Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2277
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: 31822
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Found at i:5839 original size:20 final size:20
Alignment explanation
Indices: 5792--5866 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
5782 AAAAAGACAT
*
5792 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
5811 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
5832 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
5852 AATGTATCGATACAT
1 AATGTATCGATACAT
5867 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:5860 original size:40 final size:39
Alignment explanation
Indices: 5789--5866 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
5779 GGTAAAAAGA
* *
5789 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
5828 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
5867 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:8128 original size:10 final size:10
Alignment explanation
Indices: 8113--8139 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
8103 ATGTATCAAG
8113 CAAAAACAAA
1 CAAAAACAAA
8123 CAAAAACAAA
1 CAAAAACAAA
8133 CAAAAAC
1 CAAAAAC
8140 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:12332 original size:52 final size:51
Alignment explanation
Indices: 12254--12402 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
12244 CGAAATATGA
12254 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
12306 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
12358 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
12403 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:12409 original size:13 final size:13
Alignment explanation
Indices: 12391--12415 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12381 CAAAGATCAG
12391 TGTATCGATACAA
1 TGTATCGATACAA
12404 TGTATCGATACA
1 TGTATCGATACA
12416 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:12496 original size:13 final size:13
Alignment explanation
Indices: 12478--12502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12468 CAAAAAAATA
12478 TGTATCGATACAT
1 TGTATCGATACAT
12491 TGTATCGATACA
1 TGTATCGATACA
12503 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12497 original size:33 final size:33
Alignment explanation
Indices: 12460--12522 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
12450 GCTTGAATTA
12460 TATCGATACAAAAAAATATGTATCGATACATTG
1 TATCGATACAAAAAAATATGTATCGATACATTG
* ***
12493 TATCGATACAACACTTTATGTATCGATACA
1 TATCGATACAAAAAAATATGTATCGATACA
12523 AATCGTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (33 bp):
TATCGATACAAAAAAATATGTATCGATACATTG
Found at i:26393 original size:29 final size:28
Alignment explanation
Indices: 26317--26428 Score: 163
Period size: 28 Copynumber: 4.0 Consensus size: 28
26307 CATTCCTCAC
26317 CCTTCAAAAGCCCACAAGTCAGTGGCAA
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
* *
26345 CCTTCAAAAGCCCACAAGTCAGTAGCAT
1 CCTTCAAAAGCCCACAAGTCAGTGGCAA
*
26373 CTTTTTC-AAAGCCCACAAGTCAGTGGCAA
1 C--CTTCAAAAGCCCACAAGTCAGTGGCAA
*
26402 CCTTCAAAAGCCCACAAGTCCGTGGCA
1 CCTTCAAAAGCCCACAAGTCAGTGGCA
26429 TCTTTTTTCT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
27 3 0.04
28 47 0.64
29 21 0.28
30 3 0.04
ACGTcount: A:0.33, C:0.32, G:0.17, T:0.18
Consensus pattern (28 bp):
CCTTCAAAAGCCCACAAGTCAGTGGCAA
Found at i:26408 original size:57 final size:57
Alignment explanation
Indices: 26323--26435 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
26313 TCACCCTTCA
26323 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTAGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTAGCATCTTTTTC
* *
26380 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGCATCTTTTT
1 AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTAGCATCTTTTT
26436 TCTTTTAAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (57 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTAGCATCTTTTTC
Found at i:26462 original size:33 final size:33
Alignment explanation
Indices: 26413--26735 Score: 321
Period size: 33 Copynumber: 10.1 Consensus size: 33
26403 CTTCAAAAGC
* *
26413 CCACAAGTCCGTGGCATCTTTTTTCTTTTAAGT
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
* * * *
26446 CCATAACTCCGTGGCATATTTTTCTTTTTAAAGC
1 CCACAACTCCGTGGCATCTTTTTCCTTTT-AAGT
* *
26480 CCACAACTCCGTGGCA-CCTTTTCCTTTTAAGC
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
*
26512 CCACAACTCCGCGGCA-C-----CCTTTTAAGT
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
26539 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
* *
26572 CCACAACCCCGTGGCA-C-----CCCTTTAAGT
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
*
26599 CCACAACTCCATGGCATCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
* * *
26632 CCACAACTCTGTGGCATCCTTTTCTTTTTAAGT
1 CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
* * * * *
26665 CCGCGACTCCGTGGCACCCTTTTCCCTTTTAAAGC
1 CCACAACTCCGTGGCA-TCTTTTTCCTTTT-AAGT
* *
26700 CCACAATTCCGTGGTAATCTTTTTCCTTTTAAGT
1 CCACAACTCCGTGG-CATCTTTTTCCTTTTAAGT
26734 CC
1 CC
26736 TAGTCCTCAT
Statistics
Matches: 237, Mismatches: 37, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
27 47 0.20
28 2 0.01
32 21 0.09
33 109 0.46
34 32 0.14
35 25 0.11
36 1 0.00
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
CCACAACTCCGTGGCATCTTTTTCCTTTTAAGT
Found at i:26535 original size:60 final size:60
Alignment explanation
Indices: 26381--26713 Score: 272
Period size: 60 Copynumber: 5.3 Consensus size: 60
26371 ATCTTTTTCA
* * * ** * * * *
26381 AAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCCGTGGCATCTTTTTTCTTTT
1 AAGCCCACAACTCCGTGGCACCCTT-TTAAGTCCACAACTCCGTGGCATCCTTTTCCTTTT
* * * * *
26442 AAGTCCATAACTCCGTGGCATATTTTTCTTTTTAAAGCCCACAACTCCGTGGCA-CCTTTTCCTT
1 AAGCCCACAACTCCGTGGC--A----CCCTTTT-AAGTCCACAACTCCGTGGCATCCTTTTCCTT
26506 TT
59 TT
* *
26508 AAGCCCACAACTCCGCGGCACCCTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTCCTTTT
* * * * *
26568 AAGTCCACAACCCCGTGGCACCCCTTTAAGTCCACAACTCCATGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTCCTTTT
* * * * *
26628 AAGTCCACAACTCTGTGGCATCCTTTTCTTTTTAAGTCCGCGACTCCGTGGCACCCTTTTCCCTT
1 AAGCCCACAACTCCGTGGCA-CC----C-TTTTAAGTCCACAACTCCGTGGCATCCTTTT-CCTT
26693 TT
59 TT
*
26695 AAAGCCCACAATTCCGTGG
1 -AAGCCCACAACTCCGTGG
26714 TAATCTTTTT
Statistics
Matches: 222, Mismatches: 34, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
59 19 0.09
60 89 0.40
61 17 0.08
63 1 0.00
64 1 0.00
65 1 0.00
66 51 0.23
67 28 0.13
68 15 0.07
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.32
Consensus pattern (60 bp):
AAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTCCTTTT
Found at i:26547 original size:93 final size:94
Alignment explanation
Indices: 26437--26710 Score: 310
Period size: 93 Copynumber: 2.9 Consensus size: 94
26427 CATCTTTTTT
* * *
26437 CTTTTAAGTCCATAACTCCGTGGCATATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
1 CTTTTAAGTCCACAACTCCGTGGCATCTTTTTCTTTTT-AAGTCCACAACTCCGTGGCACCTTTT
26502 CCTTTTAAGCCCACAACTCCGCGGCA-C-C
65 CCTTTTAAGCCCACAACTCCGCGGCATCTC
* *
26530 CTTTTAAGTCCACAACTCCGTGGCATCTTTTTCCTTTTAAGTCCACAACCCCGTGGCACC----C
1 CTTTTAAGTCCACAACTCCGTGGCATCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTC
* **
26591 C-TTTAAGTCCACAACTCCATGGCATCTTTTTC
66 CTTTTAAGCCCACAACTCCGCGGCATC----TC
* * * *
26623 CTTTTAAGTCCACAACTCTGTGGCATCCTTTTCTTTTTAAGTCCGCGACTCCGTGGCACCCTTTT
1 CTTTTAAGTCCACAACTCCGTGGCATCTTTTTCTTTTTAAGTCCACAACTCCGTGGCA-CCTTTT
*
26688 CCCTTTTAAAGCCCACAATTCCG
65 -CCTTTT-AAGCCCACAACTCCG
26711 TGGTAATCTT
Statistics
Matches: 150, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
87 20 0.13
88 3 0.02
92 20 0.13
93 88 0.59
94 2 0.01
99 2 0.01
100 3 0.02
101 12 0.08
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.34
Consensus pattern (94 bp):
CTTTTAAGTCCACAACTCCGTGGCATCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACCTTTTC
CTTTTAAGCCCACAACTCCGCGGCATCTC
Found at i:26833 original size:21 final size:21
Alignment explanation
Indices: 26809--26872 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
26799 ATGTCGCTGG
26809 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
* *
26830 CCTTTAAGTC--CA-ATGTCGTCGA
1 CCTTGAA-TCAGCATAT-T-GGC-A
26852 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
26873 TTTTTAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 11 0.34
22 11 0.34
23 3 0.09
24 2 0.06
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:26856 original size:43 final size:42
Alignment explanation
Indices: 26749--27250 Score: 268
Period size: 49 Copynumber: 11.1 Consensus size: 42
26739 TCCTCATCAT
* *
26749 CTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
26791 C---AAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
*
26830 CCTTTAAGTCCAATGTCG-TCGACCTTGAATCAGCATATTGGCATTTTTAA
1 -CTTTAAGTCCAATGTCGCT-GGCCTTGAATCAGCATATTGGC-------A
* ** *
26880 CTTTAAGTTCGGTATCGCTGGCCTTGAATCAGCATATTGGCATCGGCA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATA-T----T-GGCA
* * * *
26928 TCTTTAAGACCAATGTTGCTAGCCTTGAATCAGCACATTGGCA
1 -CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* * * **
26971 ---TAAGCCCAATATCGCTGGCTTTGAATTGGCATATTGGCA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* *
27010 CCTTGCCTTTAAGACCAATGTCACTGGCCTTGAATCAGCATATTGGCA
1 ------CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
* * * *
27058 C---AAGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTCA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGG------CA
* *
27103 TCTTTAAGTCCGATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCA
1 -CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATT-G----G-CA
* *
27152 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCA
1 -CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGG------CA
* * * *
27201 TCTTTAAGTCCGATATCGTTGGCCTTGAATTAGCATATTGGCA
1 -CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
27244 TCTTTAA
1 -CTTTAA
27251 CATCCTTAAG
Statistics
Matches: 362, Mismatches: 49, Indels: 97
0.71 0.10 0.19
Matches are distributed among these distances:
39 98 0.27
40 1 0.00
42 3 0.01
43 47 0.13
44 2 0.01
45 2 0.01
46 1 0.00
48 36 0.10
49 163 0.45
50 4 0.01
54 2 0.01
55 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (42 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCA
Found at i:27047 original size:87 final size:88
Alignment explanation
Indices: 26892--27146 Score: 336
Period size: 87 Copynumber: 2.9 Consensus size: 88
26882 TTAAGTTCGG
* * * *
26892 TATCGCTGGCCTTGAATCAGCATATTGGCATC-GGCATCTTTAAGACCAATGTTGCTAGCCTTGA
1 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCA-CTTTAAGACCAATGTCGCTGGCCTTGA
* *
26956 ATCAGCACATTGGCATAAGCCCAA
65 ATCAGCATATTGGCACAAGCCCAA
* ** *
26980 TATCGCTGGCTTTGAATTGGCATATTGGCACCTTGC-CTTTAAGACCAATGTCACTGGCCTTGAA
1 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCACTTTAAGACCAATGTCGCTGGCCTTGAA
27044 TCAGCATATTGGCACAAGCCCAA
66 TCAGCATATTGGCACAAGCCCAA
* * * * *
27067 TATCGTTGGCCTTGAATCAACATATTGGCACCTT-CATCTTTAAGTCCGATATCGCTGGCCTTGA
1 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCA-CTTTAAGACCAATGTCGCTGGCCTTGA
27131 ATCAGCATATTGGCAC
65 ATCAGCATATTGGCAC
27147 CGTCATCTTT
Statistics
Matches: 145, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
86 1 0.01
87 75 0.52
88 67 0.46
89 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (88 bp):
TATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCACTTTAAGACCAATGTCGCTGGCCTTGAA
TCAGCATATTGGCACAAGCCCAA
Found at i:27230 original size:273 final size:267
Alignment explanation
Indices: 26749--27244 Score: 625
Period size: 273 Copynumber: 1.8 Consensus size: 267
26739 TCCTCATCAT
* * * * *
26749 CTTTAAGTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACAAGTCCAATGTCGCTGGCCTTG
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTG
* * *** *
26814 AATCAGCATATTGGCACCTTTAAGTCCAATGTCGTCGACCTTGAATCAGCATATTGGCATTTTTA
66 AATCAACATATTGGCACCTTTAAGTCCAATATCGTCGACCTTGAATCAGCATATTGGCACCGTCA
** ** * *
26879 ACTTTAAGTTCGGTATCGCTGGCCTTGAATCAGCATATTGGCATCGGCATCTTTAAGACCAATGT
131 ACTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCATCGGCATCTTTAAGACCAATAT
*
26944 TGCTAGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCTTTGAATTGGCATATTGGC
196 CGCTAGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCTTTGAATTGGCATATTGGC
27009 ACCTTGC
261 ACCTTGC
* *
27016 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCATATTGGCACAAGCCCAATATCGTTGGCCTTG
1 CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTG
* *
27081 AATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCG-CTGGCCTTGAATCAGCATATTGGC
66 AATCAACATATTGGCA----C--CTTTAAGTCCAATATCGTC-GACCTTGAATCAGCATATTGGC
* * *** *
27145 ACCGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGT
124 ACCGTCAACTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCATCGGCATCTTTAAGA
* * * * *
27210 CCGATATCGTTGGCCTTGAATTAGCATATTGGCAT
189 CCAATATCGCTAGCCTTGAATCAGCACATTGGCAT
27245 CTTTAACATC
Statistics
Matches: 189, Mismatches: 33, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
267 73 0.39
271 1 0.01
272 1 0.01
273 114 0.60
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (267 bp):
CTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTTG
AATCAACATATTGGCACCTTTAAGTCCAATATCGTCGACCTTGAATCAGCATATTGGCACCGTCA
ACTTTAAGACCAATATCGCTGGCCTTGAATCAGCACATTGGCATCGGCATCTTTAAGACCAATAT
CGCTAGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCTTTGAATTGGCATATTGGC
ACCTTGC
Found at i:27293 original size:52 final size:49
Alignment explanation
Indices: 27063--27344 Score: 255
Period size: 49 Copynumber: 5.7 Consensus size: 49
27053 TGGCACAAGC
* * * * ** *
27063 CCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGA
* * * ***
27112 CCGATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGA
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGA
*
27161 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGT
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGA
* * * * * * *
27210 CCGATATCGTTGGCCTTGAATTAGCATATTGGCATCTTTAACATCCTTAAGC
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCAT-TTT--CATCTTTAAGA
* ** *
27262 CCAACGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTTAA-A
1 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGA
* * *
27308 TCTAATGTCGCTGGCCATGAATCAGCACATTGTCATT
1 -CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATT
27345 CTTCGCATCT
Statistics
Matches: 191, Mismatches: 36, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
47 35 0.18
49 118 0.62
50 3 0.02
52 35 0.18
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.33
Consensus pattern (49 bp):
CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGA
Found at i:27371 original size:99 final size:98
Alignment explanation
Indices: 27059--27371 Score: 319
Period size: 98 Copynumber: 3.2 Consensus size: 98
27049 ATATTGGCAC
* * *
27059 AAGCCCAATATCGTTGGCCTTGAATCAACATATTGGCACCTTCATCTTTAAGTCCGATATCGCTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGTCCGATATCGCTG
27124 GCCTTGAATCAGCATATTGGCA-C--CGTCATCTTT
65 GCCTTGAATCAGCATATTGGCATCTTCG-CATC-TT
* * * *
27157 AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTTTCATCTTTAAGTCCGATATCGTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTCATCTTTAAGTCCGATATCGCTG
* **
27222 GCCTTGAATTAGCATATTGGCATCTTTAACATCCTT
65 GCCTTGAATCAGCATATTGGCATC-TTCGCAT-CTT
** ** * * ** *
27258 AAGCCCAACGTCGCTGGCCTTGTCTCAGCACATTGGCA-TTCTTCTTTAAATCTAATGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCGATATCGCTGG
* * *
27322 CCATGAATCAGCACATTGTCATTCTTCGCATCTT
66 CCTTGAATCAGCATATTGGCA-TCTTCGCATCTT
*
27356 CGAGCCCAATATCGCT
1 -AAGCCCAATATCGCT
27372 TGCCGCATAT
Statistics
Matches: 178, Mismatches: 30, Indels: 13
0.81 0.14 0.06
Matches are distributed among these distances:
98 81 0.46
99 55 0.31
100 2 0.01
101 39 0.22
102 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (98 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTCATCTTTAAGTCCGATATCGCTGG
CCTTGAATCAGCATATTGGCATCTTCGCATCTT
Done.