35 19 0.24
36 8 0.10
37 7 0.09
38 8 0.10
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (34 bp):
TTTGAAAATGTATATATATAGTTTTAAAAACATT
Found at i:608737 original size:29 final size:31
Alignment explanation
Indices: 608695--608757 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 31
608685 TATAGTTTTG
** *
608695 AATTTTTTTAAAACA-TTTAAATAT-TATAT
1 AATTTTTGAAAAACATTTTAAAAATATATAT
608724 AATTTTTGAAAAACATTTTAAAAATATATAT
1 AATTTTTGAAAAACATTTTAAAAATATATAT
608755 AAT
1 AAT
608758 ATATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 13 0.45
30 8 0.28
31 8 0.28
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
AATTTTTGAAAAACATTTTAAAAATATATAT
Found at i:608761 original size:38 final size:38
Alignment explanation
Indices: 608623--608768 Score: 108
Period size: 38 Copynumber: 3.9 Consensus size: 38
608613 ATATAGTTTT
* * *
608623 AAAACATTTTAGAAA-ATAGAT-ATATATAGTTTTT-A
1 AAAACATTTTAAAAATATATATAATATATAATTTTTGA
* * *
608658 AAATCATTTTTGAAAACT-TATATAATATAT-AGTTTTG-
1 AAAACA-TTTT-AAAAATATATATAATATATAATTTTTGA
*** * * *
608695 -AATTTTTTTAAAACATTTAAATATTATATAATTTTTGA
1 AAAACATTTTAAAA-ATATATATAATATATAATTTTTGA
608733 AAAACATTTTAAAAATATATATAATATATAATTTTT
1 AAAACATTTTAAAAATATATATAATATATAATTTTT
608769 AAACTGTTTC
Statistics
Matches: 83, Mismatches: 18, Indels: 17
0.70 0.15 0.14
Matches are distributed among these distances:
34 4 0.05
35 10 0.12
36 17 0.20
37 17 0.20
38 25 0.30
39 10 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (38 bp):
AAAACATTTTAAAAATATATATAATATATAATTTTTGA
Found at i:608935 original size:15 final size:15
Alignment explanation
Indices: 608892--608938 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
608882 TATATATATA
608892 TATATTA-TTATTAT
1 TATATTATTTATTAT
*
608906 TATATTATTTTTTAT
1 TATATTATTTATTAT
*
608921 TTTATT-TCTTATTAT
1 TATATTAT-TTATTAT
608936 TAT
1 TAT
608939 TTGCTTTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TATATTATTTATTAT
Found at i:610323 original size:33 final size:33
Alignment explanation
Indices: 610258--610346 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
610248 TATTTTCTAC
* *
610258 TTCTTTAA-TTTATTGTTATTCATCTTTATCCATT
1 TTCTTTAATTTTATTATTA-T-ACCTTTATCCATT
610292 TTCTTTAATTTTATTATTATACCTTTATCCATT
1 TTCTTTAATTTTATTATTATACCTTTATCCATT
610325 TTCTTTAATTTTATTATTATAC
1 TTCTTTAATTTTATTATTATAC
610347 TAATATTTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
33 34 0.65
34 9 0.17
35 9 0.17
ACGTcount: A:0.24, C:0.13, G:0.01, T:0.62
Consensus pattern (33 bp):
TTCTTTAATTTTATTATTATACCTTTATCCATT
Found at i:615372 original size:165 final size:165
Alignment explanation
Indices: 615095--615923 Score: 1356
Period size: 165 Copynumber: 5.0 Consensus size: 165
615085 AAAACAAACT
* * * * **
615095 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
*
615159 GCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAGGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
615224 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
615260 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTTGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
615325 CTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGATCC
66 CTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
615390 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
*
615425 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACT
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* *
615490 CTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAATGGCTATCTGCCAAAGACCC
66 CTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
615555 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* *
615590 ATTTGCAGTATAACTTAAGTCGAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
* * *
615655 CTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAAAAGGGCTATATGCCAAAGACCC
66 CTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
615720 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
131 CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
* * * * **
615755 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTAC
*
615819 GCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
65 GCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * *
615884 CTCGGGTTCGATTACACTCAACTTCGAGGTCATATC
130 CCCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
615920 ATTT
1 ATTT
615924 ACAACATAGC
Statistics
Matches: 625, Mismatches: 37, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
164 3 0.00
165 619 0.99
166 3 0.00
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
CCGAGTTCGATTACACTCAGCTTCGAGGGCACATC
Found at i:616547 original size:37 final size:36
Alignment explanation
Indices: 616495--616629 Score: 190
Period size: 35 Copynumber: 3.8 Consensus size: 36
616485 TTTCGTCCAT
616495 TTTTTG-AAACTATATAGTATATAGTTTTTAAAA-CA
1 TTTTTGAAAACTATATA-TATATAGTTTTTAAAATCA
*
616530 TTTTAGAAAA-TATATATAATATAAAGTTTTTAAAATCA
1 TTTTTGAAAACTATATAT-ATAT--AGTTTTTAAAATCA
616568 TTTTTGAAAACTATATA-ATATAGTTTTTAAAATCA
1 TTTTTGAAAACTATATATATATAGTTTTTAAAATCA
616603 TTTTTGAAAACT-TATATATATAGTTTT
1 TTTTTGAAAACTATATATATATAGTTTT
616630 GAATATTATA
Statistics
Matches: 91, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
34 5 0.05
35 51 0.56
36 3 0.03
37 15 0.16
38 11 0.12
39 6 0.07
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (36 bp):
TTTTTGAAAACTATATATATATAGTTTTTAAAATCA
Found at i:616860 original size:2 final size:2
Alignment explanation
Indices: 616848--616877 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
616838 ATTTTTGAAA
*
616848 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
616878 TATTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:616910 original size:12 final size:12
Alignment explanation
Indices: 616875--616917 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
616865 TATATATATA
*
616875 TATTATTATTAT
1 TATTATTTTTAT
616887 TATTATTTTTAT
1 TATTATTTTTAT
616899 T-TTATTTCTTAT
1 TATTATTT-TTAT
616911 ATATTAT
1 -TATTAT
616918 GCTTTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 6 0.22
12 16 0.59
13 1 0.04
14 4 0.15
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTATTTTTAT
Found at i:619056 original size:23 final size:23
Alignment explanation
Indices: 619030--619079 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
619020 ACCTATTTTA
** *
619030 TTATATAAGTGCTACCTATTACG
1 TTATATAAACGCTACCTAATACG
*
619053 TTATATAAACGCTACCTAATATG
1 TTATATAAACGCTACCTAATACG
619076 TTAT
1 TTAT
619080 TGTGTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (23 bp):
TTATATAAACGCTACCTAATACG
Found at i:619092 original size:158 final size:158
Alignment explanation
Indices: 618885--619373 Score: 735
Period size: 158 Copynumber: 3.1 Consensus size: 158
618875 ATAATGCGCA
* * * ** *
618885 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTATGTTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
* *
618950 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTATCTAATATGTTGTAATAACAAATTAAGT
66 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTAATATGTTATAATAACAAATTAAGT
619015 AATTAACCTATTTTATTATATAAGTGCT
131 AATTAACCTATTTTATTATATAAGTGCT
*
619043 ACCTATTACGTTATATAAACGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
*
619108 TCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTATATATGTTATAATAACAAATTAAG
66 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTA-ATATGTTATAATAACAAATTAAG
* *
619173 TAATTAATCTATTTTATTATATAAGTACT
130 TAATTAACCTATTTTATTATATAAGTGCT
* * *
619202 ACCTATTACGTTATATAAGCGCTATCTAATATGTTATTGTGCTTGATACTATTAACGGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
* * * * *
619267 CCGGTTATGTTATCCTTAGTAACATTTTAGGCGTTTACCTAATATGTTATAACAACAAATTAAAT
66 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTAATATGTTATAATAACAAATTAAGT
*** *
619332 AATTAACCTATTAGGTTATATAAGCGCT
131 AATTAACCTATTTTATTATATAAGTGCT
* *
619360 ACCTAATATGTTAT
1 ACCTATTACGTTAT
619374 TGTGCTTGCT
Statistics
Matches: 300, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
158 153 0.51
159 147 0.49
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (158 bp):
ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTAATATGTTATAATAACAAATTAAGT
AATTAACCTATTTTATTATATAAGTGCT
Found at i:619231 original size:159 final size:158
Alignment explanation
Indices: 618885--619343 Score: 729
Period size: 159 Copynumber: 2.9 Consensus size: 158
618875 ATAATGCGCA
* * * ** *
618885 ACCTATTACGTTATATAAGCGCTACCTAATATATTATTATGTTTGATAATGTTTCCAGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
* *
618950 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTATCTAATATGTTGTAATAACAAATTAAGT
66 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTAATATGTTATAATAACAAATTAAGT
*
619015 AATTAACCTATTTTATTATATAAGTGCT
131 AATTAACCTATTTTATTATATAAGTACT
*
619043 ACCTATTACGTTATATAAACGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
*
619108 TCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTATATATGTTATAATAACAAATTAAG
66 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTA-ATATGTTATAATAACAAATTAAG
*
619173 TAATTAATCTATTTTATTATATAAGTACT
130 TAATTAACCTATTTTATTATATAAGTACT
* * *
619202 ACCTATTACGTTATATAAGCGCTATCTAATATGTTATTGTGCTTGATACTATTAACGGTAATTAA
1 ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
* * * * *
619267 CCGGTTATGTTATCCTTAGTAACATTTTAGGCGTTTACCTAATATGTTATAACAACAAATTAAAT
66 CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTAATATGTTATAATAACAAATTAAGT
619332 AATTAACCTATT
131 AATTAACCTATT
619344 AGGTTATATA
Statistics
Matches: 277, Mismatches: 23, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
158 130 0.47
159 147 0.53
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.42
Consensus pattern (158 bp):
ACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGTTTGATAATATTAACGGTAATTAA
CCGATTATGTTATCCTTGGTAACATTTTAGGCGTTTAACTAATATGTTATAATAACAAATTAAGT
AATTAACCTATTTTATTATATAAGTACT
Found at i:624775 original size:15 final size:15
Alignment explanation
Indices: 624755--624857 Score: 76
Period size: 15 Copynumber: 7.3 Consensus size: 15
624745 ATTATCGATG
624755 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
624770 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* *
624785 -A-TATTAT-T-GAT
1 AATTTTTATATAAAT
624796 GAATTTTTATATAAAT
1 -AATTTTTATATAAAT
*
624812 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
* ** *
624827 -A-TATTAT-CGATT
1 AATTTTTATATAAAT
624839 AATTTTTATATAAAT
1 AATTTTTATATAAAT
624854 AATT
1 AATT
624858 AGAATTTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 16
0.69 0.15 0.17
Matches are distributed among these distances:
11 2 0.03
12 3 0.05
13 12 0.18
14 12 0.18
15 35 0.53
16 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:624780 original size:21 final size:21
Alignment explanation
Indices: 624756--624822 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 21
624746 TTATCGATGA
624756 ATTTTTATATAAATAATTTTT
1 ATTTTTATATAAATAATTTTT
* * * **
624777 A--TTTAAATATATTATTGATGA
1 ATTTTTATATAAATAATT--TTT
624798 ATTTTTATATAAATAATTTTT
1 ATTTTTATATAAATAATTTTT
624819 ATTT
1 ATTT
624823 AAATATATTA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 12 0.38
21 8 0.25
23 12 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (21 bp):
ATTTTTATATAAATAATTTTT
Found at i:624789 original size:42 final size:42
Alignment explanation
Indices: 624740--624857 Score: 218
Period size: 42 Copynumber: 2.8 Consensus size: 42
624730 ATAATAAAAT
624740 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
*
624782 AATATATTATTGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
*
624824 AATATATTATCGATTAATTTTTATATAAATAATT
1 AATATATTATCGATGAATTTTTATATAAATAATT
624858 AGAATTTCAC
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
Done.