Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1306
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: 24539
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Found at i:1649 original size:32 final size:32
Alignment explanation
Indices: 1600--2134 Score: 877
Period size: 32 Copynumber: 17.2 Consensus size: 32
1590 AAAATGGTGA
* * **
1600 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1632 TTTTAAATGGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1662 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1694 TTTG-AATGGTTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1725 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1757 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1789 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1821 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1853 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1885 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1917 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1949 TTTGAAA-GGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
1980 TTTGGAATGGGTTGCCACCGACTTGTG-GGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2011 TTTGAAA-GGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
2040 TTTGAAA--GGATGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2070 TTTGAAATGGG-TGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2099 TTTGAAATGGGTTGCCA-CGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
2128 TTTGAAA
1 TTTGAAA
2135 AGGTGCCACA
Statistics
Matches: 480, Mismatches: 13, Indels: 23
0.93 0.03 0.04
Matches are distributed among these distances:
28 14 0.03
29 50 0.10
30 60 0.12
31 82 0.17
32 274 0.57
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:2179 original size:27 final size:27
Alignment explanation
Indices: 2078--3211 Score: 1950
Period size: 27 Copynumber: 42.0 Consensus size: 27
2068 GCTTTGAAAT
* * * *
2078 GGGTGCCACCGACTTGTGGGCTTTGAAAT
1 GGGTGCCACGGAGTTGTGGAC-TT-AAAA
* *
2107 GGGTTGCCAC-GACTTGTGGGCTTTGAAAA
1 GGG-TGCCACGGAGTTGTGGAC-TT-AAAA
2136 -GGTGCCAC--A-TTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2159 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2186 GGGTGCCAC-GATGTTGTGGACTTAAAA
1 GGGTGCCACGGA-GTTGTGGACTTAAAA
2213 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2240 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2267 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2294 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2321 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2348 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2375 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2402 GGGTGCCAC-GAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2428 GGGTGCCAC-GATGTTGTGGACTTAAAA
1 GGGTGCCACGGA-GTTGTGGACTTAAAA
2455 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2482 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2509 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2536 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2563 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2590 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2617 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
2644 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2671 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2698 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2725 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2752 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2779 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2806 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2833 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2860 GGGTGCCAC-GAG-T-TGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2884 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2911 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2938 GGGTGCCAC-GATGTTGTGGACTTAAAA
1 GGGTGCCACGGA-GTTGTGGACTTAAAA
2965 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
2992 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
3019 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
3046 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3073 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
3101 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
3128 GGGTACCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
3156 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
3183 GGATGCCACAGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
3211 G
1 G
3212 AAAATGCCAC
Statistics
Matches: 1072, Mismatches: 16, Indels: 35
0.95 0.01 0.03
Matches are distributed among these distances:
23 4 0.00
24 30 0.03
25 11 0.01
26 38 0.04
27 898 0.84
28 64 0.06
29 21 0.02
30 6 0.01
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:10480 original size:22 final size:23
Alignment explanation
Indices: 10432--10481 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
10422 AATATTTTTT
* *
10432 ATTTTTTAAAACAAATAAAGATC
1 ATTTTTTAAAACAAATAAACATA
10455 ATTTTTTAAAA-AAA-AAACATA
1 ATTTTTTAAAACAAATAAACATA
*
10476 AATTTT
1 ATTTTT
10482 GAACTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 3 0.12
23 11 0.46
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (23 bp):
ATTTTTTAAAACAAATAAACATA
Found at i:11035 original size:18 final size:17
Alignment explanation
Indices: 11008--11044 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
10998 CCATTTCATA
*
11008 TTTTTTCTTTTTTTTTC
1 TTTTTTCTTTTCTTTTC
11025 TTTTCTTCTTTTCTTTTC
1 TTTT-TTCTTTTCTTTTC
11043 TT
1 TT
11045 CATCTTCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTCTTTTCTTTTC
Found at i:11038 original size:13 final size:13
Alignment explanation
Indices: 11020--11045 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11010 TTTTCTTTTT
11020 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
11033 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
11046 ATCTTCCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:16711 original size:43 final size:43
Alignment explanation
Indices: 16650--16998 Score: 398
Period size: 43 Copynumber: 7.9 Consensus size: 43
16640 GATGAAGATA
* * *
16650 CCAATATGCTGATTCAAGGCC-GACAACGTTAGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAG-CGACATTGGACTTAAAGGTG
*
16693 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G--G-TG
* *
16742 CCAATGTGCTAATTCAAGGCC-GACGACATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAG-CGACATTGGACTTAAAGGTG
* *
16785 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
* *
16828 CCAATATGCTGATTCAAGGCCAGTGA-TTTGGACTTAAAGATGAAGATG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-G--G-TG
* * *
16876 CCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
*
16919 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
* * *
16962 CCAATATACTGATTCAAGGCCAGCGATATTAGACTTA
1 CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
16999 GAAGAAGATG
Statistics
Matches: 267, Mismatches: 23, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
42 8 0.03
43 172 0.64
44 7 0.03
45 2 0.01
46 3 0.01
47 2 0.01
48 32 0.12
49 41 0.15
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (43 bp):
CCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTG
Found at i:16757 original size:92 final size:90
Alignment explanation
Indices: 16592--17011 Score: 441
Period size: 92 Copynumber: 4.7 Consensus size: 90
16582 CTTAGGAATG
* * * * *** *
16592 TTAAAGATGTCAATATGCTGATTCAAAGCCAACGATATCAAACTTAAAGATGAAGATACCAATAT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGA-GAAGATGCCAATAT
* * *
16657 GCTGATTCAAGGCC-GACAACGTTAGAC
64 GCTGATTCAAGGCCAG-CGACATTGGAC
*
16684 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGT
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAGA-GAAGATGCCAATAT
*
16749 GCTAATTCAAGGCC-GACGACATTGGAC
64 GCTGATTCAAGGCCAG-CGACATTGGAC
16776 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---A-AAGATGCCAATATGC
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAGAAGATGCCAATATGC
* *
16837 TGATTCAAGGCCAGTGA-TTTGGAC
66 TGATTCAAGGCCAGCGACATTGGAC
* * * *
16861 TTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAA-AG--G-TGCCA
1 TT-AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAGAAGATGCCA
*
16922 ATATGCTGATTCAAGGCCAGCGATATTGGAC
60 ATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
16953 TTAAAGGTGCCAATATACTGATTCAAGGCCAGCGATATTAGACTT-AGAAGAAGATGCCA
1 TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAG-AGAAGATGCCA
17012 CCAACTTGTG
Statistics
Matches: 283, Mismatches: 29, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
85 9 0.03
86 61 0.22
87 5 0.02
88 2 0.01
89 2 0.01
90 7 0.02
91 63 0.22
92 133 0.47
93 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (90 bp):
TTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAGAAGATGCCAATATGC
TGATTCAAGGCCAGCGACATTGGAC
Found at i:16912 original size:134 final size:135
Alignment explanation
Indices: 16650--17011 Score: 579
Period size: 134 Copynumber: 2.7 Consensus size: 135
16640 GATGAAGATA
* ** *
16650 CCAATATGCTGATTCAAGGCC-GACAACGTTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCC
1 CCAATATGCTGATTCAAGGCCAG-CGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCC
16714 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTA
65 AGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTA
16779 AAGGTG
130 AAGGTG
*
16785 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGCCAATATGCTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
* * **
16850 GTGAT-TTGGACTTAAAGATGAAGATGCCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAA
66 GCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTAA
16914 AGGTG
131 AGGTG
*
16919 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATACTGATTCAAGGCCA
1 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
* *
16984 GCGATATTAGACTT--AGAAGAAGATGCCA
66 GCGATATTGGACTTAAAGATGAAGATGCCA
17012 CCAACTTGTG
Statistics
Matches: 211, Mismatches: 14, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
133 13 0.06
134 128 0.61
135 69 0.33
136 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (135 bp):
CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCA
GCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATTCAAGGCCGACGACATTGGACTTAA
AGGTG
Found at i:16921 original size:91 final size:92
Alignment explanation
Indices: 16691--17003 Score: 339
Period size: 91 Copynumber: 3.5 Consensus size: 92
16681 GACTTAAAGG
* * *
16691 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGCCAATGTGCTAATT
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT----A--AAGATGCCAATATGCTGATT
*
16756 CAAGGCC-GACGACATTGGACTT-AA-A-G--G-
60 CAAGGCCAG-CGATATTGGACTTAAAGATGAAGA
*
16783 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
*
16848 CAGTGAT-TTGGACTTAAAGATGAAGA
66 CAGCGATATTGGACTTAAAGATGAAGA
* * * *
16874 TGCCAATGTGCTGATTCAAGGCCGGTGACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGC
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
16939 CAGCGATATTGGACTT-AA-A-G--G-
66 CAGCGATATTGGACTTAAAGATGAAGA
* * *
16960 TGCCAATATACTGATTCAAGGCCAGCGATATTAGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
17004 AGATGCCACC
Statistics
Matches: 195, Mismatches: 17, Indels: 23
0.83 0.07 0.10
Matches are distributed among these distances:
85 8 0.04
86 62 0.32
87 6 0.03
88 2 0.01
89 1 0.01
90 2 0.01
91 68 0.35
92 46 0.24
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGATGAAGA
Found at i:16980 original size:21 final size:21
Alignment explanation
Indices: 16913--16980 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
16903 ATTGGACTTA
*
16913 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATACTGATTC
** * *
16934 AA-G-GCCAGCGATATTGGACTTA
1 AAGGTGCCA-ATATACT-GA-TTC
16956 AAGGTGCCAATATACTGATTC
1 AAGGTGCCAATATACTGATTC
16977 AAGG
1 AAGG
16981 CCAGCGATAT
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 10 0.30
22 6 0.18
23 5 0.15
24 4 0.12
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATACTGATTC
Found at i:17136 original size:58 final size:58
Alignment explanation
Indices: 17060--17261 Score: 257
Period size: 58 Copynumber: 3.5 Consensus size: 58
17050 TGTGTTTTTG
* *
17060 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
* * * * *
17118 AAGGGTACCACTAACTTGTGGGC-TTTGAAAGGGGTGCCACCGACTTATGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAA-GGATGCCACTGACTTGTGGGCTTTGAA
* * * *
17176 AGGGGTGCCACCGACTTGGGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
* *
17233 AAAGATGCCACTGACTTGT-GGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTTGAA
17262 GGGTGAGGAA
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
56 8 0.07
57 46 0.38
58 63 0.52
59 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (58 bp):
AAGGGTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
Found at i:17261 original size:29 final size:29
Alignment explanation
Indices: 17060--17257 Score: 233
Period size: 29 Copynumber: 6.9 Consensus size: 29
17050 TGTGTTTTTG
*
17060 AAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA
*
17090 AA-GATGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* *
17118 AAGGGTACCACTAACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* * *
17147 AGGGGTGCCACCGACTTATGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* * *
17176 AGGGGTGCCACCGACTTGGGGGCTTTTG--
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA
*
17204 AAGGTTGCCACTGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* *
17233 AAAGATGCCACTGACTTGT-GGCTTT
1 AAGGGTGCCACTGACTTGTGGGCTTT
17258 TGAAGGGTGA
Statistics
Matches: 147, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
27 4 0.03
28 33 0.22
29 104 0.71
30 6 0.04
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (29 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:18533 original size:15 final size:14
Alignment explanation
Indices: 18515--18560 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
18505 CATCCGGACC
18515 TTTTTTGTTGTTGTT
1 TTTTTTGTTGTT-TT
18530 TTTTTT-TT-TTTT
1 TTTTTTGTTGTTTT
18542 GTTTTTTGTTTGTTTT
1 -TTTTTTG-TTGTTTT
18558 TTT
1 TTT
18561 CCTTGTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 2 0.07
15 11 0.41
16 4 0.15
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (14 bp):
TTTTTTGTTGTTTT
Found at i:18541 original size:21 final size:22
Alignment explanation
Indices: 18515--18560 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
18505 CATCCGGACC
*
18515 TTTTTTG-TTGTTGTTTTTTTT
1 TTTTTTGTTTGTTGTTTGTTTT
*
18536 TTTTTTGTTTTTTGTTTGTTTT
1 TTTTTTGTTTGTTGTTTGTTTT
18558 TTT
1 TTT
18561 CCTTGTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (22 bp):
TTTTTTGTTTGTTGTTTGTTTT
Found at i:18557 original size:18 final size:18
Alignment explanation
Indices: 18517--18559 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
18507 TCCGGACCTT
*
18517 TTTTGTTGTTGTTTTTTTT
1 TTTT-TTGTTGTTTTTTTG
18536 TTTTTTGTT-TTTTGTTTG
1 TTTTTTGTTGTTTT-TTTG
18554 TTTTTT
1 TTTTTT
18560 TCCTTGTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 14 0.64
19 4 0.18
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (18 bp):
TTTTTTGTTGTTTTTTTG
Done.