Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1194
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: 52611
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:133 original size:2 final size:2
Alignment explanation
Indices: 128--158 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
118 TGTATGCATG
128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
159 TCTTCTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:142 original size:26 final size:26
Alignment explanation
Indices: 77--144 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
67 GTACTAGTCC
* *
77 ATATATATATATATATGTGTGTTCGT
1 ATATATATATATATATGTATGATCGT
*
103 ATATACAT-TCATATATGTATGCAT-GT
1 ATATATATAT-ATATATGTATG-ATCGT
129 ATATATATATATATAT
1 ATATATATATATATAT
145 ATATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
25 1 0.03
26 32 0.91
27 2 0.06
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (26 bp):
ATATATATATATATATGTATGATCGT
Found at i:1868 original size:2 final size:2
Alignment explanation
Indices: 1861--1889 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1851 TATTAAATTT
1861 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1890 GCATGGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2138 original size:34 final size:34
Alignment explanation
Indices: 2070--2286 Score: 285
Period size: 34 Copynumber: 6.4 Consensus size: 34
2060 GTTCTTAGTT
* * *
2070 TTGTTGATTAAAT-GGTGATTTAGTAGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
2103 TTGTTGATTAAATGGGTGATTTGGTGGTTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
*
2137 TTGTTGACTAAAT-GGAGATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
*
2170 TTGTTGATTAAATGGGAAATTTGGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* *
2204 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
2238 TTGTTGACTAAATAGGAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2272 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2287 TGGTTTTTAC
Statistics
Matches: 161, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 41 0.25
34 120 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.41
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
Found at i:2260 original size:68 final size:67
Alignment explanation
Indices: 2070--2288 Score: 312
Period size: 67 Copynumber: 3.3 Consensus size: 67
2060 GTTCTTAGTT
* * * * *
2070 TTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
2135 CA
66 CA
* * * *
2137 TTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
1 TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
2202 CA
66 CA
* * * *
2204 TTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATAGGAGATTTGGTAGGTTG
1 TTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
2269 CCA
65 CCA
2272 TTGTTGATTAAATGGTG
1 TTGTTGATTAAATGGTG
2289 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 74 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.41
Consensus pattern (67 bp):
TTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
CA
Found at i:6766 original size:34 final size:34
Alignment explanation
Indices: 6697--6914 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
6687 AAGTGGGAGA
* * *
6697 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
6730 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
6764 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
6797 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
6831 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
6865 ATTGTTGACTAAATAGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
6899 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
6915 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 42 0.26
34 120 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:6888 original size:68 final size:67
Alignment explanation
Indices: 6697--6916 Score: 314
Period size: 67 Copynumber: 3.3 Consensus size: 67
6687 AAGTGGGAGA
* * * * *
6697 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
6762 CC
66 CC
* * * *
6764 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
6829 CC
66 CC
* * * *
6831 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATAGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
6896 GCC
65 GCC
6899 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
6917 GTTTTTACCA
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 75 0.56
68 60 0.44
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:9522 original size:20 final size:20
Alignment explanation
Indices: 9497--9535 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9487 AAGAATTGAA
9497 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
**
9517 GAGGGATACTTGAGAGGGA
1 GAGGGATACAAGAGAGGGA
9536 GGAAGGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:9679 original size:24 final size:25
Alignment explanation
Indices: 9648--9705 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 25
9638 GTAACCAACA
*
9648 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
9672 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
9698 TTGTTGAC
1 TTGTTGAC
9706 TAGCCACCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 14 0.45
26 17 0.55
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:14195 original size:24 final size:26
Alignment explanation
Indices: 14159--14206 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
14149 AATAAAAATT
14159 AGCCACCAATTTTGA-AAA-ACAACA
1 AGCCACCAATTTTGACAAATACAACA
14183 AGCCA-CAATTTTTGACAAATACAA
1 AGCCACCAA-TTTTGACAAATACAA
14207 AGTAACCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 11 0.52
25 3 0.14
26 4 0.19
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.21
Consensus pattern (26 bp):
AGCCACCAATTTTGACAAATACAACA
Found at i:14249 original size:24 final size:25
Alignment explanation
Indices: 14218--14275 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
14208 GTAACCAACA
*
14218 TTGTTGACAAACAC-ATGGTGACTT
1 TTGTTGACAAACACAAGGGTGACTT
*
14242 TTGTTGACAAACACAAAGGGTGGCTT
1 TTGTTGACAAACAC-AAGGGTGACTT
14268 TTGTTGAC
1 TTGTTGAC
14276 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGACTT
Found at i:15781 original size:1 final size:1
Alignment explanation
Indices: 15737--15761 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
15727 GGGTGCGGCC
15737 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
15762 GAATAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16021 original size:26 final size:27
Alignment explanation
Indices: 15992--16044 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
15982 CACTTTTATC
15992 GGTATTACTAAATA-TGATTAATATTT
1 GGTATTACTAAATATTGATTAATATTT
16018 GGTATTACTAAATATTGATTAATATTT
1 GGTATTACTAAATATTGATTAATATTT
16045 TCTTAGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (27 bp):
GGTATTACTAAATATTGATTAATATTT
Found at i:20447 original size:3 final size:3
Alignment explanation
Indices: 20439--20469 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20429 AACACGAAGC
20439 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
20470 TTCACTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:21988 original size:64 final size:67
Alignment explanation
Indices: 21837--22010 Score: 215
Period size: 67 Copynumber: 2.7 Consensus size: 67
21827 TTAATGTATC
* *
21837 TATATTTACTA-ATTATT-TTTAATATAAAAATAAATTTTAATTATTATTATCAACATAATATTA
1 TATATTTA-TATATTATTATTTAATATAAATATAAATTTTAATAATTATTATCAACATAATATTA
21900 ATT
65 ATT
*
21903 TGATAACTTAT-TA-TATTATTTAATATAAATATAAATTTTAATAATTA-TA-CAA-ATAA-ATT
1 T-AT-ATTTATATATTATTATTTAATATAAATATAAATTTTAATAATTATTATCAACATAATA-T
21962 TAATT
63 TAATT
21967 TATATTTATATATTATTATTTAATAT-AATAT-AATTTTAATAATT
1 TATATTTATATATTATTATTTAATATAAATATAAATTTTAATAATT
22011 TTTAATTATT
Statistics
Matches: 97, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
62 18 0.19
63 10 0.10
64 24 0.25
65 3 0.03
66 7 0.07
67 31 0.32
68 4 0.04
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.51
Consensus pattern (67 bp):
TATATTTATATATTATTATTTAATATAAATATAAATTTTAATAATTATTATCAACATAATATTAA
TT
Found at i:25879 original size:21 final size:21
Alignment explanation
Indices: 25854--25918 Score: 64
Period size: 21 Copynumber: 3.1 Consensus size: 21
25844 TATCAAATAT
25854 AAATATA-ATTATAATATGAT-A
1 AAATATATATTA-AATAT-ATAA
*
25875 AAATAAATATTAAATATATAA
1 AAATATATATTAAATATATAA
**
25896 AAATATATAAAAAATA-ATAA
1 AAATATATATTAAATATATAA
25916 AAA
1 AAA
25919 AATCACATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
20 9 0.24
21 25 0.66
22 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATATATATTAAATATATAA
Found at i:25901 original size:31 final size:30
Alignment explanation
Indices: 25848--25907 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
25838 TTTAAGTATC
* *
25848 AAATATAAATATAATTATAATATGATAAAAT
1 AAATATAAATATAATAAAAATAT-ATAAAAT
25879 AAATATTAAATAT-ATAAAAATATATAAAA
1 AAATA-TAAATATAATAAAAATATATAAAA
25908 AATAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 6 0.23
31 13 0.50
32 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATATAAATATAATAAAAATATATAAAAT
Found at i:25921 original size:11 final size:11
Alignment explanation
Indices: 25886--25919 Score: 54
Period size: 10 Copynumber: 3.3 Consensus size: 11
25876 AATAAATATT
25886 AAATATAT-AA
1 AAATATATAAA
25896 AAATATATAAA
1 AAATATATAAA
25907 AAATA-ATAAA
1 AAATATATAAA
25917 AAA
1 AAA
25920 ATCACATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATATATAAA
Found at i:26347 original size:2 final size:2
Alignment explanation
Indices: 26340--26373 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
26330 CCTGGAACAA
* *
26340 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26374 TCTTGGTCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:26996 original size:21 final size:20
Alignment explanation
Indices: 26933--27001 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
26923 TCAAAAATAT
*
26933 TTTAAATTTTTTTATATAAAAA
1 TTTAAATTTTATT-TA-AAAAA
* *
26955 TTT-AATTTAATTT-ATAAA
1 TTTAAATTTTATTTAAAAAA
26973 TTTAAATTATTATTTAAAAAA
1 TTTAAATT-TTATTTAAAAAA
26994 TTTTAAAT
1 -TTTAAAT
27002 ATTAAAAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
18 7 0.18
19 4 0.11
20 6 0.16
21 11 0.29
22 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATTTTATTTAAAAAA
Found at i:29719 original size:32 final size:32
Alignment explanation
Indices: 29678--29746 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
29668 ATTTAACATA
*
29678 ATTAATATAAAAATAT-ATATCATCA-AATTCAT
1 ATTATTATAAAAATATGA-ATCAT-ATAATTCAT
* *
29710 ATTATTATAAAAGTATGAATCATATTATTCAT
1 ATTATTATAAAAATATGAATCATATAATTCAT
29742 ATTAT
1 ATTAT
29747 GAAATACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.03
32 30 0.94
33 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (32 bp):
ATTATTATAAAAATATGAATCATATAATTCAT
Found at i:31619 original size:13 final size:13
Alignment explanation
Indices: 31603--31629 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31593 TAACAATTAA
31603 TAAAAATTAAATT
1 TAAAAATTAAATT
31616 TAAAAATTAAATT
1 TAAAAATTAAATT
31629 T
1 T
31630 CATCAATTAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TAAAAATTAAATT
Found at i:32931 original size:15 final size:15
Alignment explanation
Indices: 32899--32947 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
32889 TGATTAATAT
*
32899 TAATTATAATTAATTA
1 TAATAATAATT-ATTA
*
32915 TAATAATATTTATTA
1 TAATAATAATTATTA
* *
32930 TATTAATAATTATAA
1 TAATAATAATTATTA
32945 TAA
1 TAA
32948 ATATAATATA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATAATAATTATTA
Found at i:33950 original size:16 final size:15
Alignment explanation
Indices: 33918--33967 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
33908 TAGAGAATAA
*
33918 TAATTTTTAAAAA-T
1 TAATATTTAAAAATT
33932 TAATATTTAATAAATT
1 TAATATTTAA-AAATT
33948 TAA-ATTTTAAAAATT
1 TAATA-TTTAAAAATT
33963 ATAAT
1 -TAAT
33968 TTATTTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.30
15 9 0.30
16 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATTTAAAAATT
Found at i:33968 original size:15 final size:14
Alignment explanation
Indices: 33922--33969 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
33912 GAATAATAAT
33922 TTTTAAAAA-TTAA
1 TTTTAAAAATTTAA
33935 TATTTAATAAATTTAAA
1 T-TTTAA-AAATTT-AA
33952 TTTTAAAAATTATAA
1 TTTTAAAAATT-TAA
33967 TTT
1 TTT
33970 ATTTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.03
14 5 0.17
15 13 0.43
16 8 0.27
17 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAAAAATTTAA
Found at i:34700 original size:3 final size:3
Alignment explanation
Indices: 34692--34718 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
34682 ATAACAGTAG
34692 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
34719 TATATGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:37968 original size:25 final size:24
Alignment explanation
Indices: 37940--37995 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
37930 TTAAAATTGC
*
37940 TTATTAT-TTAATTTACTAATAATAT
1 TTATTATATTAA-TTA-TAAAAATAT
37965 TTATTATAATTAATTATAAAAATAT
1 TTATTAT-ATTAATTATAAAAATAT
37990 TTATTA
1 TTATTA
37996 AATTTATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 21 0.75
26 3 0.11
27 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTATTATATTAATTATAAAAATAT
Found at i:39685 original size:34 final size:34
Alignment explanation
Indices: 39617--39832 Score: 274
Period size: 34 Copynumber: 6.4 Consensus size: 34
39607 TACTTTTTTA
* * * *
39617 TGTTGATTAAAT-GGTGATTTAGTAGTTTATCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
39650 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
39684 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
39717 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
39751 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
39785 TGTTGACTAAATGGGAGATTTGGTAGGTTGCTAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
39819 TGTTGATTAAATGG
1 TGTTGATTAAATGG
39833 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
33 40 0.25
34 120 0.75
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:39798 original size:68 final size:67
Alignment explanation
Indices: 39617--39834 Score: 301
Period size: 67 Copynumber: 3.2 Consensus size: 67
39607 TACTTTTTTA
* * * * * *
39617 TGTTGATTAAATGGTGATTTAGTAGTTTATCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
39682 AT
66 AT
* * * *
39684 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
39749 AT
66 AT
* * *
39751 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
*
39816 TAT
65 CAT
39819 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
39835 GTTTTTACCA
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
67 72 0.55
68 60 0.45
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:44316 original size:34 final size:34
Alignment explanation
Indices: 44247--44464 Score: 287
Period size: 34 Copynumber: 6.5 Consensus size: 34
44237 AAGTGGGAGA
* * *
44247 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
44280 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
44314 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
44347 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
44381 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
44415 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCT
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
44449 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
44465 TGGTTTTTAC
Statistics
Matches: 163, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
33 42 0.26
34 121 0.74
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:44355 original size:67 final size:66
Alignment explanation
Indices: 44247--44466 Score: 305
Period size: 67 Copynumber: 3.3 Consensus size: 66
44237 AAGTGGGAGA
* * *
44247 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTG
44312 CC
65 CC
* * * * *
44314 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG
44379 CC
65 CC
* *
44381 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
*
44446 GCT
64 GCC
44449 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
44467 GTTTTTACCA
Statistics
Matches: 135, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
67 74 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (66 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGC
C
Found at i:44393 original size:101 final size:101
Alignment explanation
Indices: 44247--44466 Score: 345
Period size: 101 Copynumber: 2.2 Consensus size: 101
44237 AAGTGGGAGA
* * *
44247 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
44312 CCATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
44347 ATTGTTGATTAAATGG-GAAATTTGGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
1 ATTGTTGATTAAATGGTG--ATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCT
* * *
44411 TACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCT
64 TACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
44449 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
44467 GTTTTTACCA
Statistics
Matches: 109, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
99 1 0.01
100 16 0.15
101 59 0.54
102 32 0.29
103 1 0.01
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTGTTGATTAAATGGGTGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:47238 original size:32 final size:30
Alignment explanation
Indices: 47191--47253 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 30
47181 AAAAAAATCG
* * *
47191 TTTAAAATTTTAATTAAATCTTAATTCAAAAA
1 TTTAAAAATTAAATTAAAT-TTAAAT-AAAAA
47223 TTTAAAAATTAAATTAAATTTAAATAAAAA
1 TTTAAAAATTAAATTAAATTTAAATAAAAA
47253 T
1 T
47254 AAATAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 6 0.21
31 5 0.18
32 17 0.61
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTAAAAATTAAATTAAATTTAAATAAAAA
Found at i:51647 original size:17 final size:17
Alignment explanation
Indices: 51620--51654 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
51610 GGAGAGGCAG
51620 AGGGGAGGGGGGGAGAAA
1 AGGGGAGGGGGGG-GAAA
51638 AGGGGA-GGGGGGGAAA
1 AGGGGAGGGGGGGGAAA
51654 A
1 A
51655 AAAAGGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 6 0.35
18 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (17 bp):
AGGGGAGGGGGGGGAAA
Found at i:51657 original size:19 final size:18
Alignment explanation
Indices: 51620--51656 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
51610 GGAGAGGCAG
*
51620 AGGGGAGGGGGGGAGAAA
1 AGGGGAGGGGGGGAAAAA
51638 AGGGGAGGGGGGGAAAAA
1 AGGGGAGGGGGGGAAAAA
51656 A
1 A
51657 AAGGGAGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (18 bp):
AGGGGAGGGGGGGAAAAA
Found at i:51662 original size:19 final size:18
Alignment explanation
Indices: 51622--51663 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
51612 AGAGGCAGAG
* *
51622 GGGAGGGGGGGAGAAAAG
1 GGGAGGGGGGGAAAAAAA
51640 GGGAGGGGGGGAAAAAAAA
1 GGGAGGGGGGG-AAAAAAA
51659 GGGAG
1 GGGAG
51664 AGGGATGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (18 bp):
GGGAGGGGGGGAAAAAAA
Done.