Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold927
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: 65166
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Found at i:2613 original size:22 final size:21
Alignment explanation
Indices: 2582--2629 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
2572 TTAATATTTG
*
2582 AAAAATAAATCTAAAAAATTA
1 AAAAATAAATCTAAAAAAATA
*
2603 AAAAATGAAATTTAAAAAAATA
1 AAAAAT-AAATCTAAAAAAATA
2625 AAAAA
1 AAAAA
2630 AAGAAGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (21 bp):
AAAAATAAATCTAAAAAAATA
Found at i:2870 original size:12 final size:14
Alignment explanation
Indices: 2855--2891 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
2845 TTTTTGTCTC
2855 TTTTTAA-TTT-AT
1 TTTTTAATTTTAAT
2867 TTTTTAATTTTAAT
1 TTTTTAATTTTAAT
*
2881 TTTTTACTTTT
1 TTTTTAATTTT
2892 TGATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTAATTTTAAT
Found at i:4838 original size:24 final size:24
Alignment explanation
Indices: 4810--4858 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
4800 ATTTTTTATG
4810 AATTTCTCAAAAAT-AAATTTAAAA
1 AATTT-TCAAAAATGAAATTTAAAA
*
4834 AATTTTGAAAAATGAAATTTAAAA
1 AATTTTCAAAAATGAAATTTAAAA
4858 A
1 A
4859 GAAATAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (24 bp):
AATTTTCAAAAATGAAATTTAAAA
Found at i:5103 original size:20 final size:18
Alignment explanation
Indices: 5058--5110 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 18
5048 TTTTTTTCTC
5058 TTTTTT-ATTTTTATTTT
1 TTTTTTCATTTTTATTTT
5075 TTTGATTTCATTTTTAATTTT
1 TTT--TTTCATTTTT-ATTTT
5096 TATTTTTCACTTTTT
1 T-TTTTTCA-TTTTT
5111 TTAATTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.10
19 3 0.10
20 11 0.37
21 11 0.37
22 2 0.07
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTTTCATTTTTATTTT
Found at i:5714 original size:19 final size:21
Alignment explanation
Indices: 5675--5714 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
5665 TTAATATGTA
5675 TTTTATATAAATATATTTTAT
1 TTTTATATAAATATATTTTAT
*
5696 TTTTAT-TAAA-ATTTTTTAT
1 TTTTATATAAATATATTTTAT
5715 ATATTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTATATAAATATATTTTAT
Found at i:11035 original size:2 final size:2
Alignment explanation
Indices: 11028--11062 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11018 CTCATGAATC
*
11028 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11063 ACTAAAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11088 original size:28 final size:28
Alignment explanation
Indices: 11056--11131 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
11046 ATATATGTAT
* *
11056 ATATATAACTAAAACTGAACTT-AATACC
1 ATATATAACTAAAA-TCAAATTGAATACC
* *
11084 GTATATAACCAAAATCAAATTGAATACC
1 ATATATAACTAAAATCAAATTGAATACC
* *
11112 ATATATAACTGAAATAAAAT
1 ATATATAACTAAAATCAAAT
11132 CAAACTAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (28 bp):
ATATATAACTAAAATCAAATTGAATACC
Found at i:14048 original size:117 final size:117
Alignment explanation
Indices: 13900--14131 Score: 446
Period size: 117 Copynumber: 2.0 Consensus size: 117
13890 TTTTAAATGG
*
13900 ACTTAACCTTTTTGTCTAAACCCATTTTTTTAGTATAATATTTTTGTCTAAACTCTCATAAATAT
1 ACTTAACCTTTTTGTCTAAACCCATTTTTTTAGTATAACATTTTTGTCTAAACTCTCATAAATAT
*
13965 CGAATAGGCCTTCAAGCTTGGACGAATCCAAAATAATTTTAAAAACAAAAGA
66 CGAATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAAGA
14017 ACTTAACCTTTTTGTCTAAACCCATTTTTTTAGTATAACATTTTTGTCTAAACTCTCATAAATAT
1 ACTTAACCTTTTTGTCTAAACCCATTTTTTTAGTATAACATTTTTGTCTAAACTCTCATAAATAT
14082 CGAATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAA
66 CGAATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAA
14132 AAGTCATCAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 113 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (117 bp):
ACTTAACCTTTTTGTCTAAACCCATTTTTTTAGTATAACATTTTTGTCTAAACTCTCATAAATAT
CGAATAGGCCTTCAAGCTTGGACGAATCCAAAATAATATTAAAAACAAAAGA
Found at i:15303 original size:20 final size:16
Alignment explanation
Indices: 15261--15379 Score: 78
Period size: 16 Copynumber: 7.0 Consensus size: 16
15251 TTTTTACCCA
15261 GATGTATCGATACATT
1 GATGTATCGATACATT
15277 GATGTATCGATACATGTAT
1 GATGTATCGATACA--T-T
*
15296 GAATGTATCGATATATT
1 G-ATGTATCGATACATT
* * *** * *
15313 -CTGTCTTTTTACCTA
1 GATGTATCGATACATT
*
15328 GATATATCGATACATT
1 GATGTATCGATACATT
15344 GATGTATCGATACATGTAT
1 GATGTATCGATACA--T-T
15363 GAATGTATCGATACATT
1 G-ATGTATCGATACATT
15380 CTTCAATGTA
Statistics
Matches: 76, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
15 7 0.09
16 34 0.45
17 2 0.03
18 4 0.05
19 4 0.05
20 25 0.33
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (16 bp):
GATGTATCGATACATT
Found at i:15319 original size:67 final size:67
Alignment explanation
Indices: 15211--15381 Score: 315
Period size: 67 Copynumber: 2.6 Consensus size: 67
15201 TTTTAACTAA
*
15211 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATGTATCGATACAT
1 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATATATCGATACAT
15276 TG
66 TG
*
15278 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCTAGATATATCGATACAT
1 ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATATATCGATACAT
15343 TG
66 TG
*
15345 ATGTATCGATACATGTATGAATGTATCGATACATTCT
1 ATGTATCGATACATGTATGAATGTATCGATATATTCT
15382 TCAATGTATT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 101 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (67 bp):
ATGTATCGATACATGTATGAATGTATCGATATATTCTGTCTTTTTACCCAGATATATCGATACAT
TG
Found at i:15369 original size:87 final size:83
Alignment explanation
Indices: 15261--15430 Score: 216
Period size: 87 Copynumber: 2.0 Consensus size: 83
15251 TTTTTACCCA
* * *
15261 GATGTATCGATACATTGATGTATCGATACATGT-ATGAATGTATCGATATATTCTGTCTTTTTAC
1 GATGTATCGATACATTGATGTATCGATACAT-TCATCAATGTATCGATACATTCTATCTTTTTAC
*
15325 CTAGATATATCGATACATT
65 CCAGATATATCGATACATT
* *
15344 GATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATGTATTGATACATTCTATCTTTT
1 GATGTATCGATACA--T-TG-ATGTATCGATACATTCATCAATGTATCGATACATTCTATCTTTT
* *
15409 TTCCCAGATGTATCGATACATT
62 TACCCAGATATATCGATACATT
15431 TTTTTAGTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
83 14 0.19
85 1 0.01
86 3 0.04
87 56 0.76
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (83 bp):
GATGTATCGATACATTGATGTATCGATACATTCATCAATGTATCGATACATTCTATCTTTTTACC
CAGATATATCGATACATT
Found at i:15387 original size:20 final size:20
Alignment explanation
Indices: 15345--15401 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
15335 CGATACATTG
* *
15345 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
15365 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
15385 ATGTATTGATACATTCT
1 ATGTATCGATACATTCT
15402 ATCTTTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:21740 original size:29 final size:26
Alignment explanation
Indices: 21695--21751 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 26
21685 ATAAAATTAT
21695 TATTTTATTTAATATTAATTATAAAAA
1 TATTTTATTTAATATTAA-TATAAAAA
21722 TATTTTAATATTAATATTAATATAAAAA
1 TATTTT-AT-TTAATATTAATATAAAAA
21750 TA
1 TA
21752 AAATAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 6 0.21
28 12 0.43
29 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATTTTATTTAATATTAATATAAAAA
Found at i:21758 original size:28 final size:29
Alignment explanation
Indices: 21703--21761 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
21693 ATTATTTTAT
***
21703 TTAATATTAATTATAAAAATATTTTAATA
1 TTAATATTAATTATAAAAATAAAATAATA
21732 TTAATATTAA-TATAAAAATAAAATAATA
1 TTAATATTAATTATAAAAATAAAATAATA
21760 TT
1 TT
21762 TTAATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 17 0.63
29 10 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAATATTAATTATAAAAATAAAATAATA
Found at i:22452 original size:51 final size:52
Alignment explanation
Indices: 22376--22514 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 52
22366 TTTGGAAAGA
* * *
22376 AAATGTATTGATAAATTTTTCATTGTATCGATACATTCTAG-GTTTTAACCT
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGAGTTTTAACCC
* * *
22427 AAATGTATCAATACATTTTTCATTGTATCGATACATTCTAGATTTTTGACCC
1 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGAGTTTTAACCC
* * * *
22479 AAATATATCGATACATTCTTCAATGTATCAATACAT
1 AAATGTATCGATACATTTTTCATTGTATCGATACAT
22515 GTAAGCTATT
Statistics
Matches: 76, Mismatches: 11, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
51 38 0.50
52 38 0.50
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGAGTTTTAACCC
Found at i:24931 original size:80 final size:80
Alignment explanation
Indices: 24828--25140 Score: 367
Period size: 80 Copynumber: 3.9 Consensus size: 80
24818 TCACCATCGG
* * *
24828 GGATACTTCAACCCCGTCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGAGATACTCCAACC
1 GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
* *
24893 CTATCAATTCTGAAG
66 CCATCAATTCTGAAA
* *
24908 GGATACTCCAACCCCATCGTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGACACTCCAACC
1 GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
* *
24973 CTATCAATTCCGAAA
66 CCATCAATTCTGAAA
* *** * * *
24988 GGATACTCCAACCCCGT-TCTTACTTCTAAAACATTGAATTTCTTCGTCTTTGGGGATACTCCAA
1 GGATACTCCAACCCCATCT-TTACTTCTAAAACACCAAAATT-TTCATCTTAGGGGATACTCCAA
**
25052 CCCCATCGTTTCTGAAA
64 CCCCATCAATTCTGAAA
* * * * * * *
25069 GGATACTCCAACTCCATTTTTATTTTCCAAAACATCAAAATTTTTATCTCAGGGGATACTCCAAC
1 GGATACTCCAACCCCATCTTTA-CTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAAC
25134 CCCATCA
65 CCCATCA
25141 TTTTCGAGTG
Statistics
Matches: 197, Mismatches: 32, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
80 107 0.54
81 75 0.38
82 15 0.08
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.30
Consensus pattern (80 bp):
GGATACTCCAACCCCATCTTTACTTCTAAAACACCAAAATTTTCATCTTAGGGGATACTCCAACC
CCATCAATTCTGAAA
Found at i:25235 original size:109 final size:108
Alignment explanation
Indices: 25097--25381 Score: 348
Period size: 109 Copynumber: 2.6 Consensus size: 108
25087 TTTATTTTCC
* *
25097 AAAACATCAAAATTT-TT-ATCTC-AGGGGATACTCCAACCCCATCATTTTCGAGTGGATACTCT
1 AAAACAT-TAAATTTCTTCATCTCTA-GGGATACTCCAACCCCATCATTTTCGAG-GGATACTCC
*
25159 AACCTCATCAATTCCAAAGA-GATACTTCAACACC-GTTTTTACTTCT
63 AACCTCACCAATT-CAAAGAGGATACTTCAAC-CCTGTTTTTACTTCT
* * *
25205 AAAACATTGAATTTCTTCATCTCTAGGGATACTCCAACCCCATCATTTCCAAAGGGATACTCCAA
1 AAAACATTAAATTTCTTCATCTCTAGGGATACTCCAACCCCATCATTTTC-GAGGGATACTCCAA
* ** *
25270 CCCCACCAATTCTGAGAGGATACTTCAACCCTGTTTTTACTTTT
65 CCTCACCAATTCAAAGAGGATACTTCAACCCTGTTTTTACTTCT
** *
25314 AAAACATTAAATTTCTTCATCTCTA-GGATACTCCAACGTCACCATTTTCGAGGGGATACTCCAA
1 AAAACATTAAATTTCTTCATCTCTAGGGATACTCCAACCCCATCATTTTCGA-GGGATACTCCAA
25378 CCTC
65 CCTC
25382 GATTTTCACC
Statistics
Matches: 153, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
107 6 0.04
108 50 0.33
109 94 0.61
110 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.11, T:0.31
Consensus pattern (108 bp):
AAAACATTAAATTTCTTCATCTCTAGGGATACTCCAACCCCATCATTTTCGAGGGATACTCCAAC
CTCACCAATTCAAAGAGGATACTTCAACCCTGTTTTTACTTCT
Found at i:32007 original size:2 final size:2
Alignment explanation
Indices: 32000--32034 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31990 ATTATCAATA
32000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32035 AACACCAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32784 original size:24 final size:24
Alignment explanation
Indices: 32755--32820 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
32745 TTTTTAGAAG
32755 TTTTAAA-A-TCAATAATATTTTATT
1 TTTTAAAGATTCAA-AA-ATTTTATT
*
32779 TTTTAAAGATTTAAAAATTTTATT
1 TTTTAAAGATTCAAAAATTTTATT
*
32803 TTTTAAATATTTCAAAAA
1 TTTTAAAGA-TTCAAAAA
32821 GAAATCTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 23 0.64
25 10 0.28
26 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTAAAGATTCAAAAATTTTATT
Found at i:32796 original size:33 final size:31
Alignment explanation
Indices: 32736--32796 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
32726 ACGTTAGTAT
*
32736 TAATTTTTATTTTTAGAAGTTTTAAAATCAA
1 TAATTTTTATTTTTAGAAGTTTAAAAATCAA
32767 TAATATTTTATTTTTTA-AAGATTTAAAAAT
1 TAAT-TTTTA-TTTTTAGAAG-TTTAAAAAT
32797 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 4 0.15
32 8 0.31
33 14 0.54
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (31 bp):
TAATTTTTATTTTTAGAAGTTTAAAAATCAA
Found at i:32819 original size:25 final size:24
Alignment explanation
Indices: 32771--32820 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
32761 AATCAATAAT
32771 ATTTTATTTTTTAAAGATTTAAAA
1 ATTTTATTTTTTAAAGATTTAAAA
*
32795 ATTTTATTTTTTAAATATTTCAAAA
1 ATTTTATTTTTTAAAGATTT-AAAA
32820 A
1 A
32821 GAAATCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTATTTTTTAAAGATTTAAAA
Found at i:33105 original size:12 final size:12
Alignment explanation
Indices: 33084--33116 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
33074 AGCTTTACCG
*
33084 TTTTTATTTCTC
1 TTTTTTTTTCTC
33096 TTTTTTTTTCTC
1 TTTTTTTTTCTC
33108 TTTTTTTTT
1 TTTTTTTTT
33117 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTCTC
Found at i:33813 original size:20 final size:21
Alignment explanation
Indices: 33777--33817 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
33767 GTATTTAGAT
33777 AATTAAATTAAATTTATTTTAG
1 AATTAAATT-AATTTATTTTAG
33799 AATTAAATT-ATTTATTTTA
1 AATTAAATTAATTTATTTTA
33818 TTAGATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTAAATTAATTTATTTTAG
Found at i:34970 original size:24 final size:23
Alignment explanation
Indices: 34919--34970 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
34909 TGAATTTTTC
*
34919 AAAAATAAATTTAAAAAAAATTTG
1 AAAAATAAATTTAAAAAAAA-TTA
34943 AAAAATGAAATTTAAGAAAAAA-TA
1 AAAAAT-AAATTTAA-AAAAAATTA
34967 AAAA
1 AAAA
34971 GAAGAGGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 11 0.44
25 8 0.32
26 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAAATAAATTTAAAAAAAATTA
Found at i:35163 original size:16 final size:16
Alignment explanation
Indices: 35138--35174 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
35128 GTTAGTTTGC
35138 TTTTTCTCTCT-TTTT
1 TTTTTCTCTCTCTTTT
35153 TTTTTCTTCTCTCTTTT
1 TTTTTC-TCTCTCTTTT
35170 TTTTT
1 TTTTT
35175 TTTTGATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 5 0.25
17 9 0.45
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTCTCTCTTTT
Found at i:35164 original size:18 final size:18
Alignment explanation
Indices: 35141--35175 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
35131 AGTTTGCTTT
35141 TTCTCTCTTTTTTTTTTC
1 TTCTCTCTTTTTTTTTTC
35159 TTCTCTCTTTTTTTTTT
1 TTCTCTCTTTTTTTTTT
35176 TTTGATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTCTCTTTTTTTTTTC
Found at i:40144 original size:20 final size:19
Alignment explanation
Indices: 40115--40189 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
40105 AAAAAGACAT
40115 AATGTATCGATACATTGTA
1 AATGTATCGATACATTGTA
* *
40134 GAATATATCGATACATTCATA
1 -AATGTATCGATACATT-GTA
* *
40155 AATGTATCGATATATTGAAA
1 AATGTATCGATACATTG-TA
40175 AATGTATCGATACAT
1 AATGTATCGATACAT
40190 CAGGGTATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (19 bp):
AATGTATCGATACATTGTA
Found at i:41266 original size:257 final size:256
Alignment explanation
Indices: 40703--41774 Score: 1605
Period size: 257 Copynumber: 4.2 Consensus size: 256
40693 ACAGTGGTGA
* * * *
40703 TTTGAAAAGGGTTGCCATTGACTTGCATGGGCTTTAAAAGGGTGCCACTAACTTGCGTGGGCTTT
1 TTTGAAAAGAG-TGCCACTGACTTG--TGGGCTTTGAAAGGGTGCCACTGACTT--GTGGGCTTT
** * * *
40768 GAAAGAATGCCACTAACTCGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGT
61 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGT
* * * *
40832 GCCACTGACTTGTGGGCTTTGAAAAG-GTACCACTGACTTGCGTGAGCTTTAAAAGGAGTGCCAC
126 GCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT--GTGGGCTTTGAAAGGAGTGCCAC
* *
40896 TGACTTGTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGAATTG
189 TGAC-T-TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGATTTG
40961 TGGGC
252 TGGGC
* * * * * * *
40966 TTCGCAATG-GTGCCACTGACTTGTGGGCTTCGCAATGGTGCCACTGACTTGTGGGCTTCGAAAG
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
41030 GGTGCCACTGACTTGTGGGCTCTGAAAGGGTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCAT
66 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
*
41094 TGATTTGTGGGCTTTGAAAAGAGTGCCGCTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
131 TGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
*
41159 TGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
196 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGATTTGTGGGC
*
41221 TTTGAAAAGAGTGCCACTGGCTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAA
*
41286 GGGTGCCACTGAGTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
65 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
* *
41351 CTGATTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTAACTT
130 CTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTT
* * * *
41416 GTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGC
195 GTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGATTTGTGGGC
* *
41478 TTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAGGAGTGCTACTGACTTGTGGGCTTTGAAA
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAA
*
41543 GGGTGCCACTGAGTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
65 GGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCA
*
41608 CTGATTTGTAGGCTTTG-AAAGAAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACT
130 CTGATTTGTGGGCTTTGAAAAG-AGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACT
*
41672 TGTGGGCTTGGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGC
194 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGATTTGTGGGC
*
41736 TTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
1 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGG
41775 ATGAACATTC
Statistics
Matches: 741, Mismatches: 61, Indels: 20
0.90 0.07 0.02
Matches are distributed among these distances:
254 37 0.05
255 30 0.04
256 52 0.07
257 406 0.55
258 175 0.24
259 22 0.03
261 12 0.02
262 1 0.00
263 6 0.01
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (256 bp):
TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAG
GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCAC
TGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTG
TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGATTTGTGGGC
Found at i:41772 original size:29 final size:29
Alignment explanation
Indices: 40715--41773 Score: 1483
Period size: 28 Copynumber: 36.9 Consensus size: 29
40705 TGAAAAGGGT
* *
40715 TGCCATTGACTTGCATGGGCTTTAAAAGG-G
1 TGCCACTGACTTG--TGGGCTTTGAAAGGAG
* *
40745 TGCCACTAACTTGCGTGGGCTTTGAAA-GAA
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
* *
40775 TGCCACTAACTCGTGGGCTTTGAAAGGA-
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
40803 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
40831 TGCCACTGACTTGTGGGCTTTGAAAAG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
40859 TACCACTGACTTGCGTGAGCTTTAAAAGGAG
1 TGCCACTGACTT--GTGGGCTTTGAAAGGAG
*
40890 TGCCACTGACTTGTGTGGGCTTTAAAAGG-G
1 TGCCACTGAC-T-TGTGGGCTTTGAAAGGAG
40920 TGCCACTGACTTGTGGGCTTTGAAA-GAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * * *
40948 TGCCACTGAATTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
40976 TGCCACTGACTTGTGGGCTTCGCAATG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41004 TGCCACTGACTTGTGGGCTTCGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41032 TGCCACTGACTTGTGGGCTCTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41060 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
41088 TGCCATTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41117 TGCCGCTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
41146 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
41174 TGCCACTAACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
41203 TGCCACTGATTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41232 TGCCACTGGCTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
41261 TGCCACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41289 TGCCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41317 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41346 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
41375 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41404 TGCCACTAACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41432 TGCCATTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* *
41460 TGCCACTGACTTATGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41489 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41518 TGCTACTGACTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41546 TGCCACTGAGTTGTGGGCTTTGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41574 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
* * *
41603 TGCCACTGATTTGTAGGCTTTGAAAGAAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
41632 TGCCACTGACTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41661 TGCCACTGACTTGTGGGCTTGGAAAGG-G
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41689 TGCCACTGACTTGTGGGCTTTGAAAAGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
*
41718 TGCCACTGATTTGTGGGCTTTGAAAGGAG
1 TGCCACTGACTTGTGGGCTTTGAAAGGAG
41747 TGCCACTGACTTGTGGGCTTTGAAAGG
1 TGCCACTGACTTGTGGGCTTTGAAAGG
41774 GATGAACATT
Statistics
Matches: 935, Mismatches: 75, Indels: 39
0.89 0.07 0.04
Matches are distributed among these distances:
27 3 0.00
28 446 0.48
29 404 0.43
30 55 0.06
31 24 0.03
32 2 0.00
33 1 0.00
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGAAAGGAG
Found at i:43006 original size:1 final size:1
Alignment explanation
Indices: 43002--43054 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
42992 TTTTTTGCTA
* * * * *
43002 TTTTTTCTTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
43055 GGGTGTAACG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.91
Consensus pattern (1 bp):
T
Found at i:43016 original size:11 final size:11
Alignment explanation
Indices: 43002--43055 Score: 72
Period size: 11 Copynumber: 4.6 Consensus size: 11
42992 TTTTTTGCTA
*
43002 TTTTTTCTTTT
1 TTTTTTGTTTT
43013 TTTTTTGTTTTTT
1 TTTTTTG--TTTT
43026 TTGTTTTGTTTT
1 TT-TTTTGTTTT
43038 TTTTTTGTTTT
1 TTTTTTGTTTT
43049 TTTTTTG
1 TTTTTTG
43056 GGTGTAACGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
11 22 0.56
12 6 0.15
13 6 0.15
14 5 0.13
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (11 bp):
TTTTTTGTTTT
Found at i:43016 original size:21 final size:21
Alignment explanation
Indices: 42992--43039 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42982 GACCCTTCTA
42992 TTTTTTGCTATTTTTTCTTTT-
1 TTTTTTG-TATTTTTTCTTTTG
* *
43013 TTTTTTGTTTTTTTTGTTTTG
1 TTTTTTGTATTTTTTCTTTTG
43034 TTTTTT
1 TTTTTT
43040 TTTTGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.85
Consensus pattern (21 bp):
TTTTTTGTATTTTTTCTTTTG
Found at i:43038 original size:25 final size:25
Alignment explanation
Indices: 43004--43052 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
42994 TTTTGCTATT
43004 TTTTCTTTTTTTTTTGTTTTTTTTG
1 TTTTCTTTTTTTTTTGTTTTTTTTG
*
43029 TTTTGTTTTTTTTTTGTTTTTTTT
1 TTTTCTTTTTTTTTTGTTTTTTTT
43053 TTGGGTGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (25 bp):
TTTTCTTTTTTTTTTGTTTTTTTTG
Found at i:56513 original size:44 final size:45
Alignment explanation
Indices: 56462--56557 Score: 167
Period size: 45 Copynumber: 2.2 Consensus size: 45
56452 CTCTCTTTCC
*
56462 CTTCTCTCCCACTATGGTTAGCTTG-TTTTTTTCTCTCTTTTTTT
1 CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCTATTTTTTT
*
56506 CTTCTCTCCCATTATGGTTAGCTTGCTTTTTTTCTCTATTTTTTT
1 CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCTATTTTTTT
56551 CTTCTCT
1 CTTCTCT
56558 TTTTTTATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 24 0.49
45 25 0.51
ACGTcount: A:0.07, C:0.25, G:0.08, T:0.59
Consensus pattern (45 bp):
CTTCTCTCCCACTATGGTTAGCTTGCTTTTTTTCTCTATTTTTTT
Found at i:56581 original size:22 final size:21
Alignment explanation
Indices: 56543--56610 Score: 77
Period size: 20 Copynumber: 3.2 Consensus size: 21
56533 TTTTTTCTCT
* * *
56543 ATTTTTTTCTTCTCTTTTTTT
1 ATTTTTTTTTTCACTTTTTTA
56564 ATTTTTTTATTTCAC--TTTTA
1 ATTTTTTT-TTTCACTTTTTTA
56584 ATTTTTGTTTTTCACTTTTTTA
1 ATTTTT-TTTTTCACTTTTTTA
56606 ATTTT
1 ATTTT
56611 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 16 0.40
21 10 0.25
22 14 0.35
ACGTcount: A:0.13, C:0.10, G:0.01, T:0.75
Consensus pattern (21 bp):
ATTTTTTTTTTCACTTTTTTA
Found at i:58125 original size:11 final size:11
Alignment explanation
Indices: 58109--58153 Score: 53
Period size: 9 Copynumber: 4.5 Consensus size: 11
58099 ACAATCATTT
58109 AAATATATTAA
1 AAATATATTAA
*
58120 AAATATTTTAA
1 AAATATATTAA
58131 AAAT-T-TTAA
1 AAATATATTAA
58140 AAA-A-ATTAA
1 AAATATATTAA
58149 AAATA
1 AAATA
58154 CATATATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 14 0.47
10 2 0.07
11 14 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAATATATTAA
Found at i:61159 original size:20 final size:21
Alignment explanation
Indices: 61124--61167 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
61114 CATGTCAGTA
*
61124 TTTTATCAATATTTAATGATT
1 TTTTACCAATATTTAATGATT
*
61145 TTTTACCAATA-TTAATTATT
1 TTTTACCAATATTTAATGATT
61165 TTT
1 TTT
61168 CCTTAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTACCAATATTTAATGATT
Found at i:62383 original size:2 final size:2
Alignment explanation
Indices: 62376--62405 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
62366 CTCATGAATC
62376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62406 GCATAACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62475 original size:28 final size:28
Alignment explanation
Indices: 62408--62467 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
62398 ATATATATGC
* * *
62408 ATAACCAAAACCAAACTGAATACTATAT
1 ATAACCAAAATCAAATTGAATACCATAT
62436 ATAACCAAAATCAAATTGAATACCATAT
1 ATAACCAAAATCAAATTGAATACCATAT
62464 ATAA
1 ATAA
62468 TTGAAATCGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.23
Consensus pattern (28 bp):
ATAACCAAAATCAAATTGAATACCATAT
Done.