Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2703
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: 22276
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:1770 original size:22 final size:22
Alignment explanation
Indices: 1730--1787 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
1720 CAAATAAAAG
* *
1730 AACAAAGTCA-AAATGAATAGA
1 AACAAAATCAGAATTGAATAGA
1751 AACAAAATCAGAATTGAATAGA
1 AACAAAATCAGAATTGAATAGA
1773 AACAAAATCAGAATT
1 AACAAAATCAGAATT
1788 AAGGATTACG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 9 0.26
22 25 0.74
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.17
Consensus pattern (22 bp):
AACAAAATCAGAATTGAATAGA
Found at i:4283 original size:33 final size:37
Alignment explanation
Indices: 4230--4305 Score: 106
Period size: 34 Copynumber: 2.2 Consensus size: 37
4220 AAAATAACAT
4230 AAATATATATAAATATTTTAAAATTTATAT-AATATA
1 AAATATATATAAATATTTTAAAATTTATATAAATATA
* *
4266 AAATA-ATA-AAATA-TTTAAAATTTATTTAAATATT
1 AAATATATATAAATATTTTAAAATTTATATAAATATA
4300 AAATAT
1 AAATAT
4306 TTTAAATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
33 13 0.36
34 15 0.42
35 3 0.08
36 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (37 bp):
AAATATATATAAATATTTTAAAATTTATATAAATATA
Found at i:4285 original size:63 final size:58
Alignment explanation
Indices: 4193--4336 Score: 159
Period size: 63 Copynumber: 2.4 Consensus size: 58
4183 AAAATTAAAA
*
4193 TAATAATATAAAAT-ATAATATAATATAAAAATAACATAAATATATATAAATATTTTAAAATT
1 TAATAATATAAAATAATAAAAT-ATATAAAAATAA-ATAAA-ATAT-TAAATATTTT-AAATT
* * * * *
4255 TATATAATATAAAATAATAAAATATTTAAAATTTATTTAAATATTAAATATTTTAAATT
1 TA-ATAATATAAAATAATAAAATATATAAAAATAAATAAAATATTAAATATTTTAAATT
4314 TAAT--TATAAAATAATAAAATATA
1 TAATAATATAAAATAATAAAATATA
4337 AACATGATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
56 18 0.25
58 2 0.03
59 7 0.10
60 10 0.14
61 4 0.05
62 5 0.07
63 21 0.29
64 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (58 bp):
TAATAATATAAAATAATAAAATATATAAAAATAAATAAAATATTAAATATTTTAAATT
Found at i:4792 original size:16 final size:16
Alignment explanation
Indices: 4773--4826 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
4763 CAAAATTTTA
4773 AAAATTTAAAAAATAT
1 AAAATTTAAAAAATAT
* *
4789 AAAACTCAAAAAA-ATT
1 AAAATTTAAAAAATA-T
4805 AAAATTATAAAAAATTAT
1 AAAATT-TAAAAAA-TAT
4823 AAAA
1 AAAA
4827 ATTTTGTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
15 1 0.03
16 17 0.57
17 6 0.20
18 5 0.17
19 1 0.03
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATTTAAAAAATAT
Found at i:4923 original size:28 final size:28
Alignment explanation
Indices: 4892--4958 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
4882 TTAATAATTC
*
4892 AAAAATTATTTAAAA-AT-ATAAGCCTTAT
1 AAAAATTATTTAAAATATAATAA-AC-TAT
*
4920 AAAAA-TATATAAAATATCAATAAACTAT
1 AAAAATTATTTAAAATAT-AATAAACTAT
4948 AAAAATTATTT
1 AAAAATTATTT
4959 TTTTAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.25
28 15 0.47
29 5 0.16
30 4 0.12
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAAATTATTTAAAATATAATAAACTAT
Found at i:5278 original size:20 final size:20
Alignment explanation
Indices: 5255--5303 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
5245 CAAGTTAATA
* *
5255 TATCAATACATAAGTGAATG
1 TATCAATACATAAATAAATG
5275 TATCAATACATAAATAAATG
1 TATCAATACATAAATAAATG
*
5295 TATCGATAC
1 TATCAATAC
5304 TAGGCCATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.47, C:0.12, G:0.10, T:0.31
Consensus pattern (20 bp):
TATCAATACATAAATAAATG
Found at i:10315 original size:15 final size:16
Alignment explanation
Indices: 10281--10323 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
10271 AATAAACTAA
10281 TAAAATTAATATAAAATT
1 TAAAATTAA-AT-AAATT
10299 TAAAATTAAAT-AATT
1 TAAAATTAAATAAATT
*
10314 TAAAAATAAA
1 TAAAATTAAA
10324 AAGTGAAGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 13 0.54
17 2 0.08
18 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATTAAATAAATT
Found at i:10840 original size:14 final size:15
Alignment explanation
Indices: 10821--10885 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 15
10811 CGGTGAAGTG
10821 AATTAT-ATTAAAAA
1 AATTATAATTAAAAA
* *
10835 AATTATCATTAAAGA
1 AATTATAATTAAAAA
* *
10850 TATTAT-ATTAAAAT
1 AATTATAATTAAAAA
*
10864 AATTATAAATTATAAA
1 AATTAT-AATTAAAAA
10880 AATTAT
1 AATTAT
10886 TTTTATATTA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
14 17 0.41
15 12 0.29
16 12 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
AATTATAATTAAAAA
Found at i:10892 original size:36 final size:35
Alignment explanation
Indices: 10852--10957 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 35
10842 ATTAAAGATA
* *
10852 TTATATTAAAATAATTATAAATTATAAAAATTATTT
1 TTATATTAAAATAATTA-AAATTATTAAAATTATAT
10888 TTATATT-AAATAA-TAAAATATGAATTAAAATTATAT
1 TTATATTAAAATAATTAAAAT-T--ATTAAAATTATAT
*
10924 TTATATTAAATAATAATTAAAAATATTAAAATTA
1 TTATATT-AA-AATAATTAAAATTATTAAAATTA
10958 AAAAATAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
33 4 0.07
34 3 0.05
35 6 0.10
36 25 0.42
37 10 0.17
38 1 0.02
39 6 0.10
40 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (35 bp):
TTATATTAAAATAATTAAAATTATTAAAATTATAT
Found at i:11376 original size:26 final size:26
Alignment explanation
Indices: 11338--11396 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
11328 TATTAGCTTA
* *
11338 AAATTAATTTATT-TTACATATTTTTAT
1 AAATT-ATATATTATTA-ATATTTTAAT
*
11365 ATATTATATATTATTAATATTTTAAT
1 AAATTATATATTATTAATATTTTAAT
11391 AAATTA
1 AAATTA
11397 ACCATTTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
AAATTATATATTATTAATATTTTAAT
Found at i:14942 original size:39 final size:38
Alignment explanation
Indices: 14899--15026 Score: 89
Period size: 39 Copynumber: 3.2 Consensus size: 38
14889 TAATAAGATT
* *
14899 TTAAAGATTTAGTTTTTACATAAAAATACTAAAATCATC
1 TTAAAGATTCAATTTTTACATAAAAATACTAAAAT-ATC
* * * *
14938 TTAAATG-TTCAATTTTAACATAAAAGTACTAATATAGC
1 TTAAA-GATTCAATTTTTACATAAAAATACTAAAATATC
* * * *
14976 TCT-AAGACTTGATTTTTTATATAAAAAATATTAAAATAATC
1 T-TAAAGA-TTCAATTTTTACAT-AAAAATACTAAAAT-ATC
15017 TTAAAAGATT
1 TT-AAAGATT
15027 GATTTTGACT
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
37 1 0.01
38 5 0.07
39 39 0.58
40 13 0.19
41 5 0.07
42 4 0.06
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (38 bp):
TTAAAGATTCAATTTTTACATAAAAATACTAAAATATC
Found at i:14964 original size:78 final size:77
Alignment explanation
Indices: 14872--15167 Score: 229
Period size: 78 Copynumber: 3.8 Consensus size: 77
14862 ATAAATTTAC
* * * * * *
14872 TTTTGATATGAAAGTGCTAATAAGATTTTAAAGATTTAGTTTTTACATAAAAATACTAAAATCAT
1 TTTTGACATAAAAGTACTAATAAGACTTTAAAGATTTAGTTTTGACATAAAAATACTAAAATAAT
* *
14937 CTTAAATGTTCAA
66 CTTAAAAGTT-GA
* * * * * * *
14950 TTTTAACATAAAAGTACTAATATAG-CTCT-AAGACTTGATTTTTTATATAAAAAATATTAAAAT
1 TTTTGACATAAAAGTACTAATA-AGACTTTAAAGA-TTTAGTTTTGACAT-AAAAATACTAAAAT
15013 AATCTTAAAAGATTGA
63 AATCTTAAAAG-TTGA
* * * * * * * *
15029 TTTTGACTTGAAAGTACGAATAAAACTTTAAAGA-CTAGCTTTTGATATAAAAATATTAAAATGA
1 TTTTGACATAAAAGTACTAATAAGACTTTAAAGATTTAG-TTTTGACATAAAAATACTAAAATAA
* *
15093 CCTTAAAAATTTGA
65 TCTT-AAAAGTTGA
* * * * * *
15107 TTTTGACATAAAAGTGCTAACACGATTTTAAAAATTTCGTTTTGACATAAAAATACTAAAA
1 TTTTGACATAAAAGTACTAATAAGACTTTAAAGATTTAGTTTTGACATAAAAATACTAAAA
15168 ATAACTTTAA
Statistics
Matches: 170, Mismatches: 39, Indels: 18
0.75 0.17 0.08
Matches are distributed among these distances:
77 4 0.02
78 100 0.59
79 60 0.35
80 6 0.04
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (77 bp):
TTTTGACATAAAAGTACTAATAAGACTTTAAAGATTTAGTTTTGACATAAAAATACTAAAATAAT
CTTAAAAGTTGA
Found at i:15032 original size:79 final size:78
Alignment explanation
Indices: 14838--15126 Score: 219
Period size: 78 Copynumber: 3.7 Consensus size: 78
14828 CCCAATTTCA
* * * * * * * * * * *
14838 ATATAAAAATATCAAAATGATCATATAA-ATTTACTTTTGATATGAAAGTGCTAATAAGATTTTA
1 ATATAAAAATATTAAAATAATCTTAAAAGATTGA-TTTTGACATAAAAGTACTAATAAAACTCTA
*
14902 AAGATTTAG-TTTTT
65 AAGA-CTAGCTTTTT
* * * * * * * *
14916 ACATAAAAATACTAAAATCATCTTAAATG-TTCAATTTTAACATAAAAGTACTAATATAGCTCT-
1 ATATAAAAATATTAAAATAATCTTAAAAGATT-GATTTTGACATAAAAGTACTAATAAAACTCTA
* *
14979 AAGACTTGATTTTTT
65 AAGACTAG-CTTTTT
* * * *
14994 ATATAAAAAATATTAAAATAATCTTAAAAGATTGATTTTGACTTGAAAGTACGAATAAAACTTTA
1 ATAT-AAAAATATTAAAATAATCTTAAAAGATTGATTTTGACATAAAAGTACTAATAAAACTCTA
*
15059 AAGACTAGCTTTTG
65 AAGACTAGCTTTTT
* * *
15073 ATATAAAAATATTAAAATGACCTTAAAA-ATTTGATTTTGACATAAAAGTGCTAA
1 ATATAAAAATATTAAAATAATCTTAAAAGA-TTGATTTTGACATAAAAGTACTAA
15127 CACGATTTTA
Statistics
Matches: 163, Mismatches: 40, Indels: 16
0.74 0.18 0.07
Matches are distributed among these distances:
76 2 0.01
77 5 0.03
78 93 0.57
79 54 0.33
80 9 0.06
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (78 bp):
ATATAAAAATATTAAAATAATCTTAAAAGATTGATTTTGACATAAAAGTACTAATAAAACTCTAA
AGACTAGCTTTTT
Found at i:15043 original size:157 final size:156
Alignment explanation
Indices: 14838--15126 Score: 332
Period size: 157 Copynumber: 1.8 Consensus size: 156
14828 CCCAATTTCA
* * * * * * *
14838 ATATAAAAATATCAAAATGATCATATAAATTTACTTTTGATATGAAAGTGCTAATAAGATTTTAA
1 ATATAAAAATATCAAAATAATCATAAAAATTGACTTTTGATATGAAAGTACGAATAAAACTTTAA
* * * **
14903 AGATTTAG-TTTTTACATAAAAATACTAAAATCATCTTAAATGTTCAATTTTAACATAAAAGTAC
66 AGA-CTAGCTTTTGACATAAAAATACTAAAATCACCTTAAAAATTCAATTTTAACATAAAAGTAC
14967 TAATATAGCTCTAAGACTTGATTTTTT
130 TAATATAGCTCTAAGACTTGATTTTTT
* *
14994 ATATAAAAAATATTAAAATAATCTTAAAAGATTGA-TTTTGACT-TGAAAGTACGAATAAAACTT
1 ATAT-AAAAATATCAAAATAATCATAAAA-ATTGACTTTTGA-TATGAAAGTACGAATAAAACTT
* * * ** *
15057 TAAAGACTAGCTTTTGATATAAAAATATTAAAATGACCTTAAAAATTTGATTTTGACATAAAAGT
63 TAAAGACTAGCTTTTGACATAAAAATACTAAAATCACCTTAAAAATTCAATTTTAACATAAAAGT
*
15122 GCTAA
128 ACTAA
15127 CACGATTTTA
Statistics
Matches: 108, Mismatches: 21, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
156 7 0.06
157 96 0.89
158 5 0.05
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.37
Consensus pattern (156 bp):
ATATAAAAATATCAAAATAATCATAAAAATTGACTTTTGATATGAAAGTACGAATAAAACTTTAA
AGACTAGCTTTTGACATAAAAATACTAAAATCACCTTAAAAATTCAATTTTAACATAAAAGTACT
AATATAGCTCTAAGACTTGATTTTTT
Found at i:15111 original size:39 final size:39
Alignment explanation
Indices: 14999--15265 Score: 135
Period size: 39 Copynumber: 6.8 Consensus size: 39
14989 TTTTTATATA
* *
14999 AAAAATATTAAAATAATCTTAAAAGA-TTGATTTTGACTT
1 AAAAATATTAAAATAACCTTAAAA-ATTTGATTTTGACAT
* * ** * * * * * *
15038 GAAAGTACGAATAA-AACTTTAAAGACTAGCTTTTGATAT
1 AAAAATATTAA-AATAACCTTAAAAATTTGATTTTGACAT
*
15077 AAAAATATTAAAATGACCTTAAAAATTTGATTTTGACAT
1 AAAAATATTAAAATAACCTTAAAAATTTGATTTTGACAT
* ** * ** **
15116 AAAAGTGCTAACACGATTTTAAAAATTTCG-TTTTGACAT
1 AAAAATATTAAAATAACCTTAAAAATTT-GATTTTGACAT
* * ** * *
15155 AAAAATACTAAAAATAACTTTAAAAATTCAATTTCGATAT
1 AAAAATA-TTAAAATAACCTTAAAAATTTGATTTTGACAT
* * * * * * *
15195 AAAAATATCAACACAATCTTAAGAACTTAATTTTGACAT
1 AAAAATATTAAAATAACCTTAAAAATTTGATTTTGACAT
* * * *
15234 AAAAACACTAAAATAACCTTCAAAGTTTGATT
1 AAAAATATTAAAATAACCTTAAAAATTTGATT
15266 CAACATAAGT
Statistics
Matches: 160, Mismatches: 62, Indels: 12
0.68 0.26 0.05
Matches are distributed among these distances:
38 3 0.02
39 126 0.79
40 31 0.19
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (39 bp):
AAAAATATTAAAATAACCTTAAAAATTTGATTTTGACAT
Found at i:15386 original size:19 final size:19
Alignment explanation
Indices: 15289--15387 Score: 53
Period size: 19 Copynumber: 5.3 Consensus size: 19
15279 TATGATTTTT
15289 AAAATTTAATTTTAATA-A
1 AAAATTTAATTTTAATATA
* * *
15307 AAAAATTAA--ATAACTTTA
1 AAAATTTAATTTTAA-TATA
* * * *
15325 AAAATTCATTTTTAACATG
1 AAAATTTAATTTTAATATA
* * *
15344 AAAATATTAA-TATAATCTTT
1 AAAAT-TTAATTTTAAT-ATA
15364 AAAATTTAATTTTAATATA
1 AAAATTTAATTTTAATATA
15383 AAAAT
1 AAAAT
15388 ATCAACACGA
Statistics
Matches: 55, Mismatches: 19, Indels: 13
0.63 0.22 0.15
Matches are distributed among these distances:
16 3 0.05
17 1 0.02
18 15 0.27
19 20 0.36
20 16 0.29
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (19 bp):
AAAATTTAATTTTAATATA
Found at i:15387 original size:39 final size:39
Alignment explanation
Indices: 15275--15389 Score: 139
Period size: 39 Copynumber: 3.0 Consensus size: 39
15265 TCAACATAAG
* *
15275 TTAATATGATTTTTAAAATTTAATTTTAATA-AAAAA-A
1 TTAATATAATCTTTAAAATTTAATTTTAATATAAAAATA
* * * *
15312 TTAA-ATAA-CTTTAAAAATTCATTTTTAACATGAAAATA
1 TTAATATAATCTTT-AAAATTTAATTTTAATATAAAAATA
15350 TTAATATAATCTTTAAAATTTAATTTTAATATAAAAATA
1 TTAATATAATCTTTAAAATTTAATTTTAATATAAAAATA
15389 T
1 T
15390 CAACACGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.05
36 17 0.27
37 8 0.13
38 5 0.08
39 26 0.41
40 4 0.06
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (39 bp):
TTAATATAATCTTTAAAATTTAATTTTAATATAAAAATA
Found at i:15407 original size:39 final size:38
Alignment explanation
Indices: 15283--15408 Score: 123
Period size: 39 Copynumber: 3.3 Consensus size: 38
15273 AGTTAATATG
*
15283 ATTTTTAAAATTTAATTTTAATA-AAAAA-ATTAAATA
1 ATTTTAAAAATTTAATTTTAATATAAAAATATTAAATA
* * * * *
15319 ACTTTAAAAATTCATTTTTAACATGAAAATATTAATATA
1 ATTTTAAAAATTTAATTTTAATATAAAAATATTAA-ATA
* **
15358 ATCTTT-AAAATTTAATTTTAATATAAAAATATCAACACG
1 AT-TTTAAAAATTTAATTTTAATATAAAAATATTAA-ATA
15397 ATTTTAAAAATT
1 ATTTTAAAAATT
15409 CTATTGTGAC
Statistics
Matches: 70, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
36 18 0.26
37 4 0.06
38 8 0.11
39 37 0.53
40 3 0.04
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.42
Consensus pattern (38 bp):
ATTTTAAAAATTTAATTTTAATATAAAAATATTAAATA
Found at i:17261 original size:14 final size:14
Alignment explanation
Indices: 17220--17263 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
17210 TTTTTAATTC
*
17220 TTAAAATAAATTTT
1 TTAAAATATATTTT
*
17234 TTAAAAAATATTTT
1 TTAAAATATATTTT
*
17248 TTAAAATATGTTTT
1 TTAAAATATATTTT
17262 TT
1 TT
17264 TTTACAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (14 bp):
TTAAAATATATTTT
Found at i:17620 original size:74 final size:72
Alignment explanation
Indices: 17453--17786 Score: 365
Period size: 74 Copynumber: 4.6 Consensus size: 72
17443 TATTAAAAAA
* * *
17453 TTTTTAAGGTATTATTTATCTTTATTTGTA-AAAGTTTAAATTTATTTTTGGTTATAATTATACG
1 TTTTTAA-GTATAATTTATTTTTATTTGTAGAAA-TTTAAATTTATTTTTGGGTATAATTATACG
*
17517 AGTTAAAAT
64 AGTTTAAAT
* * *
17526 TTTTAAAGTATAATTTATTTTTATTTATA-AAATTTAAATGTGT-TTTTTGGGTTATAATTATAT
1 TTTTTAAGTATAATTTATTTTTATTTGTAGAAATTTAAAT-T-TATTTTTGGG-TATAATTATAC
17589 GAGTTTAAAT
63 GAGTTTAAAT
* * *
17599 TTTTTATAGTATAATTTATTTTTATTTGTAGAAGTTTAAATGTGTTTTCTGGGTATAATTATACG
1 TTTTTA-AGTATAATTTATTTTTATTTGTAGAAATTTAAATTTATTTT-TGGGTATAATTATACG
*
17664 AGTTTATAT
64 AGTTTAAAT
* * * * **
17673 TTTTTATCA-TATGATTCATTTTTATTTGTAGAAATTTAAATTTATTTTTGAGT-TAATTACATA
1 TTTTTA--AGTATAATTTATTTTTATTTGTAGAAATTTAAATTTATTTTTGGGTATAATTATACG
*
17736 AGTATAAA-
64 AGTTTAAAT
*
17744 TTTTTAAGGTATAATTTATCTTTATTTGTAGAAATTTAAATTT
1 TTTTTAA-GTATAATTTATTTTTATTTGTAGAAATTTAAATTT
17787 TTATTTAAAA
Statistics
Matches: 223, Mismatches: 28, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
69 1 0.00
71 44 0.20
72 43 0.19
73 36 0.16
74 85 0.38
75 14 0.06
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (72 bp):
TTTTTAAGTATAATTTATTTTTATTTGTAGAAATTTAAATTTATTTTTGGGTATAATTATACGAG
TTTAAAT
Found at i:17623 original size:146 final size:145
Alignment explanation
Indices: 17450--17786 Score: 409
Period size: 146 Copynumber: 2.3 Consensus size: 145
17440 TTCTATTAAA
* *
17450 AAATTTTTAAGGTATTATTTATCTTTATTTGTAAAAGTTTAAATTTATTTT-TGGTTATAATTAT
1 AAATTTTTAAGGTATAATTTATCTTTATTTGTAAAAGTTTAAATTTATTTTCTGGGTATAATTAT
*
17514 ACGAG-TTAAAATTTTTA-AAGTATAATTTATTTTTATTTATA-AAATTTAAATGTGT-TTTTTG
66 ACGAGTTTAAAATTTTTATAA-TATAATTCATTTTTATTTATAGAAATTTAAAT-T-TATTTTTG
* * * *
17575 GGTTATAATTATATGAGTTT
128 AG-T-TAATTACATAAGTAT
* * * *
17595 AAATTTTTTATA-GTATAATTTATTTTTATTTGTAGAAGTTTAAATGTGTTTTCTGGGTATAATT
1 AAA-TTTTTA-AGGTATAATTTATCTTTATTTGTAAAAGTTTAAATTTATTTTCTGGGTATAATT
* * * * *
17659 ATACGAGTTTATATTTTTTATCATATGATTCATTTTTATTTGTAGAAATTTAAATTTATTTTTGA
64 ATACGAGTTTAAAATTTTTATAATATAATTCATTTTTATTTATAGAAATTTAAATTTATTTTTGA
17724 GTTAATTACATAAGTAT
129 GTTAATTACATAAGTAT
17741 AAATTTTTAAGGTATAATTTATCTTTATTTGTAGAAA-TTTAAATTT
1 AAATTTTTAAGGTATAATTTATCTTTATTTGTA-AAAGTTTAAATTT
17787 TTATTTAAAA
Statistics
Matches: 164, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
144 1 0.01
145 38 0.23
146 58 0.35
147 20 0.12
148 36 0.22
149 11 0.07
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.53
Consensus pattern (145 bp):
AAATTTTTAAGGTATAATTTATCTTTATTTGTAAAAGTTTAAATTTATTTTCTGGGTATAATTAT
ACGAGTTTAAAATTTTTATAATATAATTCATTTTTATTTATAGAAATTTAAATTTATTTTTGAGT
TAATTACATAAGTAT
Found at i:18907 original size:23 final size:22
Alignment explanation
Indices: 18881--18924 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
18871 ATTATTTACA
*
18881 AAATTTATAATTAATAATAATTG
1 AAATATATAATTAATAA-AATTG
18904 AAATATATAATTAATAAAATT
1 AAATATATAATTAATAAAATT
18925 ATAATACCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAATATATAATTAATAAAATTG
Found at i:19139 original size:16 final size:16
Alignment explanation
Indices: 19118--19152 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19108 TAATATAGTT
*
19118 AAAAAATTTTAAAGTA
1 AAAAAATTTAAAAGTA
19134 AAAAAATTTAAAAGTA
1 AAAAAATTTAAAAGTA
19150 AAA
1 AAA
19153 GTCACGAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AAAAAATTTAAAAGTA
Done.