Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1029
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: 106931
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4372 original size:30 final size:30
Alignment explanation
Indices: 4336--4396 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4326 TGGTATTCGC
4336 ACTGAGCATTTGCATCATACCATTTAGGGT
1 ACTGAGCATTTGCATCATACCATTTAGGGT
4366 ACTGAGCATTTGCATCATACCATTTAGGGT
1 ACTGAGCATTTGCATCATACCATTTAGGGT
4396 A
1 A
4397 TGGGGGTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (30 bp):
ACTGAGCATTTGCATCATACCATTTAGGGT
Found at i:5588 original size:21 final size:21
Alignment explanation
Indices: 5564--5608 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
5554 GCTGGCTCAT
5564 CATGTTGTTCT-GTGACTCCAG
1 CATGTTGTTCTAG-GACTCCAG
* *
5585 CATGTTTTTCTAGGACTCTAG
1 CATGTTGTTCTAGGACTCCAG
5606 CAT
1 CAT
5609 TTGATCCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (21 bp):
CATGTTGTTCTAGGACTCCAG
Found at i:22891 original size:19 final size:18
Alignment explanation
Indices: 22832--22894 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 18
22822 ATTTTATATT
*
22832 TTAAAAAATTAT-ATAAA
1 TTAAAAAATTATAAAAAA
* *
22849 TT-ATAAATTATAAAAAGT
1 TTAAAAAATTATAAAAA-A
22867 TCTAAAAAATATATAAAAAA
1 T-TAAAAAAT-TATAAAAAA
22887 TTAAAAAA
1 TTAAAAAA
22895 ATTTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
16 8 0.22
17 5 0.14
18 1 0.03
19 8 0.22
20 6 0.17
21 8 0.22
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
TTAAAAAATTATAAAAAA
Found at i:22894 original size:21 final size:20
Alignment explanation
Indices: 22853--22895 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
22843 TATAAATTAT
* **
22853 AAATTATAAAAAGTTCTAAA
1 AAATTATAAAAAATTAAAAA
22873 AAATATATAAAAAATTAAAAA
1 AAAT-TATAAAAAATTAAAAA
22894 AA
1 AA
22896 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATTATAAAAAATTAAAAA
Found at i:22903 original size:10 final size:10
Alignment explanation
Indices: 22833--22903 Score: 62
Period size: 10 Copynumber: 7.5 Consensus size: 10
22823 TTTTATATTT
22833 TAAAAAATTA
1 TAAAAAATTA
*
22843 T-ATAAATTA
1 TAAAAAATTA
22852 T---AAATTA
1 TAAAAAATTA
* *
22859 TAAAAAGTTC
1 TAAAAAATTA
22869 TAAAAAATATA
1 TAAAAAAT-TA
22880 TAAAAAATTA
1 TAAAAAATTA
*
22890 -AAAAAATTT
1 TAAAAAATTA
22899 TAAAA
1 TAAAA
22904 TAACAATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
7 7 0.14
9 16 0.32
10 18 0.36
11 9 0.18
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:24790 original size:17 final size:17
Alignment explanation
Indices: 24768--24810 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
24758 TTAAGAGGAT
24768 AAAAATAAATAAAGAAC
1 AAAAATAAATAAAGAAC
* *
24785 AAAAATAAATAAATAAG
1 AAAAATAAATAAAGAAC
24802 AAAAATAAA
1 AAAAATAAA
24811 CAAACAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAATAAATAAAGAAC
Found at i:26415 original size:41 final size:41
Alignment explanation
Indices: 26363--26463 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
26353 ACAGGGTACG
*
26363 TATGTGAAATTCAAGGGTATTGAAGTACAAACAGGGGCACA
1 TATGTGCAATTCAAGGGTATTGAAGTACAAACAGGGGCACA
* *
26404 TATGTGCAATTCAAGAGTACTGAAGTACAAACAGGGGCACA
1 TATGTGCAATTCAAGGGTATTGAAGTACAAACAGGGGCACA
26445 TATGTGCAATTC-AGGGTAT
1 TATGTGCAATTCAAGGGTAT
26464 AATTAATTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 5 0.09
41 50 0.91
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (41 bp):
TATGTGCAATTCAAGGGTATTGAAGTACAAACAGGGGCACA
Found at i:38003 original size:15 final size:15
Alignment explanation
Indices: 37983--38012 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37973 TTTTTACACA
*
37983 ACGTAAATATTAAAT
1 ACGTAAATAATAAAT
37998 ACGTAAATAATAAAT
1 ACGTAAATAATAAAT
38013 TTGGACCAAC
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:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (15 bp):
ACGTAAATAATAAAT
Found at i:38341 original size:24 final size:24
Alignment explanation
Indices: 38314--38628 Score: 242
Period size: 24 Copynumber: 13.2 Consensus size: 24
38304 TGTGAACTCT
* *
38314 TATCACTAGACACATGCGAACACC
1 TATCACCAGACACATGCGAACCCC
* ** *
38338 TATCACCACATTCCTGCGAACCCC
1 TATCACCAGACACATGCGAACCCC
* *
38362 TATCACTAGACATATGCGAACCCC
1 TATCACCAGACACATGCGAACCCC
** *
38386 TATCACCAGACATTTACGAACCCC
1 TATCACCAGACACATGCGAACCCC
*
38410 TATCACCAGAAACATGCGAA-CCC
1 TATCACCAGACACATGCGAACCCC
* * * * *
38433 TATCACTAGATACCTACTAACCCC
1 TATCACCAGACACATGCGAACCCC
** * *
38457 TATCACCAGACATTTACGAACTCC
1 TATCACCAGACACATGCGAACCCC
* * *
38481 TATCACCAAACACCTGTGAACCCC
1 TATCACCAGACACATGCGAACCCC
* ** * *
38505 TATCACTAGGTACCTACGAACCCC
1 TATCACCAGACACATGCGAACCCC
* * *
38529 TATCACCAAACATC-TGTGAACCTC
1 TATCACCAGACA-CATGCGAACCCC
* *
38553 TATCACCAGACACTTGCGAACCTC
1 TATCACCAGACACATGCGAACCCC
* * *
38577 TATCACTAGACATAT--GAATCCC
1 TATCACCAGACACATGCGAACCCC
* *
38599 TATCACCAAACATATGCGAACCCC
1 TATCACCAGACACATGCGAACCCC
38623 TATCAC
1 TATCAC
38629 AAAATATCTA
Statistics
Matches: 227, Mismatches: 59, Indels: 10
0.77 0.20 0.03
Matches are distributed among these distances:
22 18 0.08
23 19 0.08
24 189 0.83
25 1 0.00
ACGTcount: A:0.33, C:0.36, G:0.10, T:0.21
Consensus pattern (24 bp):
TATCACCAGACACATGCGAACCCC
Found at i:38397 original size:72 final size:71
Alignment explanation
Indices: 38314--38628 Score: 323
Period size: 72 Copynumber: 4.4 Consensus size: 71
38304 TGTGAACTCT
* * * * **
38314 TATCACTAGACACATGCGAACACCTATCACCACATTCCTGCGAACCCCTATCACTAGACATATGC
1 TATCACCAGACATATGCGAACCCCTATCACCAGACACCTGCGAACCCCTATCACTAGACATAT-C
38379 GAACCCC
65 GAACCCC
* * * * *
38386 TATCACCAGACATTTACGAACCCCTATCACCAGAAACATGCGAA-CCCTATCACTAGATACCTA-
1 TATCACCAGACATATGCGAACCCCTATCACCAGACACCTGCGAACCCCTATCACTAG--ACATAT
*
38449 CTAACCCC
64 CGAACCCC
* * * * * *
38457 TATCACCAGACATTTACGAACTCCTATCACCAAACACCTGTGAACCCCTATCACTAGGTACCTA-
1 TATCACCAGACATATGCGAACCCCTATCACCAGACACCTGCGAACCCCTATCACTA-G-ACATAT
38521 CGAACCCC
64 CGAACCCC
* * * * * *
38529 TATCACCAAACATCTGTGAACCTCTATCACCAGACACTTGCGAACCTCTATCACTAGACATAT-G
1 TATCACCAGACATATGCGAACCCCTATCACCAGACACCTGCGAACCCCTATCACTAGACATATCG
*
38593 AATCCC
66 AACCCC
*
38599 TATCACCAAACATATGCGAACCCCTATCAC
1 TATCACCAGACATATGCGAACCCCTATCAC
38629 AAAATATCTA
Statistics
Matches: 206, Mismatches: 32, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
70 37 0.18
71 59 0.29
72 105 0.51
73 5 0.02
ACGTcount: A:0.33, C:0.36, G:0.10, T:0.21
Consensus pattern (71 bp):
TATCACCAGACATATGCGAACCCCTATCACCAGACACCTGCGAACCCCTATCACTAGACATATCG
AACCCC
Found at i:50218 original size:19 final size:19
Alignment explanation
Indices: 50187--50223 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
50177 AATTTCTGCT
50187 TTTTATTTAAAAAAATTTC
1 TTTTATTTAAAAAAATTTC
50206 TTTT-TTTAGAAAAAATTT
1 TTTTATTTA-AAAAAATTT
50224 AAAAGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTATTTAAAAAAATTTC
Found at i:56253 original size:53 final size:53
Alignment explanation
Indices: 56173--56278 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
56163 CTTTCTTTTT
*
56173 GAATTCAAAGATTATAATGAATTTAGTTGTCAAATTTAGGTATCAATGTGGGA
1 GAATTCAAAGATTATAATAAATTTAGTTGTCAAATTTAGGTATCAATGTGGGA
56226 GAATTCAAAGATTATAATAAATTTAGTTGTCAAATTTAGGTATCAATGTGGGA
1 GAATTCAAAGATTATAATAAATTTAGTTGTCAAATTTAGGTATCAATGTGGGA
56279 AAAATATAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.36
Consensus pattern (53 bp):
GAATTCAAAGATTATAATAAATTTAGTTGTCAAATTTAGGTATCAATGTGGGA
Found at i:56791 original size:13 final size:13
Alignment explanation
Indices: 56773--56799 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
56763 TACAAGACTC
56773 AAGAGAAATGCTA
1 AAGAGAAATGCTA
56786 AAGAGAAATGCTA
1 AAGAGAAATGCTA
56799 A
1 A
56800 TATAAGACAT
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:0.56, C:0.07, G:0.22, T:0.15
Consensus pattern (13 bp):
AAGAGAAATGCTA
Found at i:57305 original size:24 final size:24
Alignment explanation
Indices: 57274--57320 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
57264 AACTTTTATC
57274 TAATAAATAAAATTGAAATTCATA
1 TAATAAATAAAATTGAAATTCATA
* *
57298 TAATAAATTAAATTTAAATTCAT
1 TAATAAATAAAATTGAAATTCAT
57321 GACTATAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
TAATAAATAAAATTGAAATTCATA
Found at i:58241 original size:21 final size:21
Alignment explanation
Indices: 58215--58258 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
58205 ACTTGCTATT
58215 GTCATTTTTGTTAGTGTCGGA
1 GTCATTTTTGTTAGTGTCGGA
* *
58236 GTCATTTTTGTTCGTGTTGGA
1 GTCATTTTTGTTAGTGTCGGA
58257 GT
1 GT
58259 TGAAAGAGGG
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:0.11, C:0.09, G:0.30, T:0.50
Consensus pattern (21 bp):
GTCATTTTTGTTAGTGTCGGA
Found at i:58793 original size:30 final size:31
Alignment explanation
Indices: 58726--58793 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
58716 ACTGTTAATC
* * *
58726 AGTGACTATTTTGTCACTTTTTTATAACGTT
1 AGTGACTATTTTGTAACTTTTTCATAAAGTT
58757 AGTGACTATTTTGTAAC-TTTTCA-AAAGTT
1 AGTGACTATTTTGTAACTTTTTCATAAAGTT
58786 GAGTGACT
1 -AGTGACT
58794 GAAATGAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 12 0.36
31 16 0.48
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (31 bp):
AGTGACTATTTTGTAACTTTTTCATAAAGTT
Found at i:63044 original size:45 final size:44
Alignment explanation
Indices: 62982--63148 Score: 175
Period size: 45 Copynumber: 3.9 Consensus size: 44
62972 TTATGCTATG
62982 TGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTT
1 TGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTT
* *
63026 ATGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCAATA-TG
1 -TGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTT
* * * * * *
63070 TGGTTACGAGTAAGACCATGTCTGGGACATCGGCATCG-TA-TT
1 TGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTT
* *
63112 TG-ATTCGTGTAATACC-CTGTCTGGGACAG-TGGCATCG
1 TGTTTTCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCG
63149 GTATGAGATC
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
41 26 0.25
42 5 0.05
43 31 0.30
44 1 0.01
45 40 0.39
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (44 bp):
TGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGATATTT
Found at i:63097 original size:43 final size:45
Alignment explanation
Indices: 62991--63107 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 45
62981 GTGTTTTCGT
* * * *
62991 GTAAGACCACGTCTGGGACGTTGGCATCGATATTTATGTTTTCGT
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATATATGGTTACGA
*
63036 GTAAGACCACGTCTGGGACGTTGGCATC-A-ATATGTGGTTACGA
1 GTAAGACCACGTCTGGGACGTTGGCATCGATATATATGGTTACGA
* * *
63079 GTAAGACCATGTCTGGGACATCGGCATCG
1 GTAAGACCACGTCTGGGACGTTGGCATCG
63108 TATTTGATTC
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
43 34 0.54
44 1 0.02
45 28 0.44
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28
Consensus pattern (45 bp):
GTAAGACCACGTCTGGGACGTTGGCATCGATATATATGGTTACGA
Found at i:63189 original size:84 final size:89
Alignment explanation
Indices: 62990--63189 Score: 211
Period size: 84 Copynumber: 2.3 Consensus size: 89
62980 TGTGTTTTCG
*
62990 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTATGTTTTCGTGTAAGACCACGTCTGGGAC
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTATGTATTCGTGTAAGACCACGTCTGGGAC
* *
63055 GTTGGCATCAATATGTGGTTACGA
66 GTTGGCATCAATATGTAGATACGA
* * * *
63079 -GTAAGACCATGTCTGGGACATCGGCATCG-TA-TT-TG-ATTCGTGTAATACC-CTGTCTGGGA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTATGTATTCGTGTAAGACCAC-GTCTGGGA
**
63138 CAG-TGGCATCGGTATG-AGAT-CGCA
65 C-GTTGGCATCAATATGTAGATACG-A
* *
63162 TGTAGGACCACATCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
63190 TGTTCGATAT
Statistics
Matches: 93, Mismatches: 14, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
82 2 0.02
83 4 0.04
84 54 0.58
85 3 0.03
86 2 0.02
87 2 0.02
88 26 0.28
ACGTcount: A:0.23, C:0.20, G:0.29, T:0.29
Consensus pattern (89 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATTTATGTATTCGTGTAAGACCACGTCTGGGAC
GTTGGCATCAATATGTAGATACGA
Found at i:64244 original size:14 final size:14
Alignment explanation
Indices: 64222--64255 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
64212 AATTGGTGAA
64222 TATAAATATTGAGT
1 TATAAATATTGAGT
*
64236 TATATATATTGAGT
1 TATAAATATTGAGT
64250 TGATAA
1 T-ATAA
64256 TGTATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 14 0.82
15 3 0.18
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (14 bp):
TATAAATATTGAGT
Found at i:78123 original size:48 final size:46
Alignment explanation
Indices: 78064--78384 Score: 236
Period size: 48 Copynumber: 6.7 Consensus size: 46
78054 TATGTGTGCT
* *
78064 AGTGTAAGACCATGTTTGGAACATGGCATCAGCAATGCTATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GC-CTGCTATGAGAGCC
* ** * * * *
78112 AGAGTAAGACCAAATTTGGGGCATGGCATTGGCTTCGAC-ATGTGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCA-TCGCCT-G-CTATGAGAGCC
* * *
78160 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAC-ATGTGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GCCT-G-CTATGAGAGCC
* *
78208 AGTGTAAGACCATGTCTGGGACATGGCATCAGCCT-CAATATGCGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GCCTGC--TATGAGAGCC
* * * * *
78256 AGTGTAAGACCATGTTTGGAACATGGCATCGACATTGTTAT-ATGTGTC
1 AGTGTAAGACCATGTTTGGGACATGGCATCG-C-CTGCTATGA-GAGCC
* * *
78304 AATGTAAGACCATGTCTGGGACATGGCATCGACACTGATGAATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCG-C-CTGCT--ATGAGAGCC
* *
78354 AGTGTAAGACCTTGTTTGAGACATGGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
78385 GCATTTTACC
Statistics
Matches: 222, Mismatches: 37, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
45 1 0.00
47 3 0.01
48 182 0.82
49 3 0.01
50 32 0.14
51 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGCCTGCTATGAGAGCC
Found at i:78219 original size:96 final size:96
Alignment explanation
Indices: 78055--78387 Score: 275
Period size: 96 Copynumber: 3.4 Consensus size: 96
78045 TTTGGTTGAT
* * *
78055 ATGTGTGCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCAATGCTATGAGAGCCAGAGTAAG
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGCTATGAGAGCCAGAGTAAG
* * ** * *
78120 ACCAAATTTGGGGCATGGCATTGGCTTCGAC
66 ACCAAATCTGGGACATGGCATCAGCCTCAAC
* * * * * *
78151 ATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAC-ATGTGAGCTAGTGTA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAAT-G-CTATGAGAGCCAGAGTA
** *
78214 AGACCATGTCTGGGACATGGCATCAGCCTCAAT
64 AGACCAAATCTGGGACATGGCATCAGCCTCAAC
* * * * * *
78247 ATGCGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTGTTAT-ATGTGTCA-ATGTA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGCTATGA-GAGCCAGA-GTA
** *
78310 AGACCATGTCTGGGACATGGCATC-GACACTGATGA-
64 AGACCAAATCTGGGACATGGCATCAG-C-CTCA--AC
* *
78345 ATGAGAGCCAGTGTAAGACCTTGTTT-GAGACATGGCATCGGCA
1 ATGTGAGCCAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCA
78388 TTTTACCCTT
Statistics
Matches: 193, Mismatches: 33, Indels: 20
0.78 0.13 0.08
Matches are distributed among these distances:
95 2 0.01
96 146 0.76
97 7 0.04
98 37 0.19
99 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (96 bp):
ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCAATGCTATGAGAGCCAGAGTAAG
ACCAAATCTGGGACATGGCATCAGCCTCAAC
Found at i:78315 original size:144 final size:145
Alignment explanation
Indices: 78055--78383 Score: 362
Period size: 144 Copynumber: 2.3 Consensus size: 145
78045 TTTGGTTGAT
* *
78055 ATGTGTGCTAGTGTAAGACCATGTTTGGAACATGGCATCAGCAATGCTATGAGAGCCAGAGTAAG
1 ATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCAATGCTATGAGAGCCAGAGTAAG
** * * * *
78120 ACCAAATTTGGGGCATGGCATTGGCTTCGACATGTGAGCCAGTGTAAGACCATGTCTGGGACATG
66 ACCAAATTTGGAACATGGCATCGACTTCGACATATGAGCCAATGTAAGACCATGTCTGGGACATG
* *
78185 GCATCGGC-CTCGA-C
131 GCATCGACACT-GAGA
* * * *
78199 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CT-CAATATGCGAGCCAGTGTA
1 ATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCAATGC--TATGAGAGCCAGAGTA
** ** * *
78262 AGACCATGTTTGGAACATGGCATCGACATT-GTTATATGTGTCAATGTAAGACCATGTCTGGGAC
64 AGACCAAATTTGGAACATGGCATCGAC-TTCGACATATGAGCCAATGTAAGACCATGTCTGGGAC
78326 ATGGCATCGACACTGATGA
128 ATGGCATCGACACTGA-GA
* * * *
78345 ATGAGAGCCAGTGTAAGACCTTGTTTGAGACATGGCATC
1 ATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATC
78384 GGCATTTTAC
Statistics
Matches: 154, Mismatches: 25, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
142 1 0.01
143 1 0.01
144 114 0.74
145 4 0.03
146 34 0.22
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (145 bp):
ATGTGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCAGCAATGCTATGAGAGCCAGAGTAAG
ACCAAATTTGGAACATGGCATCGACTTCGACATATGAGCCAATGTAAGACCATGTCTGGGACATG
GCATCGACACTGAGA
Found at i:78961 original size:21 final size:19
Alignment explanation
Indices: 78928--78966 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
78918 CCCTTGTCTT
*
78928 AAATTTGGAAAATCATTAA
1 AAATTTGGAAAATAATTAA
78947 AAATTTCGTGAAAATAATTA
1 AAATTT-G-GAAAATAATTA
78967 TGGGTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 1 0.06
21 10 0.59
ACGTcount: A:0.51, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
AAATTTGGAAAATAATTAA
Found at i:86845 original size:8 final size:8
Alignment explanation
Indices: 86832--86856 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
86822 CTAAAGTGCA
86832 AAAATGTG
1 AAAATGTG
86840 AAAATGTG
1 AAAATGTG
86848 AAAATGTG
1 AAAATGTG
86856 A
1 A
86857 GGGCTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (8 bp):
AAAATGTG
Found at i:87355 original size:43 final size:43
Alignment explanation
Indices: 87220--87373 Score: 163
Period size: 43 Copynumber: 3.6 Consensus size: 43
87210 ACATAAGATC
* * * *
87220 CGATATGTGTTTTCGTGTAAGACCACGTCTGGGAC-GTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTTTGGGACAG-TGGCAT
* *
87263 CGACT-TATGATTTACGTGTAAGACCATGTTTGGGACA-TCGACAT
1 CGA-TATTTGATTT-CGTGTAAGACCATGTTTGGGACAGT-GGCAT
*
87307 C-ATATTTGATTTCGTGTAAGACCTTGTTTGGGACAGTGGCAT
1 CGATATTTGATTTCGTGTAAGACCATGTTTGGGACAGTGGCAT
* *
87349 CGATATTTGATTACATGTAAGACCA
1 CGATATTTGATTTCGTGTAAGACCA
87374 CACCTGGGAC
Statistics
Matches: 93, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
42 28 0.30
43 39 0.42
44 26 0.28
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (43 bp):
CGATATTTGATTTCGTGTAAGACCATGTTTGGGACAGTGGCAT
Found at i:90425 original size:15 final size:16
Alignment explanation
Indices: 90405--90436 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
90395 CCTTGCTCTA
90405 TTGGC-AATCATTATG
1 TTGGCAAATCATTATG
90420 TTGGCAAATCATTATG
1 TTGGCAAATCATTATG
90436 T
1 T
90437 AATTTAGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (16 bp):
TTGGCAAATCATTATG
Found at i:92752 original size:31 final size:31
Alignment explanation
Indices: 92711--92774 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
92701 CCTTTTCATA
*
92711 TTTCATATTTCACAACACTGGGCCGAAGCCT
1 TTTCAAATTTCACAACACTGGGCCGAAGCCT
* **
92742 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCACAACACTGGGCCGAAGCCT
92773 TT
1 TT
92775 ACTGTAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (31 bp):
TTTCAAATTTCACAACACTGGGCCGAAGCCT
Found at i:93020 original size:24 final size:24
Alignment explanation
Indices: 92968--93228 Score: 332
Period size: 24 Copynumber: 11.0 Consensus size: 24
92958 GCTTTATCAT
*
92968 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
92993 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
93017 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* * *
93040 ATAACTGGGGCGTACGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
93064 ATAACTGGGGCATAAGCCTTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
93088 ATAATTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
93111 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
93135 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
93159 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* * *
93182 ATAACTAGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
93206 ATAACTGGGGCATAATCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
93229 CCACTTCCTC
Statistics
Matches: 207, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
23 60 0.29
24 135 0.65
25 12 0.06
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:93044 original size:47 final size:47
Alignment explanation
Indices: 92989--93227 Score: 336
Period size: 47 Copynumber: 5.1 Consensus size: 47
92979 CCTAGCCTCT
* *
92989 TTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
* * *
93036 TTTAATAACTGGGGCGTACGCCCTTTTGATAACTGGGGCATAAGCCTT
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCC-C
* * * *
93084 TTTGATAATTGGGGCATAAGCCC-TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
*
93130 TTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
* * *
93178 TTTAATAACTAGGGCGTAAGCCCTTTTGATAACTGGGGCATAATCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
93225 TTT
1 TTT
93228 TCCACTTCCT
Statistics
Matches: 170, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
47 130 0.76
48 40 0.24
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCC
Found at i:93068 original size:71 final size:71
Alignment explanation
Indices: 92968--93228 Score: 409
Period size: 71 Copynumber: 3.7 Consensus size: 71
92958 GCTTTATCAT
* * *
92968 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCGTAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAA
93032 GCCCTTTA
64 GCCCTTTA
* *
93040 ATAACTGGGGCGTACGCCCTTTTGATAACTGGGGCATAAG-CCTTTTTGATAATTGGGGCATAAG
1 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTT-ATAACTGGGGCATAAG
93104 CCCTTTA
65 CCCTTTA
*
93111 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
93176 CCTTTA
66 CCTTTA
* *
93182 ATAACTAGGGCGTAAGCCCTTTTGATAACTGGGGCATAATCCCTTTT
1 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
93229 CCACTTCCTC
Statistics
Matches: 176, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
70 7 0.04
71 152 0.86
72 17 0.10
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (71 bp):
ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
CCTTTA
Found at i:93306 original size:20 final size:20
Alignment explanation
Indices: 93278--93336 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
93268 TTATGAATAC
93278 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
93298 ATTATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
93318 GTCATGTGCATATCATACA
1 ATCATGTGCATATCATACA
93337 AACTGTGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:93413 original size:25 final size:25
Alignment explanation
Indices: 93381--93428 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
93371 ATACATAAAC
* * *
93381 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
93406 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
93429 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:100978 original size:30 final size:31
Alignment explanation
Indices: 100938--101000 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
100928 TCTATTCATA
100938 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
100969 TTTCA-ATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
100999 TT
1 TT
101001 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:101245 original size:24 final size:24
Alignment explanation
Indices: 101193--101422 Score: 301
Period size: 24 Copynumber: 9.8 Consensus size: 24
101183 GCTTTATCAT
* *
101193 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* *
101218 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTG
*
101242 ATAACTGGGGCATAAGCCC--TTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
101264 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
* *
101288 ATAATTGGGGCATAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTG
101312 ATAACTGGGGCATAAGCCC--TT-
1 ATAACTGGGGCATAAGCCCTTTTG
* *
101333 ATAACTAGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
101357 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
101381 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
101405 ATAACTGGGGCATAAGCC
1 ATAACTGGGGCATAAGCC
101423 TTTCCACTTT
Statistics
Matches: 182, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
21 17 0.09
22 22 0.12
23 2 0.01
24 129 0.71
25 12 0.07
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:101369 original size:69 final size:70
Alignment explanation
Indices: 101207--101401 Score: 320
Period size: 69 Copynumber: 2.8 Consensus size: 70
101197 CTGGAGGCCT
* * *
101207 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCCTTAATAACTGG
1 AGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCCCTTAATAACTAG
101272 GGCGTA
65 GGCGTA
*
101278 AGCCCTTTTGATAATTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCCCTT-ATAACTAGG
1 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCCCTTAATAACTAGG
101342 GCGTA
66 GCGTA
* *
101347 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCGTAAGCCCTT
1 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCCCTT
101402 TTGATAACTG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
69 65 0.56
70 48 0.41
71 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.29
Consensus pattern (70 bp):
AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCCCTTAATAACTAGG
GCGTA
Found at i:101382 original size:93 final size:92
Alignment explanation
Indices: 101193--101422 Score: 302
Period size: 93 Copynumber: 2.5 Consensus size: 92
101183 GCTTTATCAT
* * *
101193 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCC--TTTATAACTAGGGCATAA
*
101257 GCCCTTAATAACTGGGGCGTAAGCCCTTTTG
62 GCCCTTAATAACTGGGGCATAAGCCCTTTTG
* * *
101288 ATAATTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGCCC-TTATAACTAGGGCGTAAGCCC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTATAACTAGGGCATAAGCCC
*
101352 TTTTGATAACTGGGGCATAAGCCCTTTTG
66 --TTAATAACTGGGGCATAAGCCCTTTTG
* *
101381 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCC
101423 TTTCCACTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
91 19 0.16
93 64 0.53
94 27 0.22
95 11 0.09
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.28
Consensus pattern (92 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTATAACTAGGGCATAAGCCC
TTAATAACTGGGGCATAAGCCCTTTTG
Found at i:101501 original size:20 final size:20
Alignment explanation
Indices: 101476--101542 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
101466 TTATGAATAC
101476 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
101496 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
101516 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
101536 ACCATGT
1 ATCATGT
101543 TTATCAAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:101507 original size:11 final size:11
Alignment explanation
Indices: 101476--101531 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
101466 TTATGAATAC
101476 ATCATGTGCAT
1 ATCATGTGCAT
*
101487 ATCA--TACAT
1 ATCATGTGCAT
101496 ATCATGTGCAT
1 ATCATGTGCAT
*
101507 ATCA--TACAT
1 ATCATGTGCAT
*
101516 GTCATGTGCAT
1 ATCATGTGCAT
101527 ATCAT
1 ATCAT
101532 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Done.