Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006571.1 Hibiscus syriacus cultivar Beakdansim tig00016085_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: 72487
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:2863 original size:15 final size:15
Alignment explanation
Indices: 2840--2877 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2830 TAACTTCATT
*
2840 GGAGCCATTTGATAC
1 GGAGCCATTCGATAC
*
2855 GGAGTCATTCGATAC
1 GGAGCCATTCGATAC
2870 GGAGCCAT
1 GGAGCCAT
2878 AAAAACAGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (15 bp):
GGAGCCATTCGATAC
Found at i:5429 original size:60 final size:60
Alignment explanation
Indices: 5359--5733 Score: 531
Period size: 60 Copynumber: 6.2 Consensus size: 60
5349 TACATTGTTC
* *
5359 TAACTTTTCATCTAACTTGTATTAGTGGCACCTTTTTGCCAAAATGCACCA-TTAGGCATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCA-CAGTTAGGCATT
* * *
5419 GAACTTTTCATCTAACTTGCATTTGTGGCACCTTTCTGCCAAAATGCACAGTTAGACATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATT
* * *
5479 TAA-TATTTCATCTAACTTGAATTAGTGGCACCTTTCTACCAAAATGCATAGTTAGGCATT
1 TAACT-TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATT
* * * *
5539 TAACTTTTCATCTAACTTGCATTAGTGCCACATTTCTGTCAAAATGCACAGTTAGACATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATT
* *
5599 TAATTTTTCATCTAACTTGCATTAGTGGCACCTTTTCTTCCAAAATGCACAG-TAGGCATT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACC-TTTCTGCCAAAATGCACAGTTAGGCATT
* * * * *
5659 TAACTTTTCATCTAACTTGCATTAGTGGCATCTTTATGCTAAAATGCACAATTAGGCAAT
1 TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATT
5719 TAACTTTTCATCTAA
1 TAACTTTTCATCTAA
5734 TAGCAGTTCC
Statistics
Matches: 279, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
59 18 0.06
60 243 0.87
61 18 0.06
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (60 bp):
TAACTTTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACAGTTAGGCATT
Found at i:5689 original size:32 final size:32
Alignment explanation
Indices: 5595--5689 Score: 83
Period size: 32 Copynumber: 3.1 Consensus size: 32
5585 CACAGTTAGA
*
5595 CATTTAATTTTTCATCTAACTTGCATTAGTGG
1 CATTTAACTTTTCATCTAACTTGCATTAGTGG
* * * ** *
5627 C----ACCTTTTCTTCCAAAATGCA-CAGTAGG
1 CATTTAACTTTTCATCTAACTTGCATTAGT-GG
5655 CATTTAACTTTTCATCTAACTTGCATTAGTGG
1 CATTTAACTTTTCATCTAACTTGCATTAGTGG
5687 CAT
1 CAT
5690 CTTTATGCTA
Statistics
Matches: 44, Mismatches: 13, Indels: 12
0.64 0.19 0.17
Matches are distributed among these distances:
27 3 0.07
28 17 0.39
32 21 0.48
33 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (32 bp):
CATTTAACTTTTCATCTAACTTGCATTAGTGG
Found at i:11017 original size:31 final size:31
Alignment explanation
Indices: 10980--11039 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
10970 CTTCCCCTAG
10980 TTTTCTCGAACACTAAAGATCAAAACTTAGT
1 TTTTCTCGAACACTAAAGATCAAAACTTAGT
* *
11011 TTTTCTCGAACATTAAGGATCAAAACTTA
1 TTTTCTCGAACACTAAAGATCAAAACTTA
11040 AAAAATAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (31 bp):
TTTTCTCGAACACTAAAGATCAAAACTTAGT
Found at i:23213 original size:3 final size:3
Alignment explanation
Indices: 23200--23294 Score: 50
Period size: 3 Copynumber: 32.3 Consensus size: 3
23190 AAACATAAGC
* * ** ** ** *
23200 AAT ATT AAT AAT AAT ACT AAT AAT AAT TTT AAT TTT AAT TGT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
23248 AAT AAT AAT AAT AGT TAT AAT -AT CAT ATT AAT AAT TAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23294 A
1 A
23295 TTTATAACCC
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (3 bp):
AAT
Found at i:23232 original size:12 final size:12
Alignment explanation
Indices: 23200--23301 Score: 56
Period size: 12 Copynumber: 8.9 Consensus size: 12
23190 AAACATAAGC
23200 AATATTAATAAT
1 AATATTAATAAT
*
23212 AATACTAATAAT
1 AATATTAATAAT
* **
23224 AATTTTAATTTT
1 AATATTAATAAT
*
23236 AAT-TGTTATAAT
1 AATAT-TAATAAT
*
23248 AATAATAATAAT
1 AATATTAATAAT
*
23260 AGT-TATAAT-AT
1 AATAT-TAATAAT
*
23271 CATATTAATAAT
1 AATATTAATAAT
23283 --TA-TAAT-AT
1 AATATTAATAAT
*
23291 AATATTTATAA
1 AATATTAATAA
23302 CCCGGACAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
8 2 0.03
9 4 0.06
10 4 0.06
11 11 0.17
12 45 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (12 bp):
AATATTAATAAT
Found at i:23285 original size:20 final size:20
Alignment explanation
Indices: 23241--23301 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
23231 ATTTTAATTG
* *
23241 TTATAATAATAATAATAATAG
1 TTATAAT-ATAATATTAATAA
*
23262 TTATAATATCATATTAATAA
1 TTATAATATAATATTAATAA
*
23282 TTATAATATAATATTTATAA
1 TTATAATATAATATTAATAA
23302 CCCGGACAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 28 0.80
21 7 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TTATAATATAATATTAATAA
Found at i:23510 original size:53 final size:52
Alignment explanation
Indices: 23449--23578 Score: 172
Period size: 53 Copynumber: 2.4 Consensus size: 52
23439 CCTCTTCTTT
* *
23449 GAACAATCTTCGACC-AGTGGGTTCACTCCCTCTTGCTTCAGGGAGTAGAACTC
1 GAACAATCTTCG-CCTA-CGGGTTCACTCCCTCTTACTTCAGGGAGTAGAACTC
* *
23502 GAACAATCTTTTGCCTACGGGTTTACTCCCTCTTACTTCAGGGAGTAGAACTC
1 GAACAATC-TTCGCCTACGGGTTCACTCCCTCTTACTTCAGGGAGTAGAACTC
*
23555 GAACAATCTTCTTCCTACGGGTTC
1 GAACAATCTTC-GCCTACGGGTTC
23579 GCTTCACTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
52 2 0.03
53 61 0.91
54 4 0.06
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (52 bp):
GAACAATCTTCGCCTACGGGTTCACTCCCTCTTACTTCAGGGAGTAGAACTC
Found at i:24056 original size:36 final size:36
Alignment explanation
Indices: 24000--24087 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
23990 ATCATGCTCG
* *
24000 GAAGGCTTACTGATGGTTTGCTTCACTACTCTTCCGT
1 GAAGGCTTAAT-ATGGTTTGCATCACTACTCTTCCGT
24037 GAAGGCTTAATATGGTTTGCATCACTACTCTTCCGT
1 GAAGGCTTAATATGGTTTGCATCACTACTCTTCCGT
*
24073 GAAGGCTTAAGATGG
1 GAAGGCTTAATATGG
24088 CCCGGAAGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 38 0.79
37 10 0.21
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (36 bp):
GAAGGCTTAATATGGTTTGCATCACTACTCTTCCGT
Found at i:24100 original size:114 final size:114
Alignment explanation
Indices: 23896--24131 Score: 350
Period size: 114 Copynumber: 2.1 Consensus size: 114
23886 TCTGATGATA
* * *
23896 TGATGGTTTACTCCAACACTCTTCCGAGAAGGCTTAAAATGGTTAGCTTTATTACTCTTCCGTGA
1 TGATGGTTTACTCCAACACTCTTCCGAGAAGGCTTAAAATGGTTAGCATCACTACTCTTCCGTGA
*
23961 ATGCTTAAGATGGCCCAGAGAACTTAATCATCATGCTCGGAAGGCTTAC
66 AGGCTTAAGATGGCCCAGAGAACTTAATCATCATGCTCGGAAGGCTTAC
* * * * *
24010 TGATGGTTTGCTTC-ACTACTCTTCCGTGAAGGCTTAATATGGTTTGCATCACTACTCTTCCGTG
1 TGATGGTTTACTCCAAC-ACTCTTCCGAGAAGGCTTAAAATGGTTAGCATCACTACTCTTCCGTG
*
24074 AAGGCTTAAGATGGCCCGGA-AGACTTAATCATCATGCTCGGAAGGCTTAC
65 AAGGCTTAAGATGGCCCAGAGA-ACTTAATCATCATGCTCGGAAGGCTTAC
24124 TGATGGTT
1 TGATGGTT
24132 CAAAAGACTT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
113 3 0.03
114 107 0.97
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (114 bp):
TGATGGTTTACTCCAACACTCTTCCGAGAAGGCTTAAAATGGTTAGCATCACTACTCTTCCGTGA
AGGCTTAAGATGGCCCAGAGAACTTAATCATCATGCTCGGAAGGCTTAC
Found at i:24116 original size:22 final size:22
Alignment explanation
Indices: 24093--24164 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
24083 GATGGCCCGG
*
24093 AAGACTTAATCATCATGCTCGG
1 AAGACTTAATCATCATGCTCGA
* * * *
24115 AAGGCTT-A-C-TGATGGTTCAA
1 AAGACTTAATCATCAT-GCTCGA
*
24135 AAGACTTCATCATCATGCTCGA
1 AAGACTTAATCATCATGCTCGA
24157 AAGACTTA
1 AAGACTTA
24165 CTGATGGCAC
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
19 3 0.08
20 10 0.28
21 2 0.06
22 18 0.50
23 3 0.08
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (22 bp):
AAGACTTAATCATCATGCTCGA
Found at i:24178 original size:13 final size:13
Alignment explanation
Indices: 24160--24184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24150 TGCTCGAAAG
24160 ACTTACTGATGGC
1 ACTTACTGATGGC
24173 ACTTACTGATGG
1 ACTTACTGATGG
24185 GATTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:24271 original size:42 final size:42
Alignment explanation
Indices: 24225--24305 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
24215 ACAAATTACC
**
24225 CGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGACA
1 CGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATGACA
* *
24267 CGAAGGATTTAAGAATCGTGCTCGAAAGACTTACTGATG
1 CGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATG
24306 GGATTACTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (42 bp):
CGAAGGATTTAAGAATCATGCTCAAAAGACTTACTGATGACA
Found at i:24377 original size:42 final size:42
Alignment explanation
Indices: 24330--24421 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
24320 CTCTTCCGTG
* * *
24330 AAGGCTTAC-AAATTACCCGAAGGATTTAATCATCATGCTCGA
1 AAGGCTTACTAAA-GACCCCAAGGATTTAAGCATCATGCTCGA
*
24372 AAGGCTTACTGAAGACCCCAAGGATTTAAGCATCATGCTCGA
1 AAGGCTTACTAAAGACCCCAAGGATTTAAGCATCATGCTCGA
*
24414 AAGACTTA
1 AAGGCTTA
24422 TTGATGGCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (42 bp):
AAGGCTTACTAAAGACCCCAAGGATTTAAGCATCATGCTCGA
Found at i:24395 original size:122 final size:122
Alignment explanation
Indices: 24173--24428 Score: 422
Period size: 122 Copynumber: 2.1 Consensus size: 122
24163 TACTGATGGC
*
24173 ACTTACTGATGGGATTGCTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGGATTACTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
* * *
24238 CATCATGCTCAAAAGACTTACTGATGACACGAAGGATTTAAGAATCGTGCTCGAAAG
66 CATCATGCTCAAAAGACTTACTGAAGACACCAAGGATTTAAGAATCATGCTCGAAAG
*
24295 ACTTACTGATGGGATTACTTCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
1 ACTTACTGATGGGATTACTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
* * * *
24360 CATCATGCTCGAAAGGCTTACTGAAGACCCCAAGGATTTAAGCATCATGCTCGAAAG
66 CATCATGCTCAAAAGACTTACTGAAGACACCAAGGATTTAAGAATCATGCTCGAAAG
*
24417 ACTTATTGATGG
1 ACTTACTGATGG
24429 CCCGAAGGAC
Statistics
Matches: 124, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
122 124 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (122 bp):
ACTTACTGATGGGATTACTTCACTACTCTTCCATGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCATGCTCAAAAGACTTACTGAAGACACCAAGGATTTAAGAATCATGCTCGAAAG
Found at i:24437 original size:42 final size:42
Alignment explanation
Indices: 24344--24437 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
24334 CTTACAAATT
* *
24344 ACCCGAAGGATTTAATCATCATGCTCGAAAGGCTTACTGAAG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGAAG
* * *
24386 ACCCCAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATG
1 ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGAAG
*
24428 GCCCGAAGGA
1 ACCCGAAGGA
24438 CTTAGTAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (42 bp):
ACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGAAG
Found at i:30715 original size:12 final size:12
Alignment explanation
Indices: 30694--30739 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
30684 AAGCTAATAA
30694 GAATGCAAATGT
1 GAATGCAAATGT
* *
30706 GAATGAAAATGA
1 GAATGCAAATGT
*
30718 AAATGCAAATGT
1 GAATGCAAATGT
30730 GAATGCAAAT
1 GAATGCAAAT
30740 ACAAATGCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.50, C:0.07, G:0.22, T:0.22
Consensus pattern (12 bp):
GAATGCAAATGT
Found at i:30722 original size:24 final size:24
Alignment explanation
Indices: 30695--30748 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
30685 AGCTAATAAG
30695 AATGCAAATGTGAATGAAAATGA-A
1 AATGCAAATGTGAATGAAAAT-ACA
*
30719 AATGCAAATGTGAATGCAAATACA
1 AATGCAAATGTGAATGAAAATACA
30743 AATGCA
1 AATGCA
30749 CAAGGTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.20
Consensus pattern (24 bp):
AATGCAAATGTGAATGAAAATACA
Found at i:34036 original size:3 final size:3
Alignment explanation
Indices: 34023--34117 Score: 50
Period size: 3 Copynumber: 32.3 Consensus size: 3
34013 AAACATAAAC
* * * * ** ** *
34023 AAT ATT AAT AAT AAT ACT ATT AAT AAT TAT AAT TTT AAT TGT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
34071 AAT AAC AAT AAT AGT TAT AAT -AT AAT ATT AAT AAT TAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34117 A
1 A
34118 TTTATAACCC
Statistics
Matches: 65, Mismatches: 25, Indels: 4
0.69 0.27 0.04
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:34124 original size:20 final size:20
Alignment explanation
Indices: 34045--34124 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
34035 AATACTATTA
* **
34045 ATAATTATAATTTTAATTGTT
1 ATAA-TATAATATTAATAATT
* * *
34066 ATAATAATAACAATAATAGTT
1 ATAAT-ATAATATTAATAATT
34087 ATAATATAATATTAATAATT
1 ATAATATAATATTAATAATT
*
34107 ATAATATAATATTTATAA
1 ATAATATAATATTAATAA
34125 CCCGGACAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 30 0.60
21 20 0.40
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (20 bp):
ATAATATAATATTAATAATT
Found at i:35501 original size:35 final size:35
Alignment explanation
Indices: 35427--35526 Score: 103
Period size: 36 Copynumber: 2.7 Consensus size: 35
35417 TTTCGTCCTA
*
35427 CTAGGATTCAAACT-CTCAAGAATATGATAGAATTCTG
1 CTAGGATTC-AACTCCT-AA-AATAGGATAGAATTCTG
*
35464 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
35499 CTATGTTTTAAACTCCTAAATATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
35527 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
35 18 0.33
36 19 0.35
37 18 0.33
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:35957 original size:11 final size:11
Alignment explanation
Indices: 35937--36023 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
35927 TTAATTATTT
*
35937 TTATTCTAATA
1 TTATTTTAATA
*
35948 TTATTTTAATG
1 TTATTTTAATA
*
35959 TTTTTTTAA-A
1 TTATTTTAATA
35969 GTTATTATATATATA
1 -TTATT-T-TA-ATA
35984 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
35998 TTATATTTATTA
1 TTAT-TTTAATA
*
36010 TTATTTTACTA
1 TTATTTTAATA
36021 TTA
1 TTA
36024 ACATATATAA
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
11 30 0.49
12 7 0.11
13 8 0.13
14 11 0.18
15 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:36215 original size:16 final size:16
Alignment explanation
Indices: 36194--36227 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
36184 CATGTATTTA
36194 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
36210 TATTATTTTACTTTAT
1 TATTATATTACATTAT
36226 TA
1 TA
36228 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:36232 original size:21 final size:22
Alignment explanation
Indices: 36208--36258 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
36198 ATATTACATT
*
36208 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
36229 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
36251 TTTATTAT
1 ATTATTAT
36259 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:40952 original size:21 final size:21
Alignment explanation
Indices: 40928--40989 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
40918 AACAAAAAGG
40928 GCAAAAAGAAAAAAAAAAGAA
1 GCAAAAAGAAAAAAAAAAGAA
* *
40949 GCAAAAAGGAAAAAATAAGAA
1 GCAAAAAGAAAAAAAAAAGAA
40970 -CAAAAAAGAAAGAACAAAAA
1 GC-AAAAAGAAA-AA-AAAAA
40990 TAAAAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 27 0.79
22 2 0.06
23 4 0.12
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (21 bp):
GCAAAAAGAAAAAAAAAAGAA
Found at i:41634 original size:22 final size:22
Alignment explanation
Indices: 41606--41656 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
41596 CCCCATCAAT
41606 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
**
41628 CCTTTGAGCATCAAATGTCAAA
1 CCTTTGAGCATCAAATACCAAA
41650 CCTTTGA
1 CCTTTGA
41657 CCAAACACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:42604 original size:37 final size:37
Alignment explanation
Indices: 42510--42619 Score: 150
Period size: 37 Copynumber: 3.0 Consensus size: 37
42500 GTGCTCACCA
*
42510 TTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* *
42546 TTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
42583 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
42620 ATTGAAAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 29 0.45
37 32 0.50
38 3 0.05
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:42704 original size:102 final size:102
Alignment explanation
Indices: 42528--42985 Score: 781
Period size: 102 Copynumber: 4.5 Consensus size: 102
42518 CTTGAGATAG
** * * * *
42528 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTTAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
42593 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAATA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
42630 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
42695 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
42732 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
42797 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
42834 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
42899 TAAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
42936 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
42986 TAAACATTGA
Statistics
Matches: 336, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 336 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:42705 original size:37 final size:37
Alignment explanation
Indices: 42646--42920 Score: 159
Period size: 37 Copynumber: 7.9 Consensus size: 37
42636 TTGAAATGAG
*
42646 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
42683 TTTCGTCTCCATTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
42721 ---------CATTGGAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATT-GAGACAGTTTCCCTTGAAACAAAA
*
42748 TTTTGTCTCTC-TTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* *
42785 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA-AAA
* **
42823 ---------CATTGAAAACA-TTTCCCTTGAAA-TGAA
1 TTTTGTCTCCATTG-AGACAGTTTCCCTTGAAACAAAA
* *
42850 TTTTGTCTCTC-TTGAGATAGTTTCCCTCGAAACAAAA
1 TTTTGTCTC-CATTGAGACAGTTTCCCTTGAAACAAAA
* * *
42887 TTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACA
42921 TAAACATTGA
Statistics
Matches: 180, Mismatches: 27, Indels: 62
0.67 0.10 0.23
Matches are distributed among these distances:
27 4 0.02
29 30 0.17
30 9 0.05
35 7 0.04
36 31 0.17
37 93 0.52
38 6 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
TTTTGTCTCCATTGAGACAGTTTCCCTTGAAACAAAA
Found at i:42975 original size:65 final size:65
Alignment explanation
Indices: 42885--43050 Score: 296
Period size: 65 Copynumber: 2.6 Consensus size: 65
42875 CTCGAAACAA
* * *
42885 AATTTTGTCTCCCTTAAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
*
42950 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
43015 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACA
43051 AAATTTTGTC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 96 1.00
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (65 bp):
AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:42986 original size:167 final size:169
Alignment explanation
Indices: 42768--43085 Score: 532
Period size: 167 Copynumber: 1.9 Consensus size: 169
42758 CTTGAGATAG
*
42768 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
42833 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
42898 TTAAGACAG-TTTCTCTTGAAACATAAACATTGAAAACA
131 TTAAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
** * *
42936 TTTCCCTTGAAA-TGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
43000 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
*
43065 TTGAGACAGTTTTCTCTTGAA
131 TTAAGACAGTTTTCTCTTGAA
43086 GCATCATCTT
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 116 0.83
168 23 0.17
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
TTAAGACAGTTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:43823 original size:98 final size:98
Alignment explanation
Indices: 43582--44447 Score: 725
Period size: 98 Copynumber: 8.4 Consensus size: 98
43572 TAGCTAGAGT
* *
43582 CAATTTCGACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * * *
43647 GGACGGCTGGTTGTCAACAATAATTTCCCAGTTTCAGTGC
66 GGACGGCTGATTGTCAAC-A-AA-----CAATTTCGGAGC
* * * * * *
43687 CAATTTCAACTTCACGGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * *
43752 GGGCGGCTGACTGTCGACAAACAATTTCGGAGC
66 GGACGGCTGATTGTCAACAAACAATTTCGGAGC
* * * * * *
43785 CAATCTCAACTTCACAGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * * *
43850 GGGCGGCTGACTGTCGACAAGCAATTTCGGAGC
66 GGACGGCTGATTGTCAACAAACAATTTCGGAGC
* * *
43883 CAATCTCAACTTCACAGCGAAGGATATTGGATTCGAGACAACACAAGTTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * *
43948 GGACAGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGC
66 GGACGGCTGATTGTCAACAAACAA--T-----TT-CGGAGC
* * * *
43989 CGATTTCAACTCCA-AGACGGAGGATATCGTG-CTACCTGAGACAACACAAGTTCAACTTCACAA
1 CAATTTCAACTTCACAG-CGAAGGATATTG-GACT--C-GAGACAACACAAGTTCAACTTCACAA
* * *
44052 CGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGGTTCATC
61 CGAAGGGACGGCTGATTGTCAACAAACAA--TTTC-GG---AGC
* * * *
44096 TGCGATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAACTTCACA
1 --CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACA
* * *
44160 ACGAAGGGACGGCTGGTTGTCAACAAATATTTTTTAAATTTCAGAGC
60 ACGAAGGGACGGCTGATTGTCAAC-AA-A------CAATTTCGGAGC
* *
44207 CAATTTCAACTTCGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAAATTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * *
44272 GGATGGCTGATTGTCAAC-AA-GATTTCGTTCAGAGT
66 GGACGGCTGATTGTCAACAAACAATTTCG----GAGC
* * *
44307 CAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* *
44372 GGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAAC
66 GGACGGCTGATTGTCAACAAACAATTT--CGG----AG--C
*
44413 CAATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCG
44448 GAACAATATT
Statistics
Matches: 643, Mismatches: 72, Indels: 91
0.80 0.09 0.11
Matches are distributed among these distances:
96 5 0.01
98 182 0.28
100 80 0.12
101 2 0.00
102 4 0.01
103 4 0.01
104 9 0.01
105 75 0.12
106 110 0.17
107 5 0.01
108 1 0.00
109 150 0.23
110 3 0.00
111 4 0.01
112 2 0.00
114 1 0.00
115 4 0.01
117 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (98 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
GGACGGCTGATTGTCAACAAACAATTTCGGAGC
Found at i:44390 original size:424 final size:409
Alignment explanation
Indices: 43616--44439 Score: 1026
Period size: 424 Copynumber: 2.0 Consensus size: 409
43606 TATTGGACTC
* *
43616 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAATAATTTCCCAGTTT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGGTT
* * * * *
43681 CAGTGCCAATTTCAACTTCACGGCGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACA
66 CACTGCCAATTTCAACTCCACGACGAAGGATATTGCACCCAAGACAACACAAGCTCAACTTCACA
* * * * *
43746 GCGAAGGGGCGGCTGACTGTCGACAAACAATTTCGGAGCCAATCTCAACTTCACAGCGAAGGATA
131 ACGAAGGGACGGCTGACTGTCAACAAAAAATTTCAGAGCCAATCTCAACTTCACAGCGAAGGATA
* * * * *
43811 TTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATT
196 TTGGACCCAAGACAACACAAGCTCAAATTCACAACGAAGGGACGGCTGACTGTCAACAAG-AATT
* * *
43876 TCGGAGCCAATCTCAACTTCACAGCGAAGGATATTGGATTCGAGACAACACAAGTTCAACTTCAC
260 TCGGAGCCAATCTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCAC
** * *
43941 AGCGAAGGGACAGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGCCGATTTCAACTCCA-AG
325 AGCGAAGGGACAGCTGACTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTCCACAG
44005 ACGGAGGATATCGTGCTACCT
390 -CGGAGGATATCGTGCTACCT
*
44026 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACGAACAACTTT-TCAGG
1 GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAA-TTTCCCAGG
* * * * *
44090 TTCATCTG-CGATTTCAACTCCACGACGGAGGATATCGTGCCACTCGAGACAACACAAGTTCAAC
64 TTCA-CTGCCAATTTCAACTCCACGACGAAGGATAT--TG-CACCCAAGACAACACAAGCTCAAC
** *
44154 TTCACAACGAAGGGACGGCTGGTTGTCAACAAATATTTTTTAAATTTCAGAGCCAATTTCAACTT
125 TTCACAACGAAGGGACGGCTGACTGTCAAC-AA-A------AAATTTCAGAGCCAATCTCAACTT
* * * * * *
44219 CGCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAAATTCACAACGAAGGGATGGCTGATT
182 CACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAAATTCACAACGAAGGGACGGCTGACT
* *
44284 GTCAACAAG-ATTTCGTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAA
247 GTCAACAAGAATTTCG----GAGCCAATCTCAACTTCACAGCGAAGGATATTAGACTCGAGACAA
* * **
44348 CACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCCAGAAC
308 CACAAGCTCAACTTCACAGCGAAGGGACAGCTGACTGTCAACAAACAATTTCCCAATTCCAGAAC
*
44413 CAATTTCAACTTCACAGCGGAGGATAT
373 CAATTTCAACTCCACAGCGGAGGATAT
44440 TGGACTCGGA
Statistics
Matches: 349, Mismatches: 46, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
410 49 0.14
411 34 0.10
412 5 0.01
413 2 0.01
414 44 0.13
415 2 0.01
416 1 0.00
420 6 0.02
422 84 0.24
424 120 0.34
425 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (409 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCCCAGGTT
CACTGCCAATTTCAACTCCACGACGAAGGATATTGCACCCAAGACAACACAAGCTCAACTTCACA
ACGAAGGGACGGCTGACTGTCAACAAAAAATTTCAGAGCCAATCTCAACTTCACAGCGAAGGATA
TTGGACCCAAGACAACACAAGCTCAAATTCACAACGAAGGGACGGCTGACTGTCAACAAGAATTT
CGGAGCCAATCTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACA
GCGAAGGGACAGCTGACTGTCAACAAACAATTTCCCAATTCCAGAACCAATTTCAACTCCACAGC
GGAGGATATCGTGCTACCT
Found at i:44973 original size:35 final size:35
Alignment explanation
Indices: 44908--45007 Score: 112
Period size: 35 Copynumber: 2.7 Consensus size: 35
44898 TTTCGTCCTA
44908 CTAGGATTCAAACT-CTCAAGAATAGGATAGAATTCTG
1 CTAGGATTC-AACTCCT-AA-AATAGGATAGAATTCTG
*
44945 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
44980 CTATGTTTTAAACTCCTAAATATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
45008 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
35 19 0.34
36 19 0.34
37 18 0.32
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:45697 original size:16 final size:16
Alignment explanation
Indices: 45676--45709 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45666 CATGTATTTA
45676 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
45692 TATTATTTTACTTTAT
1 TATTATATTACATTAT
45708 TA
1 TA
45710 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:45714 original size:21 final size:22
Alignment explanation
Indices: 45690--45740 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
45680 ATATTACATT
*
45690 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
* *
45711 ATTATTTTTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
45733 TTTATTAT
1 ATTATTAT
45741 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:45745 original size:2 final size:2
Alignment explanation
Indices: 45729--45767 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
45719 TTTTCGTTAT
*
45729 TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- 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
45768 CATAATATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:48353 original size:37 final size:38
Alignment explanation
Indices: 48303--48385 Score: 159
Period size: 37 Copynumber: 2.2 Consensus size: 38
48293 TTTGACTTAT
48303 GACCTCCATTCCTTCCTTTTCTTC-TTTTGTTTATATC
1 GACCTCCATTCCTTCCTTTTCTTCTTTTTGTTTATATC
48340 GACCTCCATTCCTTCCTTTTCTTCTTTTTGTTTATATC
1 GACCTCCATTCCTTCCTTTTCTTCTTTTTGTTTATATC
48378 GACCTCCA
1 GACCTCCA
48386 ACAATCTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 24 0.53
38 21 0.47
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.51
Consensus pattern (38 bp):
GACCTCCATTCCTTCCTTTTCTTCTTTTTGTTTATATC
Found at i:49541 original size:22 final size:23
Alignment explanation
Indices: 49515--49558 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
49505 TCGATCTATT
*
49515 AATTTTATCACT-TAATTATTTA
1 AATTTTATCAATCTAATTATTTA
49537 AATTTTATCAATCTAATTATTT
1 AATTTTATCAATCTAATTATTT
49559 GTTGTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (23 bp):
AATTTTATCAATCTAATTATTTA
Found at i:49851 original size:22 final size:22
Alignment explanation
Indices: 49820--49863 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
49810 AATAATTTTT
49820 TTATAATAAAT-AATATTAATTA
1 TTATAATAAATAAATA-TAATTA
*
49842 TTATATTAAATAAATATAATTA
1 TTATAATAAATAAATATAATTA
49864 ATCATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTATAATAAATAAATATAATTA
Found at i:49878 original size:26 final size:26
Alignment explanation
Indices: 49824--49878 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
49814 ATTTTTTTAT
* *
49824 AATAAATAATATTAATTATTATATTA
1 AATAAATAATATTAATCATTATATAA
*
49850 AATAAAT-ATAATTAATCATTTTATAA
1 AATAAATAAT-ATTAATCATTATATAA
49876 AAT
1 AAT
49879 TACCAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAATAATATTAATCATTATATAA
Found at i:53349 original size:136 final size:136
Alignment explanation
Indices: 53056--53682 Score: 842
Period size: 138 Copynumber: 4.6 Consensus size: 136
53046 ACTATTCACA
* ** *
53056 TGAAGGCGCGTTCCCGGAGAAGCTCCTTTCATTATTTTGTCACAGAGAATATGTTATCATTGCCC
1 TGAAAGCGCGTTCCCGG-GGGGCACCTTTCATTATTTTGT--CAGAGAATATGTTATCATTGCCC
* * * * *
53121 TATTATGTCAGTCATGTCCCCAGGAAACTATTCATATCAGTACCTATTATTTTTTAGGAGACTTG
63 TATTATGTCACTCATGTCCCCCGGAAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTG
53186 GCAAAGTGG
128 GCAAAGTGG
* ** * *
53195 TGAAAGCGCATTTTCGGGGGGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTAT
1 TGAAAGCGCGTTCCCGGGGGGCACCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
53260 TATGTCACTCATGTCCCCCGGAAACTATTCATATTAGTACCTATTATTTCTGAGGGGACTTGGCA
66 TATGTCACTCATGTCCCCCGGAAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGGCA
53325 AAGTGG
131 AAGTGG
*
53331 TGAAAGCGCGTTCCCGGGGGTGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGGGGG-GCACCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * * * *
53396 TTATGTCACTCATGTCTCCCGGGGAACTATTCATGTTAGAACCTATTATTTCTGAGAGGACTTGG
65 TTATGTCACTCATGTC-CCCCGGAAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGG
53461 CAAAGTGG
129 CAAAGTGG
* * * *
53469 TGAAAACGCGTTCCCGGGGGCGCACCTTTTATTATTTTGTCAGAGAATATATTATCATTGTCCTA
1 TGAAAGCGCGTTCCCGGGGG-GCACCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* ** * * * * *
53534 TTATGTCATTTTTGTCTCCCGGAGAACTATTCATGTCCGTACCTATTATTT-TTAGGGGACTTGA
65 TTATGTCACTCATGTCCCCCGGA-AACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGG
53598 CAAAGTGG
129 CAAAGTGG
* * * *
53606 TGAAAGCGCGTTCTCGGGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTAT
1 TGAAAGCGCGTTCCCGGGGGGCACCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
53671 TATGTCACTCAT
66 TATGTCACTCAT
53683 ATTCCCCAGA
Statistics
Matches: 430, Mismatches: 55, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
136 155 0.36
137 97 0.23
138 165 0.38
139 13 0.03
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (136 bp):
TGAAAGCGCGTTCCCGGGGGGCACCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCCCGGAAACTATTCATATCAGTACCTATTATTTCTGAGGGGACTTGGCA
AAGTGG
Found at i:53593 original size:275 final size:272
Alignment explanation
Indices: 53056--53691 Score: 889
Period size: 275 Copynumber: 2.3 Consensus size: 272
53046 ACTATTCACA
* ** *
53056 TGAAGGCGCGTTCCCGGAGAAGCTCCTTTCATTATTTTGTCACAGAGAATATGTTATCATTGCCC
1 TGAAAGCGCGTTCCCGG-GGGGCGCCTTTCATTATTTTGT--CAGAGAATATGTTATCATTGCCC
* * * *
53121 TATTATGTCAGTCATGTCCCCAGGAAACTATTCATATCAGTACCTATTATTTTTTAGGAGACTTG
63 TATTATGTCACTCATGTCCCCAGGAAACTATTCATATCAGAACCTATTATTTCTGAGGAGACTTG
* ** *
53186 GCAAAGTGGTGAAAGCGCATTTTCGGGGGGCACCTTCCATTATTTTGTCAGAGAATATGTTATCA
128 GCAAAGTGGTGAAAACGCATTCCCGGGGGGCACCTTCCATTATTTTGTCAGAGAATATATTATCA
*
53251 TTGTCCTATTATGTCACTCATGTCCCCCGGAAACTATTCATATTAGTACCTATTATTTCTGAGGG
193 TTGTCCTATTATGTCACTCATGTCCCCCGGAAACTATTCATATCAGTACCTATTATTTCTGAGGG
*
53316 GACTTGGCAAAGTGG
258 GACTTGACAAAGTGG
53331 TGAAAGCGCGTTCCCGGGGGTGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAAGCGCGTTCCCGGGGG-GCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
* * * *
53396 TTATGTCACTCATGTCTCCCGGGGAACTATTCATGTTAGAACCTATTATTTCTGA-GAGGACTTG
65 TTATGTCACTCATGTC-CCCAGGAAACTATTCATATCAGAACCTATTATTTCTGAGGA-GACTTG
* **
53460 GCAAAGTGGTGAAAACGCGTTCCCGGGGGCGCACCTTTTATTATTTTGTCAGAGAATATATTATC
128 GCAAAGTGGTGAAAACGCATTCCCGGGGG-GCACCTTCCATTATTTTGTCAGAGAATATATTATC
* ** * * * *
53525 ATTGTCCTATTATGTCATTTTTGTCTCCCGGAGAACTATTCATGTCCGTACCTATTATTT-TTAG
192 ATTGTCCTATTATGTCACTCATGTCCCCCGGA-AACTATTCATATCAGTACCTATTATTTCTGAG
53589 GGGACTTGACAAAGTGG
256 GGGACTTGACAAAGTGG
* * *
53606 TGAAAGCGCGTTCTCGGGGGGCGCCTTCCATTATTTTGTCAGATAATATGTTATCATTGCCCTAT
1 TGAAAGCGCGTTCCCGGGGGGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
*
53671 TATGTCACTCATATTCCCCAG
66 TATGTCACTCAT-GTCCCCAG
53692 AGACGCAGAG
Statistics
Matches: 322, Mismatches: 33, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
273 42 0.13
274 122 0.38
275 134 0.42
276 24 0.07
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (272 bp):
TGAAAGCGCGTTCCCGGGGGGCGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTGCCCTAT
TATGTCACTCATGTCCCCAGGAAACTATTCATATCAGAACCTATTATTTCTGAGGAGACTTGGCA
AAGTGGTGAAAACGCATTCCCGGGGGGCACCTTCCATTATTTTGTCAGAGAATATATTATCATTG
TCCTATTATGTCACTCATGTCCCCCGGAAACTATTCATATCAGTACCTATTATTTCTGAGGGGAC
TTGACAAAGTGG
Found at i:53861 original size:23 final size:22
Alignment explanation
Indices: 53835--53939 Score: 76
Period size: 23 Copynumber: 4.9 Consensus size: 22
53825 TAAAGTTTGA
53835 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGGAT-AAATGTTATGG
* * *
53858 ATAAATTGAATAAATGTGAAGTG
1 ATAAATTGGATAAATGTTATG-G
* * *
53881 ATAAGTTGG-T---TGCT-TGA
1 ATAAATTGGATAAATGTTATGG
*
53898 ATAAATTGGATAAAATGCTATGG
1 ATAAATTGGAT-AAATGTTATGG
*
53921 ATAAATTGAATAAATGTTA
1 ATAAATTGGATAAATGTTA
53940 AGAGATAAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
17 8 0.13
18 2 0.03
19 2 0.03
22 20 0.32
23 30 0.48
ACGTcount: A:0.43, C:0.02, G:0.21, T:0.34
Consensus pattern (22 bp):
ATAAATTGGATAAATGTTATGG
Found at i:53909 original size:63 final size:63
Alignment explanation
Indices: 53831--53955 Score: 223
Period size: 63 Copynumber: 2.0 Consensus size: 63
53821 TATGTAAAGT
* *
53831 TTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTGC
1 TTGAATAAATTGGATAAAATGCTATGGATAAATTGAATAAATGTGAAGAGATAAGTTGGTTGC
*
53894 TTGAATAAATTGGATAAAATGCTATGGATAAATTGAATAAATGTTAAGAGATAAGTTGGTTG
1 TTGAATAAATTGGATAAAATGCTATGGATAAATTGAATAAATGTGAAGAGATAAGTTGGTTG
53956 TGACATTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (63 bp):
TTGAATAAATTGGATAAAATGCTATGGATAAATTGAATAAATGTGAAGAGATAAGTTGGTTGC
Found at i:53946 original size:23 final size:23
Alignment explanation
Indices: 53898--53947 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
53888 GGTTGCTTGA
* *
53898 ATAAATTGGATAAAATGCTATGG
1 ATAAATTGAATAAAATGCTAAGG
*
53921 ATAAATTGAAT-AAATGTTAAGAG
1 ATAAATTGAATAAAATGCTAAG-G
53944 ATAA
1 ATAA
53948 GTTGGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (23 bp):
ATAAATTGAATAAAATGCTAAGG
Found at i:54138 original size:19 final size:19
Alignment explanation
Indices: 54114--54192 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
54104 ACTATAATTA
54114 GAATATAACTTTT-AATTTC
1 GAATATAA-TTTTAAATTTC
54133 GAATATAATTTTAAATTTC
1 GAATATAATTTTAAATTTC
*
54152 -AAT-TGGAATATTAAATTT-
1 GAATAT--AATTTTAAATTTC
* *
54170 -AATTTAATGTTAAATTTC
1 GAATATAATTTTAAATTTC
54188 GAATA
1 GAATA
54193 CTATAATTTG
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
17 12 0.24
18 10 0.20
19 29 0.57
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.46
Consensus pattern (19 bp):
GAATATAATTTTAAATTTC
Found at i:54227 original size:34 final size:34
Alignment explanation
Indices: 54165--54244 Score: 110
Period size: 34 Copynumber: 2.4 Consensus size: 34
54155 TGGAATATTA
*
54165 AATTTA-A-TTTAATGTTAAATTTCGAATACTAT
1 AATTTATATTTTAATGTTAAATTTCAAATACTAT
* * *
54197 AATTTGTATTTTAATTTTAATTTTCAAATACTAT
1 AATTTATATTTTAATGTTAAATTTCAAATACTAT
54231 AATTTATATTTTAA
1 AATTTATATTTTAA
54245 AAACATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 5 0.12
33 1 0.02
34 35 0.85
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (34 bp):
AATTTATATTTTAATGTTAAATTTCAAATACTAT
Found at i:56434 original size:23 final size:24
Alignment explanation
Indices: 56398--56447 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
56388 ATAATTAATA
*
56398 TAAAAATATGATAAAT-TTAA-AT
1 TAAAAATATAATAAATATTAACAT
56420 TAAAAATAATAATAAATATTAACAT
1 TAAAAAT-ATAATAAATATTAACAT
56445 TAA
1 TAA
56448 TTATAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 4 0.17
25 5 0.21
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
TAAAAATATAATAAATATTAACAT
Found at i:56553 original size:21 final size:20
Alignment explanation
Indices: 56529--56569 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
56519 CACTTTCTAT
*
56529 TATAACTATAGACAAAAAATA
1 TATAACTA-ACACAAAAAATA
*
56550 TATAATTAACACAAAAAATA
1 TATAACTAACACAAAAAATA
56570 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (20 bp):
TATAACTAACACAAAAAATA
Found at i:56565 original size:20 final size:20
Alignment explanation
Indices: 56540--56578 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
56530 ATAACTATAG
56540 ACAAAAAAT-ATATAATTAAC
1 ACAAAAAATAAT-TAATTAAC
56560 ACAAAAAATAATTAATTAA
1 ACAAAAAATAATTAATTAA
56579 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAAC
Found at i:56629 original size:31 final size:31
Alignment explanation
Indices: 56562--56670 Score: 82
Period size: 31 Copynumber: 3.6 Consensus size: 31
56552 TAATTAACAC
* * *
56562 AAAAAATAATTA-ATTAATA-AATTTAAAT-
1 AAAAAATAATTATATAAATATTATTTTAATA
*
56590 AAATAATAATTATATAAATATTATTTTAATA
1 AAAAAATAATTATATAAATATTATTTTAATA
* * *
56621 AAAAAATAA-TATTTATATAATTATATTAATA
1 AAAAAATAATTATATAAAT-ATTATTTTAATA
* * *
56652 TAAAATATAAGTATTTAAA
1 -AAAAAATAATTATATAAA
56671 AAATACTAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
28 11 0.17
29 6 0.09
30 14 0.22
31 19 0.29
32 8 0.12
33 7 0.11
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAAAATAATTATATAAATATTATTTTAATA
Found at i:58854 original size:16 final size:16
Alignment explanation
Indices: 58835--58868 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
58825 CGGGTTCATG
* *
58835 TCGGATCATTTTCAGT
1 TCGGATCAATGTCAGT
58851 TCGGATCAATGTCAGT
1 TCGGATCAATGTCAGT
58867 TC
1 TC
58869 AGGTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (16 bp):
TCGGATCAATGTCAGT
Found at i:59562 original size:15 final size:15
Alignment explanation
Indices: 59544--59661 Score: 77
Period size: 13 Copynumber: 7.9 Consensus size: 15
59534 TATAAAATTA
59544 TATATAAACTATATTT
1 TATATAAACTATA-TT
59560 ATATTATAAACTATATAAT
1 -TA-TATAAACTATAT--T
59579 TATTATAAACTATA--
1 TA-TATAAACTATATT
* *
59593 TATATAAATTATGTT
1 TATATAAACTATATT
* *
59608 TATGTGAACTATA--
1 TATATAAACTATATT
*
59621 TATATAAAC--TATG
1 TATATAAACTATATT
*
59634 TATATAAACTATATA
1 TATATAAACTATATT
*
59649 TGTATAAACTATA
1 TATATAAACTATA
59662 AAAAGTATAA
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.02
13 25 0.30
14 2 0.02
15 24 0.29
17 3 0.04
18 25 0.30
19 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (15 bp):
TATATAAACTATATT
Found at i:59596 original size:20 final size:20
Alignment explanation
Indices: 59533--59596 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 20
59523 AATATATATA
*
59533 ATATAAAATTATATATAAACT
1 ATATATAATTAT-TATAAACT
*
59554 ATAT-TTA-TATTATAAAC-
1 ATATATAATTATTATAAACT
59571 -TATATAATTATTATAAACT
1 ATATATAATTATTATAAACT
59590 ATATATA
1 ATATATA
59597 TAAATTATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
16 3 0.08
17 2 0.06
18 17 0.47
19 3 0.08
20 7 0.19
21 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATATAATTATTATAAACT
Found at i:59603 original size:20 final size:20
Alignment explanation
Indices: 59542--59604 Score: 82
Period size: 18 Copynumber: 3.4 Consensus size: 20
59532 AATATAAAAT
59542 TATA-TATAAACTATAT-T-
1 TATATTATAAACTATATATA
59559 TATATTATAAACTATATA-A
1 TATATTATAAACTATATATA
59578 T-TATTATAAACTATATATA
1 TATATTATAAACTATATATA
*
59597 TAAATTAT
1 TATATTAT
59605 GTTTATGTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
17 4 0.10
18 28 0.70
19 3 0.08
20 5 0.12
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATTATAAACTATATATA
Found at i:59659 original size:41 final size:41
Alignment explanation
Indices: 59519--59661 Score: 110
Period size: 41 Copynumber: 3.3 Consensus size: 41
59509 AATTAAAAAA
*
59519 ATATAATA-TATATAATATAAAAT-TATATATAAACTATATTTAT
1 ATATAA-ACTATAT-ATATAAACTATATATATAAACTATA--TAT
* * *
59562 ATTATAAACTATATAATTATTATAAACTATATATATAAATTATGTTT
1 A-TATAAAC--TAT-A-TA-TATAAACTATATATATAAACTATATAT
* * *
59609 ATGTGAACTATATATATAAACTATGTATATAAACTATATAT
1 ATATAAACTATATATATAAACTATATATATAAACTATATAT
*
59650 GTATAAACTATA
1 ATATAAACTATA
59662 AAAAGTATAA
Statistics
Matches: 79, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
41 32 0.41
42 2 0.03
43 3 0.04
44 8 0.10
46 8 0.10
47 5 0.06
48 8 0.10
49 13 0.16
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (41 bp):
ATATAAACTATATATATAAACTATATATATAAACTATATAT
Found at i:59681 original size:18 final size:18
Alignment explanation
Indices: 59654--59688 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
59644 ATATATGTAT
59654 AAACTATAAAAAGTATAA
1 AAACTATAAAAAGTATAA
*
59672 AAACTGTAAAAAGTATA
1 AAACTATAAAAAGTATA
59689 TAGTTTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (18 bp):
AAACTATAAAAAGTATAA
Found at i:59726 original size:15 final size:15
Alignment explanation
Indices: 59708--59781 Score: 52
Period size: 15 Copynumber: 5.3 Consensus size: 15
59698 AAATATTATT
*
59708 TATATTAATATAATA
1 TATATTAATATACTA
59723 TATA-T-ATATACTA
1 TATATTAATATACTA
*
59736 TAT-GTAA-A-ACTA
1 TATATTAATATACTA
* * *
59748 TATA-AAATATAGTT
1 TATATTAATATACTA
*
59762 TATATTAATATAGTA
1 TATATTAATATACTA
59777 TATAT
1 TATAT
59782 ATGTATGCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 12
0.72 0.09 0.18
Matches are distributed among these distances:
12 9 0.19
13 13 0.28
14 8 0.17
15 17 0.36
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (15 bp):
TATATTAATATACTA
Found at i:60781 original size:2 final size:2
Alignment explanation
Indices: 60774--60824 Score: 59
Period size: 2 Copynumber: 25.5 Consensus size: 2
60764 TATGTTTAAT
* * *
60774 TA TA TA TA TA TA TT TA TG TA TA TA CT- TT 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
60816 TA TA TA TA T
1 TA TA TA TA T
60825 TATTCAAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.95
3 1 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:60790 original size:14 final size:14
Alignment explanation
Indices: 60773--60828 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
60763 TTATGTTTAA
60773 TTATATATATATAT
1 TTATATATATATAT
*
60787 TTATGTATATACT-T
1 TTATATATATA-TAT
60801 TTATATATATATAT
1 TTATATATATATAT
*
60815 ATATATATAT-TAT
1 TTATATATATATAT
60828 T
1 T
60829 CAAAGTGAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 4 0.11
14 31 0.86
15 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (14 bp):
TTATATATATATAT
Found at i:60924 original size:20 final size:20
Alignment explanation
Indices: 60899--60948 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
60889 TTTATTTGGG
60899 AATTTAGAGAGAAATTAGGA
1 AATTTAGAGAGAAATTAGGA
*
60919 AATTTAGAGGGAAATTAGGA
1 AATTTAGAGAGAAATTAGGA
*
60939 AATTTTGAGA
1 AATTTAGAGA
60949 ATATAGGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (20 bp):
AATTTAGAGAGAAATTAGGA
Found at i:61467 original size:14 final size:14
Alignment explanation
Indices: 61448--61518 Score: 61
Period size: 14 Copynumber: 5.7 Consensus size: 14
61438 ATTTTTTCTT
61448 TATATAAATTAAAC
1 TATATAAATTAAAC
61462 TATAT-AATT----
1 TATATAAATTAAAC
61471 TATATAAATTAAAC
1 TATATAAATTAAAC
*
61485 TATATTAATT----
1 TATATAAATTAAAC
61495 TATATAAATTAAAC
1 TATATAAATTAAAC
*
61509 TATATTAATT
1 TATATAAATT
61519 TTCCTTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 18
0.68 0.05 0.27
Matches are distributed among these distances:
9 5 0.11
10 13 0.29
13 4 0.09
14 23 0.51
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:61498 original size:24 final size:24
Alignment explanation
Indices: 61446--61519 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
61436 TTATTTTTTC
61446 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
61469 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
61493 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
61517 TTT
1 TTT
61520 TCCTTTGCGT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 20 0.40
24 30 0.60
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:61590 original size:13 final size:13
Alignment explanation
Indices: 61558--61584 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
61548 TAATTTACAT
61558 TTAAATAATTTTA
1 TTAAATAATTTTA
61571 TTAAATAATTTTA
1 TTAAATAATTTTA
61584 T
1 T
61585 ATAATAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:61787 original size:16 final size:16
Alignment explanation
Indices: 61766--61808 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
61756 CGGATTATTT
61766 ACAGGTCATGTTAAAA
1 ACAGGTCATGTTAAAA
* *
61782 ACAGGTCAGGTTGAAA
1 ACAGGTCATGTTAAAA
61798 ACAGGTCATGT
1 ACAGGTCATGT
61809 AATACCAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (16 bp):
ACAGGTCATGTTAAAA
Found at i:62516 original size:22 final size:22
Alignment explanation
Indices: 62491--62662 Score: 128
Period size: 22 Copynumber: 7.5 Consensus size: 22
62481 TTTTAAAATA
*
62491 ATTTATTATAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
** *
62513 ATTTATTTTAAAATAATTTATTTT
1 ATTTATTTTAAAAT-ATGGA-TTG
** * * *
62537 AAATAATTTATTAGTATGGATTG
1 ATTTATTTTA-AAATATGGATTG
*
62560 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
** *
62582 ATTTATTTTAAAATAATTTATTTT
1 ATTTATTTTAAAAT-ATGGA-TTG
** * * *
62606 AAATAATTTATTAGTATGGATTG
1 ATTTATTTTA-AAATATGGATTG
62629 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
62651 ATTTATTTTAAA
1 ATTTATTTTAAA
62663 TAATTTATTA
Statistics
Matches: 110, Mismatches: 34, Indels: 12
0.71 0.22 0.08
Matches are distributed among these distances:
22 58 0.53
23 24 0.22
24 24 0.22
25 4 0.04
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:62542 original size:14 final size:15
Alignment explanation
Indices: 62371--62617 Score: 246
Period size: 15 Copynumber: 15.5 Consensus size: 15
62361 TAATAAGGTT
62371 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
62386 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
62401 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
62416 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
62431 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
62446 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
62461 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
62476 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
62491 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
62510 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
62528 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
** * *
62542 ATTTATTAGTATGGATTG
1 ATTTATT--T-TAAAATA
62560 ATTTATTTTAAAATATGAA
1 ATTTATTTT-AAA-AT--A
62579 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
62597 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
62611 ATTTATT
1 ATTTATT
62618 AGTATGGATT
Statistics
Matches: 201, Mismatches: 13, Indels: 37
0.80 0.05 0.15
Matches are distributed among these distances:
14 24 0.12
15 127 0.63
16 7 0.03
17 4 0.02
18 11 0.05
19 1 0.00
20 4 0.02
21 7 0.03
22 16 0.08
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:62583 original size:69 final size:70
Alignment explanation
Indices: 62446--62914 Score: 400
Period size: 69 Copynumber: 6.3 Consensus size: 70
62436 TTATAAAATA
* ** * * *
62446 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAATTTATTATAAAATATG
1 ATTTATTTTAAAATAATTTATTATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
62508 GATTG
66 GATTG
62513 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
*
62577 AATTG
66 GATTG
62582 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
62646 GATTG
66 GATTG
* *
62651 ATTTATTTT-AAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTGATTTATTTTA
1 ATTTATTTTAAAATAATTTATTA-T-T-AAATAATTTA--TT--AGTATGGATTGATTTA-TTT-
62715 AATAATTTATTAGTATGGATTG
57 --TAA---A--A-TATGGATTG
** ** * *
62737 ATTTATTTTAAAATAA-AGATTGATTTTATTATTGTAGTT-GTATGAATTGATTTATTTTAAATA
1 ATTTATTTTAAAATAATTTATT-ATTAAATAATT-TA-TTAGTATGGATTGATTTATTTT-AA-A
62800 ATTTATTAGTATAGATTG
61 A--TA-T-G----GATTG
*
62818 ATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA
1 ATTTATTTTAAAATA---ATTTA-TTA--TTAAATAATTTATTAGTATGGATTGATTTATTTTAA
62883 AATATGGATTG
60 AATATGGATTG
62894 ATTTATTTT-AAATAA-TTATTA
1 ATTTATTTTAAAATAATTTATTA
62915 GTATAGATTG
Statistics
Matches: 336, Mismatches: 26, Indels: 77
0.77 0.06 0.18
Matches are distributed among these distances:
66 13 0.04
67 22 0.07
68 13 0.04
69 100 0.30
70 4 0.01
71 3 0.01
72 10 0.03
74 3 0.01
75 7 0.02
76 32 0.10
77 5 0.01
78 2 0.01
80 7 0.02
81 34 0.10
82 2 0.01
83 1 0.00
84 9 0.03
85 11 0.03
86 44 0.13
87 14 0.04
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (70 bp):
ATTTATTTTAAAATAATTTATTATTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
GATTG
Found at i:62659 original size:54 final size:54
Alignment explanation
Indices: 62597--63250 Score: 395
Period size: 54 Copynumber: 12.1 Consensus size: 54
62587 TTTTAAAATA
62597 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
62651 ATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
**
62705 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAAAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * *
62759 ATTT-TATT--AT--TGTAGTT-GTATGAATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * **
62804 A-TTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * *
62863 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTTAAATAATTATTAGTATAGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA-TA-T-G----GATTG
* * ***
62925 ATTTATTTT-AA-AA--TA-TA-TAT-GATTTA-TTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTG
*
62972 ATTTA-TTTAAATAATTTATTAGTATGGATTAATTTA-TTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
63024 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
63078 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-TTT---TAA---A--A-TATGGATTG
** ** * ** * * *
63136 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTG
* *
63190 ATTTATTTTAAATAATTTATTTGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
63244 ATTTATT
1 ATTTATT
63251 ATTGTAGTTA
Statistics
Matches: 470, Mismatches: 67, Indels: 126
0.71 0.10 0.19
Matches are distributed among these distances:
44 2 0.00
45 5 0.01
46 3 0.01
47 12 0.03
48 26 0.06
49 26 0.06
50 9 0.02
51 7 0.01
52 23 0.05
53 43 0.09
54 215 0.46
55 19 0.04
56 9 0.02
57 8 0.02
58 22 0.05
59 8 0.02
60 6 0.01
61 4 0.01
62 9 0.02
63 11 0.02
64 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:62689 original size:32 final size:32
Alignment explanation
Indices: 62642--62748 Score: 126
Period size: 32 Copynumber: 3.7 Consensus size: 32
62632 TATTTTAAAA
62642 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* *
62674 TATGAATTAATTTA-TTT---TAA---A--A-
1 TATGGATTGATTTATTTTAAATAATTTATTAG
62696 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
62728 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
62749 ATAAAGATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
22 12 0.20
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.07
32 33 0.54
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:62699 original size:22 final size:22
Alignment explanation
Indices: 62674--62716 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
62664 AATTTATTAG
62674 TATGAATTAATTTATTTTAAAA
1 TATGAATTAATTTATTTTAAAA
* *
62696 TATGGATTGATTTATTTTAAA
1 TATGAATTAATTTATTTTAAA
62717 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGAATTAATTTATTTTAAAA
Found at i:62819 original size:32 final size:30
Alignment explanation
Indices: 62776--62936 Score: 156
Period size: 32 Copynumber: 5.7 Consensus size: 30
62766 TATTGTAGTT
62776 GTATGAATTGATTTATTTTAAATAATTTATTA
1 GTATG-ATTGATTTATTTTAAATAA-TTATTA
62808 GTATAGATTGATTTATTTT-AA-AA-TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTATTA
62834 G---GATTGATTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAA-TTATTA
62862 GTATGGATTGATTTATTTT-AA-AA-TA-T-
1 GTAT-GATTGATTTATTTTAAATAATTATTA
62888 G---GATTGATTTATTTTAAATAATTATTA
1 GTATGATTGATTTATTTTAAATAATTATTA
62915 GTATAGATTGATTTATTTTAAA
1 GTAT-GATTGATTTATTTTAAA
62937 ATATATATGA
Statistics
Matches: 109, Mismatches: 0, Indels: 41
0.73 0.00 0.27
Matches are distributed among these distances:
22 28 0.26
23 4 0.04
24 4 0.04
25 2 0.02
26 5 0.05
27 4 0.04
28 5 0.05
30 4 0.04
31 21 0.19
32 31 0.28
33 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (30 bp):
GTATGATTGATTTATTTTAAATAATTATTA
Found at i:62888 original size:22 final size:22
Alignment explanation
Indices: 62863--62905 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
62853 AATTTATTAG
62863 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
62885 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
62906 TAATTATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:62979 original size:78 final size:77
Alignment explanation
Indices: 62885--63030 Score: 224
Period size: 78 Copynumber: 1.9 Consensus size: 77
62875 TATTTTAAAA
*
62885 TATGGATTGATTTATTTTAAATAA-TTATTAGTATAGATTGATTTATTTTAAAATAT-ATATGAT
1 TATGGATTGATTTA-TTTAAATAATTTATTAGTATAGATTAATTTA-TTTAAAATATGAT-TGAT
62948 TTATTATTGTAGTTG
63 TTATTATTGTAGTTG
*
62963 TATGGATTGATTTATTTAAATAATTTATTAGTATGGATTAATTTATTTAAAATATGGATTGATTT
1 TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTAATTTATTTAAAATAT-GATTGATTT
63028 ATT
65 ATT
63031 TTAAATAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
77 19 0.30
78 42 0.67
79 2 0.03
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (77 bp):
TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTAATTTATTTAAAATATGATTGATTTA
TTATTGTAGTTG
Found at i:62997 original size:31 final size:31
Alignment explanation
Indices: 62962--63063 Score: 116
Period size: 31 Copynumber: 3.6 Consensus size: 31
62952 TATTGTAGTT
62962 GTATGGATTGATTTATTTAAATAATTTATTA
1 GTATGGATTGATTTATTTAAATAATTTATTA
*
62993 GTATGGATTAATTTA-TT---TAA---A--A
1 GTATGGATTGATTTATTTAAATAATTTATTA
63015 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTA-TTTAAATAATTTATTA
63046 GTATGGATTGATTTATTT
1 GTATGGATTGATTTATTT
63064 TAAAATATGG
Statistics
Matches: 58, Mismatches: 2, Indels: 22
0.71 0.02 0.27
Matches are distributed among these distances:
21 13 0.22
22 1 0.02
23 2 0.03
24 1 0.02
26 3 0.05
27 3 0.05
29 1 0.02
30 2 0.03
31 18 0.31
32 14 0.24
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (31 bp):
GTATGGATTGATTTATTTAAATAATTTATTA
Found at i:63020 original size:21 final size:21
Alignment explanation
Indices: 62994--63037 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
62984 AATTTATTAG
62994 TATGGATTAATTTATTTAAAA
1 TATGGATTAATTTATTTAAAA
* *
63015 TATGGATTGATTTATTTTAAA
1 TATGGATTAATTTATTTAAAA
63036 TA
1 TA
63038 ATTTATTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (21 bp):
TATGGATTAATTTATTTAAAA
Found at i:63135 original size:32 final size:32
Alignment explanation
Indices: 63094--63233 Score: 192
Period size: 32 Copynumber: 4.7 Consensus size: 32
63084 TATTGTAGTT
63094 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
63126 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
63149 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
63180 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
63212 GTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
63234 ATATGGATTG
Statistics
Matches: 96, Mismatches: 2, Indels: 20
0.81 0.02 0.17
Matches are distributed among these distances:
22 14 0.15
23 4 0.04
25 1 0.01
26 3 0.03
28 3 0.03
29 1 0.01
31 4 0.04
32 66 0.69
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:63152 original size:22 final size:22
Alignment explanation
Indices: 63127--63169 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
63117 AATTTATTAG
63127 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
63149 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
63170 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:63317 original size:22 final size:22
Alignment explanation
Indices: 63292--63333 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
63282 ATTTATTAGT
63292 ATGGATTGATTTATTTTAAAAC
1 ATGGATTGATTTATTTTAAAAC
63314 ATGGATTGATTTATTTTAAA
1 ATGGATTGATTTATTTTAAA
63334 TAATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGGATTGATTTATTTTAAAAC
Found at i:63343 original size:54 final size:54
Alignment explanation
Indices: 63095--63343 Score: 287
Period size: 54 Copynumber: 4.6 Consensus size: 54
63085 ATTGTAGTTG
63095 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
63149 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
* * * * * * **
63202 TA---ATTTATTT-GTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTA
1 TATGGATTGATTTATTTTA-AATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAA
63261 TATGGATTGA-TTA-TTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
*
63313 CATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
63344 TTGTAGTTTT
Statistics
Matches: 163, Mismatches: 16, Indels: 32
0.77 0.08 0.15
Matches are distributed among these distances:
49 3 0.02
50 14 0.09
52 12 0.07
53 10 0.06
54 83 0.51
55 2 0.01
56 17 0.10
57 1 0.01
58 2 0.01
59 3 0.02
60 7 0.04
61 5 0.03
62 4 0.02
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
Done.