Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1379
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: 58234
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:21 original size:12 final size:12
Alignment explanation
Indices: 1--30 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1 AAAAAAGAAAAT
1 AAAAAAGAAAAT
*
13 AAAAGAGAAAAT
1 AAAAAAGAAAAT
25 AAAAAA
1 AAAAAA
31 CACTAAAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (12 bp):
AAAAAAGAAAAT
Found at i:1882 original size:20 final size:20
Alignment explanation
Indices: 1857--1910 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1847 TTTTGAAGCA
* *
1857 ATGTATCGATACAATTTATC
1 ATGTATCGATACAATGTACC
*
1877 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTACC
1897 ATGTATCGATACAA
1 ATGTATCGATACAA
1911 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1968 original size:20 final size:19
Alignment explanation
Indices: 1943--1991 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1933 TAGTTTCATA
**
1943 TATCGATACAATTGTGCATG
1 TATCGATACAA-TGAACATG
*
1963 TATCGATATAATGAACATG
1 TATCGATACAATGAACATG
1982 TATCGATACA
1 TATCGATACA
1992 TCTAGATGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (19 bp):
TATCGATACAATGAACATG
Found at i:4087 original size:14 final size:14
Alignment explanation
Indices: 4068--4098 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
4058 AAAACTTAAA
4068 CTAGGAGTGTTTGT
1 CTAGGAGTGTTTGT
4082 CTAGGAGTGTTTGT
1 CTAGGAGTGTTTGT
4096 CTA
1 CTA
4099 TGGAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.10, G:0.32, T:0.42
Consensus pattern (14 bp):
CTAGGAGTGTTTGT
Found at i:8963 original size:12 final size:11
Alignment explanation
Indices: 8941--9016 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
8931 AGAGAAAGAA
*
8941 GAGAGAGGAGG
1 GAGATAGGAGG
8952 GATGATAGGAGG
1 GA-GATAGGAGG
*
8964 AGAGACAGGA--
1 -GAGATAGGAGG
*
8974 GAGATAGTA--
1 GAGATAGGAGG
8983 GAGATAGGAGG
1 GAGATAGGAGG
8994 GATGATAGGAGG
1 GA-GATAGGAGG
*
9006 AGAGACAGGAG
1 -GAGATAGGAG
9017 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:8973 original size:24 final size:24
Alignment explanation
Indices: 8940--9025 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
8930 AAGAGAAAGA
*
8940 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
8964 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
8982 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
9006 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
9026 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:8992 original size:42 final size:42
Alignment explanation
Indices: 8931--9049 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
8921 TAGCCCTCAA
* *
8931 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
8973 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
9015 AGAGATAATAGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
9050 GAGAGAATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:14462 original size:20 final size:19
Alignment explanation
Indices: 14437--14490 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
14427 CTGCCAGTTT
**
14437 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
*
14457 CATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
*
14476 CGTGTATCGATACAA
1 CATGTATCGATACAA
14491 AGTATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:19032 original size:16 final size:17
Alignment explanation
Indices: 19013--19052 Score: 57
Period size: 15 Copynumber: 2.4 Consensus size: 17
19003 AAGAGGGGTC
19013 AAAAAAAT-AAAAAGA-
1 AAAAAAATCAAAAAGAT
19028 AAAAAAATCAAAAAGAAT
1 AAAAAAATCAAAAAG-AT
19046 AAAAAAA
1 AAAAAAA
19053 AGTCAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 6 0.27
17 1 0.05
18 7 0.32
ACGTcount: A:0.85, C:0.03, G:0.05, T:0.07
Consensus pattern (17 bp):
AAAAAAATCAAAAAGAT
Found at i:19966 original size:28 final size:28
Alignment explanation
Indices: 19926--19986 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
19916 TTTATGTCAT
* * *
19926 ATCCCCAATGGAGTCTGGATAACCTGCA
1 ATCCCCAATGGAGCCTGGACAACCTACA
*
19954 ATCCCCAATGGAGCCTTGACAACCTACA
1 ATCCCCAATGGAGCCTGGACAACCTACA
19982 ATCCC
1 ATCCC
19987 TAGTGGAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (28 bp):
ATCCCCAATGGAGCCTGGACAACCTACA
Found at i:20338 original size:14 final size:13
Alignment explanation
Indices: 20321--20385 Score: 62
Period size: 14 Copynumber: 4.9 Consensus size: 13
20311 GTCAAAGTGC
*
20321 CATTATCAAGAAA
1 CATTGTCAAGAAA
*
20334 TCATTGTTAAGAAA
1 -CATTGTCAAGAAA
20348 CTATTGTCAAG-AA
1 C-ATTGTCAAGAAA
20361 CATTTGTC-AGAAA
1 CA-TTGTCAAGAAA
*
20374 CTTTGTCAAGAA
1 CATTGTCAAGAA
20386 TTTTGTCAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
12 8 0.19
13 16 0.37
14 19 0.44
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
CATTGTCAAGAAA
Found at i:20369 original size:13 final size:12
Alignment explanation
Indices: 20326--20407 Score: 67
Period size: 12 Copynumber: 6.3 Consensus size: 12
20316 AGTGCCATTA
20326 TCAAGAAATCATTG
1 TCAAGAAAT--TTG
*
20340 TTAAGAAACTATTG
1 TCAAGAAA-T-TTG
20354 TCAAGAACATTTG
1 TCAAGAA-ATTTG
20367 TC-AGAAACTTTG
1 TCAAGAAA-TTTG
*
20379 TCAAGAATTTTG
1 TCAAGAAATTTG
*
20391 TCAAGAACTTATG
1 TCAAGAAATT-TG
20404 TCAA
1 TCAA
20408 AACCCTTTCA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.02
12 23 0.39
13 15 0.25
14 18 0.31
15 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (12 bp):
TCAAGAAATTTG
Found at i:20378 original size:12 final size:12
Alignment explanation
Indices: 20346--20407 Score: 72
Period size: 12 Copynumber: 4.9 Consensus size: 12
20336 ATTGTTAAGA
20346 AACTATTGTCAAG
1 AACT-TTGTCAAG
20359 AACATTTGTC-AG
1 AAC-TTTGTCAAG
20371 AAACTTTGTCAAG
1 -AACTTTGTCAAG
*
20384 AATTTTGTCAAG
1 AACTTTGTCAAG
20396 AACTTATGTCAA
1 AACTT-TGTCAA
20408 AACCCTTTCA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 23 0.53
13 19 0.44
14 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (12 bp):
AACTTTGTCAAG
Found at i:25038 original size:103 final size:100
Alignment explanation
Indices: 24807--25038 Score: 272
Period size: 103 Copynumber: 2.3 Consensus size: 100
24797 GCCACCACCT
* *
24807 TGAGGGGATACTCCAACGCCA-CTTTCCAAAATCATCAGAATTAAATTTTCCTTTGGTCAAATCT
1 TGAGGGGATACTCCAACCCCACCTTT-CAAAATCATCAGAATTAAATCTTCCTTTGGTCAAATCT
*
24871 TTTATCATCCGTGGGGATACTCCAACCCCAACCTTC
65 TTTATCATCCATGGGGATACTCCAACCCCAACCTTC
* * * ** *
24907 TGAGGGGATACTCCAACCGCGCCATTCAAAATTGTCAAGATTTAAAACTCTTCCTTT-GTCAAAA
1 TGAGGGGATACTCCAACCCCACCTTTCAAAATCATC-AGAATT-AAA-TCTTCCTTTGGTC-AAA
* * * *
24971 T-TATTTGTCATCCATGGGGATACTCTAACCCCATCTTTC
62 TCT-TTTATCATCCATGGGGATACTCCAACCCCAACCTTC
25010 TGAGGGGATACTCCAACCCCACCTTTCAA
1 TGAGGGGATACTCCAACCCCACCTTTCAA
25039 TTATGATTAA
Statistics
Matches: 110, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
100 26 0.24
101 8 0.07
102 7 0.06
103 69 0.63
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (100 bp):
TGAGGGGATACTCCAACCCCACCTTTCAAAATCATCAGAATTAAATCTTCCTTTGGTCAAATCTT
TTATCATCCATGGGGATACTCCAACCCCAACCTTC
Found at i:27683 original size:82 final size:80
Alignment explanation
Indices: 27544--27698 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 80
27534 CTAAACAAGA
* *
27544 ACAATCCTATCCAATAAGGAAAAGTCTATTCCTTATCCTAATATGATTAGGACTTATCTAAACAA
1 ACAATCCTATCCAATAAGGAAAAGTCTATTCCTTATCCTAATATGATTAGAAATTATCTAAACAA
*
27609 CTTAAAATCCTAAAC
66 ATTAAAATCCTAAAC
*
27624 ACAATCCTAAT-CAATAAGGATAAAGTCTAACTT-CTTATCAC-AATCTGATTAGAAATTATCTA
1 ACAATCCT-ATCCAATAAGGA-AAAGTCT-A-TTCCTTATC-CTAATATGATTAGAAATTATCTA
27686 AACAAATTAAAAT
61 AACAAATTAAAAT
27699 TGAAAGGTCA
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
80 17 0.26
81 9 0.14
82 37 0.56
83 3 0.05
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.30
Consensus pattern (80 bp):
ACAATCCTATCCAATAAGGAAAAGTCTATTCCTTATCCTAATATGATTAGAAATTATCTAAACAA
ATTAAAATCCTAAAC
Found at i:35932 original size:18 final size:18
Alignment explanation
Indices: 35902--35948 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
35892 ATTTTTTTCT
35902 CTCCTC-CTCCTATCATCC
1 CTCCTCTCT-CTATCATCC
* *
35920 CTCCTCTCTCTATTATCT
1 CTCCTCTCTCTATCATCC
*
35938 CTCCTATCTCT
1 CTCCTCTCTCT
35949 CGTTCTGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.11, C:0.47, G:0.00, T:0.43
Consensus pattern (18 bp):
CTCCTCTCTCTATCATCC
Found at i:35945 original size:9 final size:9
Alignment explanation
Indices: 35933--36014 Score: 50
Period size: 9 Copynumber: 9.8 Consensus size: 9
35923 CTCTCTCTAT
35933 TATCTCTCC
1 TATCTCTCC
*
35942 TATCTCTCG
1 TATCTCTCC
*
35951 T-TCTGT-C
1 TATCTCTCC
* *
35958 -ATCTGTTC
1 TATCTCTCC
**
35966 TATCTCTAT
1 TATCTCTCC
35975 TATCTCTCC
1 TATCTCTCC
35984 TATCTCTCC
1 TATCTCTCC
*
35993 T-TCTAT-C
1 TATCTCTCC
*
36000 -ATCCCTCC
1 TATCTCTCC
36008 TATCTCT
1 TATCTCT
36015 TCTTTCTCTT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
7 9 0.16
8 10 0.18
9 36 0.65
ACGTcount: A:0.12, C:0.37, G:0.04, T:0.48
Consensus pattern (9 bp):
TATCTCTCC
Found at i:36023 original size:42 final size:42
Alignment explanation
Indices: 35905--36014 Score: 157
Period size: 42 Copynumber: 2.6 Consensus size: 42
35895 TTTTTCTCTC
* *
35905 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTATCT
1 CTCCTTCTATCATCCCTCCTATCTCTATTATCTCTCCTATCT
* * ** *
35947 CTCGTTCTGTCATCTGTTCTATCTCTATTATCTCTCCTATCT
1 CTCCTTCTATCATCCCTCCTATCTCTATTATCTCTCCTATCT
35989 CTCCTTCTATCATCCCTCCTATCTCT
1 CTCCTTCTATCATCCCTCCTATCTCT
36015 TCTTTCTCTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.12, C:0.40, G:0.03, T:0.45
Consensus pattern (42 bp):
CTCCTTCTATCATCCCTCCTATCTCTATTATCTCTCCTATCT
Found at i:42998 original size:158 final size:157
Alignment explanation
Indices: 42830--43122 Score: 356
Period size: 157 Copynumber: 1.9 Consensus size: 157
42820 CCAAAGCTTT
* * *
42830 AATACCTTGTATCCAAATAAGAG-GAACATGTGTTCGTTG-CTCAATCACAAAAAGACCAGAATT
1 AATACCTTGTATCCAAA-AAGAGAGAACATGTGTTCGTAGCCT-AATCACAAAAACAACAG-ATT
* * * *
42893 ATTACGAGAATTCATGTATGTCTCATTTGGTAGACGAACTTTGATTCTAAGGGAAATGGCGAAAA
63 ATTACGAGAATGCATGTATATCTCATTTGATAGACGAACTTTGATTCTAAGGAAAATGGCGAAAA
42958 GAAAAGCTTTTCCAATGATACCAATGCATC
128 GAAAAGCTTTTCCAATGATACCAATGCATC
* * * * * * *
42988 AATATCTTGTATCCAAACAGGGAGAACATGTTTTTGTAGCCTAATCACAAAAACAATAGTTTATT
1 AATACCTTGTATCCAAAAAGAGAGAACATGTGTTCGTAGCCTAATCACAAAAACAACAGATTATT
* * * * * * *
43053 ACTAGAATGCATGTTTATCTCATTTGATAGATGAATTTTGATTCTATGTAAAATGGTGAAAAGAA
66 ACGAGAATGCATGTATATCTCATTTGATAGACGAACTTTGATTCTAAGGAAAATGGCGAAAAGAA
43118 AAGCT
131 AAGCT
43123 CTTCTTGGGA
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
157 67 0.60
158 43 0.38
159 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (157 bp):
AATACCTTGTATCCAAAAAGAGAGAACATGTGTTCGTAGCCTAATCACAAAAACAACAGATTATT
ACGAGAATGCATGTATATCTCATTTGATAGACGAACTTTGATTCTAAGGAAAATGGCGAAAAGAA
AAGCTTTTCCAATGATACCAATGCATC
Found at i:43197 original size:157 final size:157
Alignment explanation
Indices: 42838--43188 Score: 339
Period size: 157 Copynumber: 2.2 Consensus size: 157
42828 TTAATACCTT
* * * * * * ** *
42838 GTATCCAAATAA-GAGGAACATGTGTTCGTTGCTCAATCACAAAAAGACCAGAATTATTACGAGA
1 GTATCCAAACAAGGA-GAACATGTTTTGGTAGCCCAATCACAAAAACAATAG-TTTATTACGAGA
* * * * *
42902 ATTCATGTATGTCTCATTTGGTAGACGAACTTTGATTCTAAGGGAAATGGCGAAAAGAAAAGCTT
64 ATGCATGTATATCTCATTTGATAGACGAACTTTGATTCTAAGGAAAATGGCGAAAAGAAAAGCTC
* * **
42967 TTCCAATGATACCAATGCATCAATATCTT
129 TTCCAAGGAAACCAATGCATCAATATCAA
* * * *
42996 GTATCCAAACAGGGAGAACATGTTTTTGTAGCCTAATCACAAAAACAATAGTTTATTACTAGAAT
1 GTATCCAAACAAGGAGAACATGTTTTGGTAGCCCAATCACAAAAACAATAGTTTATTACGAGAAT
* * * * * *
43061 GCATGTTTATCTCATTTGATAGATGAATTTTGATTCTATGTAAAATGGTGAAAAGAAAAGCTCTT
66 GCATGTATATCTCATTTGATAGACGAACTTTGATTCTAAGGAAAATGGCGAAAAGAAAAGCTCTT
***
43126 CTTGGGAAACCAA-GCATCAATATCAA
131 CCAAGGAAACCAATGCATCAATATCAA
* * **
43152 GTATCCTAACAAGGATAATGTGTTTATGGT-GCCCAAT
1 GTATCCAAACAAGGAGAACATGTTT-TGGTAGCCCAAT
43189 TATGAAAAAA
Statistics
Matches: 154, Mismatches: 37, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
156 37 0.24
157 77 0.50
158 38 0.25
159 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (157 bp):
GTATCCAAACAAGGAGAACATGTTTTGGTAGCCCAATCACAAAAACAATAGTTTATTACGAGAAT
GCATGTATATCTCATTTGATAGACGAACTTTGATTCTAAGGAAAATGGCGAAAAGAAAAGCTCTT
CCAAGGAAACCAATGCATCAATATCAA
Found at i:43556 original size:20 final size:20
Alignment explanation
Indices: 43519--43556 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43509 TGGAGATTAT
*
43519 TACTAGAATCCATGTTTGTC
1 TACTAGAATCCATATTTGTC
*
43539 TACTAGAATCTATATTTG
1 TACTAGAATCCATATTTG
43557 CCTCATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (20 bp):
TACTAGAATCCATATTTGTC
Found at i:44627 original size:159 final size:159
Alignment explanation
Indices: 44343--45058 Score: 455
Period size: 159 Copynumber: 4.5 Consensus size: 159
44333 TACACATTCA
* * *
44343 TCTCATTTAAGGGATGAATTTTTATTCTAAGGAAAATGTTGGAAAAAAAAGCTTTTCTTGCAAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAAAAAAGCTTTTCTTGCAAAA
* * ** * *
44408 CCAAAGCATTAATATCATGTATCCAAATGAGAAAAATGTGCTTTTGCTGCCTAACCATGAATAGA
66 CCAAAGCATCAATATCATGTATCCAAATAAGAAAAATGCACTTTTGCTGCCCAACCATGAAAAGA
* *
44473 CTAGAGATTACTACAAGAATCCATGTTTG
131 CTAGAGATTACTACAAGAAACCATATTTG
* * * * *
44502 TCTTATTTAAGGGATGAACTTTGATTCTAAGGAATATGGTGGAAAAAGATGGTTTTCTTGCAAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAAAAAAGCTTTTCTTGCAAAA
* * * * *** * ** **
44567 GCAAAGTATCAATATCGTGTATCCTAATAAGGGGAATGCATTTTTTTTGCCCAATTATGAAAAGA
66 CCAAAGCATCAATATCATGTATCCAAATAAGAAAAATGCACTTTTGCTGCCCAACCATGAAAAGA
* **
44632 CTAGAGATTATTATGAGAAACCATATTTG
131 CTAGAGATTACTACAAGAAACCATATTTG
* * * * * * * * **
44661 TCTCATTTGAGGCATGAA-TTT-ACATCTTAGAAAAATAGT-GAAAACAAAATCATTTCTTGGGA
1 TCTCATTTAAGGGATGAACTTTGA-TTCTAAGGAAAATGGTGGAAAA-AAAAGCTTTTCTTGCAA
** * * * * * *
44723 AATTAAAGCATCATTATCATGTATCTC-AATGACAAGAA--CACTTTTGCAGTGCCAAATCTAT-
64 AACCAAAGCATCAATATCATGTATC-CAAATAAGAAAAATGCACTTTTGC--TGCCCAA-CCATG
* * * * *
44784 AAAAGAATGGAGATTATTACAAGAATCCATCTTTG
125 AAAAGACTAGAGATTACTACAAGAAACCATATTTG
* * * ** * * **
44819 CCTCATTTAAGGGATTAACTATGATTCTAAGGAAAATAATGGAAAGAAAAGCCTTTTTTTGTGAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAAAAAAG-CTTTTCTTGCAAA
* * * ** * * * *
44884 ACCAAAGTATCAATA-C-TGTTTATCCCAATTAGGAAAACAT--TTTTTTGTTGCCAAATCTTGA
65 ACCAAAGCATCAATATCATG--TAT-CCAAATAAGAAAA-ATGCACTTTTGCTGCCCAACCATGA
* ** * * * * *
44945 AAAGAATTCAGATTATTACATGAATCCATGTTTC
126 AAAGACTAGAGATTACTACAAGAAACCATATTTG
* * * * * **
44979 TCTCATTTAAGTGATGAACTTTGATTATAAGGAAAATGGTAGAAAGAAAAGCTTTTTTTGTGAAA
1 TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAAAAAAGCTTTTCTTGCAAAA
* *
45044 CTAAAACATCAATAT
66 CCAAAGCATCAATAT
45059 TGTATATCCT
Statistics
Matches: 428, Mismatches: 111, Indels: 35
0.75 0.19 0.06
Matches are distributed among these distances:
156 6 0.01
157 6 0.01
158 102 0.24
159 192 0.45
160 110 0.26
161 6 0.01
162 6 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (159 bp):
TCTCATTTAAGGGATGAACTTTGATTCTAAGGAAAATGGTGGAAAAAAAAGCTTTTCTTGCAAAA
CCAAAGCATCAATATCATGTATCCAAATAAGAAAAATGCACTTTTGCTGCCCAACCATGAAAAGA
CTAGAGATTACTACAAGAAACCATATTTG
Found at i:44950 original size:160 final size:157
Alignment explanation
Indices: 44772--45142 Score: 444
Period size: 160 Copynumber: 2.4 Consensus size: 157
44762 ACTTTTGCAG
* *
44772 TGCCAAATCTAT-AAAAGAATGGAGATTATTACAAGAATCCATCTTTGCCTCATTTAAGGGATTA
1 TGCCAAATCT-TGAAAAGAATGGAGATTATTACAAGAATCCATGTTTGCCTCATTTAAGGGATGA
* * **
44836 ACTATGATTCTAAGGAAAATAATGGAAAGAAAAGCCTTTTTTTGTGAAACCAAAGTATCAATACT
65 ACTATGATTATAAGGAAAATAATAGAAAGAAAAG-CTTTTTTTGTGAAACCAAAACATCAATACT
* *
44901 GTTTATCCCAATTAGGAAAACATTTTTTTGT
129 GTATATCCCAATT-GGAAAACATGTTTTT-T
** * *
44932 TGCCAAATCTTGAAAAGAATTCAGATTATTACATGAATCCATGTTT-CTCTCATTTAAGTGATGA
1 TGCCAAATCTTGAAAAGAATGGAGATTATTACAAGAATCCATGTTTGC-CTCATTTAAGGGATGA
* ** * *
44996 ACTTTGATTATAAGGAAAATGGTAGAAAGAAAAGCTTTTTTTGTGAAACTAAAACATCAATATTG
65 ACTATGATTATAAGGAAAATAATAGAAAGAAAAGCTTTTTTTGTGAAACCAAAACATCAATACTG
* *
45061 TATATCCTAATTGGAGAACATGTTTTTT
130 TATATCCCAATTGGAAAACATGTTTTTT
* * * * *
45089 AGCCTAATCATGAAAA-AATGGAGATT-TATATAAGAATCCATGTTTGTCTCATTT
1 TGCCAAATCTTGAAAAGAATGGAGATTAT-TACAAGAATCCATGTTTGCCTCATTT
45143 GAGAGACAAA
Statistics
Matches: 180, Mismatches: 27, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
155 1 0.01
156 30 0.17
157 14 0.08
158 13 0.07
159 39 0.22
160 83 0.46
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (157 bp):
TGCCAAATCTTGAAAAGAATGGAGATTATTACAAGAATCCATGTTTGCCTCATTTAAGGGATGAA
CTATGATTATAAGGAAAATAATAGAAAGAAAAGCTTTTTTTGTGAAACCAAAACATCAATACTGT
ATATCCCAATTGGAAAACATGTTTTTT
Found at i:45233 original size:149 final size:149
Alignment explanation
Indices: 44954--45386 Score: 360
Period size: 149 Copynumber: 2.8 Consensus size: 149
44944 AAAAGAATTC
* * * * *
44954 AGATTATTACATGAATCCATGTTTCTCTCATTTAAGTG-ATGAACTTTGATTATAAGGAAAATGG
1 AGATTATTACAAGAATCCATGTTTGTCTCATTTGA-TGAACGAA--AT--TTATAAGGAAAATGG
* * * * * * * * * *
45018 TAGAAAGAAAAGCTTTTTTTGTGAAACTAAAACATCAATATTGTATATCCTAAT-TGGAGAACAT
61 T-GAAAAAAAAGCTTTTCTTG-GAAACCAAAGCATC-ATATTATGTATCCCAATGAGGAAAAAAT
* *
45082 GTTTTTTA-GCCTAATCATGAAAAAA-TGG
123 G-TTTATAGGCCT-ATCA-CAAAAAAGTGG
* *
45110 AGATT-TATATAAGAATCCATGTTTGTCTCATTTGA-GAGAC-AAATTT-TAAGAAAAATGGTGA
1 AGATTAT-TACAAGAATCCATGTTTGTCTCATTTGATGA-ACGAAATTTATAAGGAAAATGGTGA
45171 AAAAAAAGCTTTTCTTGGAAGACCAAAGCATCATATTATGTATCCCAATGAGGAAAAAATGTTTA
64 AAAAAAAGCTTTTCTTGGAA-ACCAAAGCATCATATTATGTATCCCAATGAGGAAAAAATGTTTA
45236 TAGGGCCTATCACAAAAAAGTGG
128 TA-GGCCTATCACAAAAAAGTGG
* *
45259 AGATTATTACAAGAATCTATGTTTGTCTCATTTGATGAACGAACTTTGACTCCAAGGAAAATGGT
1 AGATTATTACAAGAATCCATGTTTGTCTCATTTGATGAACGAAATTT-A-T--AAGGAAAATGGT
* * * * *
45324 GAAAAGAAAAGTTTTTCTTGCAAAACCAAGGCATATCAGTATTATGTATCGCAATGAAGAAAA
62 GAAAA-AAAAGCTTTTCTTG-GAAACCAAAGC--ATCA-TATTATGTATCCCAATGAGGAAAA
45387 TGTGTTTTCA
Statistics
Matches: 228, Mismatches: 28, Indels: 39
0.77 0.09 0.13
Matches are distributed among these distances:
148 28 0.12
149 74 0.32
150 24 0.11
151 2 0.01
153 2 0.01
154 1 0.00
155 19 0.08
156 50 0.22
157 2 0.01
158 4 0.02
159 22 0.10
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.31
Consensus pattern (149 bp):
AGATTATTACAAGAATCCATGTTTGTCTCATTTGATGAACGAAATTTATAAGGAAAATGGTGAAA
AAAAAGCTTTTCTTGGAAACCAAAGCATCATATTATGTATCCCAATGAGGAAAAAATGTTTATAG
GCCTATCACAAAAAAGTGG
Found at i:57563 original size:251 final size:252
Alignment explanation
Indices: 57093--57600 Score: 876
Period size: 251 Copynumber: 2.0 Consensus size: 252
57083 AAGCAAGTCA
*
57093 CAACCAGCAGGCCCTTTATTACAAAATAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
1 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
*
57158 TCCAAATATATGCAATTAACTAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
66 TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
*
57223 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTTATTGGACCTT
131 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
* * * *
57288 GAAATCCTTCCAACGCCTTCAGGTCTTTGTCTTCAATGGACCTTCCTTGGTTTTCAT
196 GAAATCCTTCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
57345 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
1 CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
* * *
57410 TCCAAATATATGCAATTGACCAGCTTGGGCTCTTCTAGCTCC-AATTGGGTTTACTTTCAAATAG
66 TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
* * *
57474 GGCAGCAACCGTCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGTCCTT
131 GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
57539 GAAA-CCTTCCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
196 GAAATCCTT-CCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
57596 CAACC
1 CAACC
57601 CTTCCTTCTT
Statistics
Matches: 242, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
250 4 0.02
251 135 0.56
252 103 0.43
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (252 bp):
CAACCAGCAGGCCCTTTATTACAAAAAAACCCAAGTCCTAATTCAATCCATTGGAGCCCATATCT
TCCAAATATATGCAATTAACCAGCTTGGGCTCTTCTAACTCCAAATTGGGTCTACTTTCAAATAG
GCCAGCAACCATCTTCTCTAGGTCTTCCTTTATCCTCTTTGCCTTTGCCCTCGTCATTGGACCTT
GAAATCCTTCCAACGCCTTCAGGTCGTTGTCTTCAACGGACCATCCTTGGTTCTCAT
Done.