Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold597
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: 93966
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2157 original size:20 final size:20
Alignment explanation
Indices: 2119--2170 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2109 CTATGATTTG
*
2119 TATCGATACAAATAGTGAATA
1 TATCGATACATA-AGTGAATA
* *
2140 TATTGATACATAAGTGAATG
1 TATCGATACATAAGTGAATA
2160 TATCGATACAT
1 TATCGATACAT
2171 GTTTGAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (20 bp):
TATCGATACATAAGTGAATA
Found at i:2306 original size:20 final size:20
Alignment explanation
Indices: 2279--2333 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2269 TTTTAACCCA
2279 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
* *
2299 ATTGTATCGATACATTTTTC
1 AATGTATCGATACATTATTC
2319 AATGTATCGATACAT
1 AATGTATCGATACAT
2334 GTAGGCAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:9165 original size:52 final size:52
Alignment explanation
Indices: 9096--9215 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
9086 AAAATTTATT
*
9096 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
* *
9148 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGTC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
9200 TGCATGTATCGATACA
1 TGCATGTATCGATACA
9216 AAGATCAGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:9228 original size:52 final size:51
Alignment explanation
Indices: 9087--9235 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
9077 CGAAATATGA
* *
9087 AAATTTATTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
9139 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGTCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
9191 AAATTTGTCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGTCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
9236 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (51 bp):
AAATTTGTCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:9242 original size:13 final size:13
Alignment explanation
Indices: 9224--9248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9214 CAAAGATCAG
9224 TGTATCGATACAA
1 TGTATCGATACAA
9237 TGTATCGATACA
1 TGTATCGATACA
9249 TGTGAGTAAT
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:9330 original size:33 final size:33
Alignment explanation
Indices: 9288--9357 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
9278 GGCAGTAGCT
9288 TACATTGTATCGATACAAAAAAATATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
* ***
9321 TACATTGTATCGATACAACATTTTATGTATCGA
1 TACATTGTATCGATACAAAAAAATATGTATCGA
9354 TACA
1 TACA
9358 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.34
Consensus pattern (33 bp):
TACATTGTATCGATACAAAAAAATATGTATCGA
Found at i:9331 original size:13 final size:13
Alignment explanation
Indices: 9313--9337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9303 CAAAAAAATA
9313 TGTATCGATACAT
1 TGTATCGATACAT
9326 TGTATCGATACA
1 TGTATCGATACA
9338 ACATTTTATG
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:11538 original size:45 final size:45
Alignment explanation
Indices: 11474--11563 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
11464 TATGAAAGAC
*
11474 GTCAAAAAAATAAATTTCCAAGCCATAACGCTTAGCCAAAACCTT
1 GTCAAAAAAATAAATTTCCAAGCCAGAACGCTTAGCCAAAACCTT
* * * *
11519 GTCAAAAGAATAAATTTCCAAGCTAGAAGGCTTGGCCAAAACCTT
1 GTCAAAAAAATAAATTTCCAAGCCAGAACGCTTAGCCAAAACCTT
11564 TCTTTAAGAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.22
Consensus pattern (45 bp):
GTCAAAAAAATAAATTTCCAAGCCAGAACGCTTAGCCAAAACCTT
Found at i:11890 original size:12 final size:12
Alignment explanation
Indices: 11875--11905 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
11865 TTCTTTTTGA
11875 TTTTTTTCTCTC
1 TTTTTTTCTCTC
*
11887 TTTTTTTCTTTC
1 TTTTTTTCTCTC
11899 TTTTTTT
1 TTTTTTT
11906 TACTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTCTCTC
Found at i:14007 original size:13 final size:13
Alignment explanation
Indices: 13989--14023 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
13979 CAATTCTTCA
13989 TGTGTCGATACAT
1 TGTGTCGATACAT
14002 TGTGTCGATACAT
1 TGTGTCGATACAT
*
14015 TGTATCGAT
1 TGTGTCGAT
14024 GCAATATGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (13 bp):
TGTGTCGATACAT
Found at i:15591 original size:11 final size:11
Alignment explanation
Indices: 15539--15593 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
15529 AAGAGATGTT
*
15539 TTGATGTAAAA
1 TTGATGAAAAA
*
15550 TTGATG-AAAT
1 TTGATGAAAAA
* * *
15560 TTTAAGAAAAT
1 TTGATGAAAAA
15571 TTGA-GAAAAA
1 TTGATGAAAAA
15581 TTGATGAAAAA
1 TTGATGAAAAA
15592 TT
1 TT
15594 ATTAGGGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 16 0.43
11 21 0.57
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (11 bp):
TTGATGAAAAA
Found at i:19165 original size:27 final size:27
Alignment explanation
Indices: 19124--19192 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
19114 TATCATTATC
* *
19124 GGGGACACTCTAACCCCATGT-CTTCGA
1 GGGGACACTCCAACCCCAT-TCCTCCGA
*
19151 GGGGACACTCCAACCCTATTCCTCCGA
1 GGGGACACTCCAACCCCATTCCTCCGA
*
19178 GAGGACACTCCAACC
1 GGGGACACTCCAACC
19193 TCGTTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.03
27 36 0.97
ACGTcount: A:0.25, C:0.38, G:0.20, T:0.17
Consensus pattern (27 bp):
GGGGACACTCCAACCCCATTCCTCCGA
Found at i:23980 original size:17 final size:16
Alignment explanation
Indices: 23966--24013 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
23956 AGTCAAAAGT
23966 AAAAACACAAAAAAAAC
1 AAAAACA-AAAAAAAAC
23983 AAAAACAAAAAAAAAC
1 AAAAACAAAAAAAAAC
*
23999 AACACACAAAAAAAA
1 AA-AAACAAAAAAAA
24014 GAGTGCAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 11 0.38
17 18 0.62
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAAAAC
Found at i:23986 original size:16 final size:16
Alignment explanation
Indices: 23967--24013 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
23957 GTCAAAAGTA
23967 AAAACACAAAAAAAAC
1 AAAACACAAAAAAAAC
23983 AAAA-ACAAAAAAAAAC
1 AAAACAC-AAAAAAAAC
*
23999 AACACACAAAAAAAA
1 AAAACACAAAAAAAA
24014 GAGTGCAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAACACAAAAAAAAC
Found at i:27971 original size:52 final size:51
Alignment explanation
Indices: 27893--28041 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
27883 CGAAATATGA
27893 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
27945 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
27997 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
28042 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:28132 original size:33 final size:33
Alignment explanation
Indices: 28095--28161 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
28085 AGTAGCTTAA
28095 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
28128 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
28161 A
1 A
28162 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:28135 original size:13 final size:13
Alignment explanation
Indices: 28117--28141 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28107 CAAAAAAATA
28117 TGTATCGATACAT
1 TGTATCGATACAT
28130 TGTATCGATACA
1 TGTATCGATACA
28142 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:28900 original size:30 final size:31
Alignment explanation
Indices: 28831--29383 Score: 505
Period size: 30 Copynumber: 17.7 Consensus size: 31
28821 ATCTCTCTTC
* *
28831 TCAAAGTCCACGACCCAGTGGCAATCTCTTCT
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCT
* *
28863 T-AAAGTCCATGACTCAGTGGCATCTTGTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
28892 CCAAAGTCCAAGACTGAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
28923 TCAAAATCCACAACTCAGTGGCATCTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
28953 TCTAAGTCCACGACTTAGTGGCATCCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTCT
* * *
28985 TCCAAGTCCACAACTCAATGGCATCTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC--TTTTCT
* *
29018 TCAAAGTTCACGACTCAGTGGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
29048 CCAAAGTCCACAACTCAATGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* * *
29079 CCAAAGTTCACAACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
** *
29110 TCAAAGTCCATAACTCAGTGGCATCTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
29140 TCTAAGTCCACGACTTAGTGGCATCTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATC-TTTTCT
*
29172 TCCAAGTCCACGACTC-GATGGCATCTTTTTTCT
1 TCAAAGTCCACGACTCAG-TGGCATC--TTTTCT
* *
29205 TCAAAGTCCACGACTTAGTGGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
29235 CCAAAGTCCATGACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* ** * *
29266 TCAAATTTTATGACTCAATGGCAATCTTTTC-
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCT
* * * *
29297 TCAAAGTCCACGACTTAATAGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCT
* *
29327 CCAAAGTCCACGACTCTA-TGGCACCTTTTTCTTT
1 TCAAAGTCCACGACTC-AGTGGCATC-TTTTC--T
* *
29361 TCAAAGTCCACAACTCTGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
29384 CCCTTTTAAG
Statistics
Matches: 428, Mismatches: 73, Indels: 38
0.79 0.14 0.07
Matches are distributed among these distances:
30 151 0.35
31 150 0.35
32 52 0.12
33 55 0.13
34 20 0.05
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.33
Consensus pattern (31 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCT
Found at i:28913 original size:61 final size:62
Alignment explanation
Indices: 28831--29602 Score: 531
Period size: 61 Copynumber: 12.4 Consensus size: 62
28821 ATCTCTCTTC
* * ** *
28831 TCAAAGTCCACGACCCAGTGGCAATCTCTTCTT-AAAGTCCATGACTCAGTGGCATCTTGTC-
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
* * * * *
28892 CCAAAGTCCAAGACTGAGTGGCATCTTTTCTTCAAAATCCACAACTCAGTGGCATCTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
* * * *
28953 TCTAAGTCCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAATGGCATCTTTTTTCT
1 TCAAAGTCCACGACTCAGTGGCAT-CTTTTCTTCAAAGTCCACAACTCAGTGGCATC--TTTTCT
* * * *
29018 TCAAAGTTCACGACTCAGTGGCATCTCTTC-CCAAAGTCCACAACTCAATGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
* * * * *
29079 CCAAAGTTCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATAACTCAGTGGCATCTCTT-T
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
* * * *
29140 TCTAAGTCCACGACTTAGTGGCATCTTTTTCTTCCAAGTCCACGACTC-GATGGCATCTTTTTTC
1 TCAAAGTCCACGACTCAGTGGCATC-TTTTCTTCAAAGTCCACAACTCAG-TGGCATC--TTTTC
29204 T
62 T
* * * **
29205 TCAAAGTCCACGACTTAGTGGCATCTCTTC-CCAAAGTCCATGACTCAGTGGCATCTTTTCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
* ** * * * * * * *
29266 TCAAATTTTATGACTCAATGGCAATCTTTTC-TCAAAGTCCACGACTTAATAGCATCTCTTC-
1 TCAAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
* * * **
29327 CCAAAGTCCACGACTCTA-TGGCACCTTTTTCTTTTCAAAGTCCACAACTCTGTGGCA-CCCTT-
1 TCAAAGTCCACGACTC-AGTGGCATC-TTTTC--TTCAAAGTCCACAACTCAGTGGCATCTTTTC
29389 T
62 T
* * * * *
29390 T--AAGTCCACAACTCCGTGGCA-CATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TCAAAGTCCACGACTCAGTGGCATC--TTTTC--TTCAAAGTCCACAACTCAGTGGCA-TC-TTT
29452 TCCT
60 T-CT
** * * ** *
29456 TTTAAGTCCACAACTC-CTGGCA-CCCTT-TT--AAGTCCACAACTCCGTGGCATCTTTTTCCT
1 TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATC-TTTT-CT
** * * * ** * *
29515 TTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTCTT
1 TCAAAGTCCACGACTCAGTGGCATCTT-TT-CTTCAAAGTCCACAACTCAGTGGCATCTTTTC-T
** * *
29580 TTTAAGTCCATGACTCTGTGGCA
1 TCAAAGTCCACGACTCAGTGGCA
29603 CCATTTTCCC
Statistics
Matches: 584, Mismatches: 90, Indels: 70
0.78 0.12 0.09
Matches are distributed among these distances:
59 26 0.04
60 36 0.06
61 204 0.35
62 116 0.20
63 48 0.08
64 39 0.07
65 74 0.13
66 22 0.04
67 6 0.01
68 13 0.02
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (62 bp):
TCAAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCT
Found at i:29146 original size:187 final size:186
Alignment explanation
Indices: 28831--29376 Score: 722
Period size: 187 Copynumber: 2.9 Consensus size: 186
28821 ATCTCTCTTC
* ** *
28831 TCAAAGTCCACGACCCAGTGGCAATCTCTTCTTAAAGTCCATGACTCAGTGGCATCTTGTC-CCA
1 TCAAAGTCCACGACTCAGTGGC-ATCTCTTCCCAAAGTCCATGACTCAGTGGCATCTTTTCTCCA
* * *
28895 AAGTCCAAGACTGAGTGGCATCTTTTCTTCAAAATCCACAACTCAGTGGCATCTCTTTTCTAAGT
65 AAGTTCAA-ACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGT
28960 CCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAATGGCATCTTTTTTCT
129 CCACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAATGGCATCTTTTTTCT
* ** *
29018 TCAAAGTTCACGACTCAGTGGCATCTCTTCCCAAAGTCCACAACTCAATGGCATCTTTTCTCCAA
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCATGACTCAGTGGCATCTTTTCTCCAA
*
29083 AGTTCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATAACTCAGTGGCATCTCTTTTCTAAGTC
66 AGTTCA-AACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTC
* * *
29148 CACGACTTAGTGGCATCTTTTTCTTCCAAGTCCACGACTCGATGGCATCTTTTTTCT
130 CACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAATGGCATCTTTTTTCT
* *
29205 TCAAAGTCCACGACTTAGTGGCATCTCTTCCCAAAGTCCATGACTCAGTGGCATCTTTTCTTCAA
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCATGACTCAGTGGCATCTTTTCTCCAA
* * * * * * * * ** *
29270 ATTTTATGACTCAATGGCAATCTTTTC-TCAAAGTCCACGACTTAATAGCATCTCTTCCCAAAGT
66 AGTTCA-AACTCAGTGGC-ATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGT
*
29334 CCACGACTCTA-TGGCA-CCTTTTTCTTTTCAAAGTCCACAACTC
129 CCACGACT-TAGTGGCATCC-TTTTC--TTCCAAGTCCACAACTC
29377 TGTGGCACCC
Statistics
Matches: 315, Mismatches: 37, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
186 33 0.10
187 256 0.81
188 11 0.03
189 15 0.05
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.33
Consensus pattern (186 bp):
TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCATGACTCAGTGGCATCTTTTCTCCAA
AGTTCAAACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCC
ACGACTTAGTGGCATCCTTTTCTTCCAAGTCCACAACTCAATGGCATCTTTTTTCT
Found at i:29383 original size:95 final size:93
Alignment explanation
Indices: 28831--29383 Score: 568
Period size: 92 Copynumber: 5.9 Consensus size: 93
28821 ATCTCTCTTC
* ** * * *
28831 TCAAAGTCCACGACCCAGTGGCAATCTCTTCTTAAAGTCCATGACTC-AGTGGCATCTTGTC-CC
1 TCAAAGTCCACGACTCAGTGGC-ATCTCTTCCCAAAGTCCACGACTCTAGTGGCATCTTTTCTTC
*
28894 AAAGTCCA-AGACTGAGTGGCATCTTTTCT
65 AAAGTCCACA-ACTCAGTGGCATCTTTTCT
* * ** *
28923 TCAAAATCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACT-TAGTGGCATCCTTTTCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCTAGTGGCAT-CTTTTCTTC
* *
28987 CAAGTCCACAACTCAATGGCATCTTTTTTCT
65 AAAGTCCACAACTCAGTGGCATC--TTTTCT
* * * *
29018 TCAAAGTTCACGACTCAGTGGCATCTCTTCCCAAAGTCCACAACTC-AATGGCATCTTTTCTCCA
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCTAGTGGCATCTTTTCTTCA
*
29082 AAGTTCACAACTCAGTGGCATCTTTTCT
66 AAGTCCACAACTCAGTGGCATCTTTTCT
** ** *
29110 TCAAAGTCCATAACTCAGTGGCATCTCTTTTCTAAGTCCACGACT-TAGTGGCATCTTTTTCTTC
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCTAGTGGCATC-TTTTCTTC
* *
29174 CAAGTCCACGACTC-GATGGCATCTTTTTTCT
65 AAAGTCCACAACTCAG-TGGCATC--TTTTCT
* *
29205 TCAAAGTCCACGACTTAGTGGCATCTCTTCCCAAAGTCCATGACTC-AGTGGCATCTTTTCTTCA
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCTAGTGGCATCTTTTCTTCA
* ** ** *
29269 AATTTTATGACTCAATGGCAATCTTTTC-
66 AAGTCCACAACTCAGTGGC-ATCTTTTCT
* * * *
29297 TCAAAGTCCACGACTTAATAGCATCTCTTCCCAAAGTCCACGACTCTA-TGGCACCTTTTTCTTT
1 TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCTAGTGGCATC-TTTTC--T
*
29361 TCAAAGTCCACAACTCTGTGGCA
63 TCAAAGTCCACAACTCAGTGGCA
29384 CCCTTTTAAG
Statistics
Matches: 382, Mismatches: 60, Indels: 36
0.80 0.13 0.08
Matches are distributed among these distances:
91 27 0.07
92 126 0.33
93 55 0.14
94 51 0.13
95 123 0.32
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.33
Consensus pattern (93 bp):
TCAAAGTCCACGACTCAGTGGCATCTCTTCCCAAAGTCCACGACTCTAGTGGCATCTTTTCTTCA
AAGTCCACAACTCAGTGGCATCTTTTCT
Found at i:29482 original size:26 final size:27
Alignment explanation
Indices: 29453--29576 Score: 117
Period size: 33 Copynumber: 4.2 Consensus size: 27
29443 CACTCTTTTT
29453 CCTTTTAAGTCCACAACTCC-TGGCAC
1 CCTTTTAAGTCCACAACTCCGTGGCAC
29479 CCTTTTAAGTCCACAACTCCGTGGCATC
1 CCTTTTAAGTCCACAACTCCGTGGCA-C
29507 TTTTTCCTTTTAAGTCCACAACTCCGTGGCACC
1 -----CCTTTTAAGTCCACAACTCCGTGGCA-C
*
29540 TTGTTCCTTTTAAGTCCACAACTCTGTGGCA-
1 -----CCTTTTAAGTCCACAACTCCGTGGCAC
29571 CCTTTT
1 CCTTTT
29577 CTTTTTAAGT
Statistics
Matches: 88, Mismatches: 3, Indels: 14
0.84 0.03 0.13
Matches are distributed among these distances:
26 26 0.30
27 5 0.06
28 1 0.01
33 56 0.64
ACGTcount: A:0.19, C:0.33, G:0.13, T:0.35
Consensus pattern (27 bp):
CCTTTTAAGTCCACAACTCCGTGGCAC
Found at i:29484 original size:33 final size:33
Alignment explanation
Indices: 29330--29675 Score: 339
Period size: 34 Copynumber: 10.8 Consensus size: 33
29320 TCTCTTCCCA
* **
29330 AAGTCCACGACTCTATGGCACCTTTTT-CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
29362 CAAAGTCCACAACTCTGTGGCA-C-----CCTTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
29391 AAGTCCACAACTCCGTGGCACATTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
29424 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCAC-CTTTTTCCTTTT
29459 AAGTCCACAACTCC-TGGCA-C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
29485 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
29518 AAGTCCACAACTCCGTGGCACCTTGTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
29551 AAGTCCACAACTCTGTGGCACC-TTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
** * *
29583 AAGTCCATGACTCTGTGGCACCATTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCACC-TTTTTCCTTTT
* *
29617 AAG-CTCACACCTCCGTGGCATACCTTTTTCC-TAT
1 AAGTC-CACAACTCCGTGGC--ACCTTTTTCCTTTT
*
29651 AAGTCCACAACTCCGTGGAACCTTT
1 AAGTCCACAACTCCGTGGCACCTTT
29676 AATTCCAATA
Statistics
Matches: 264, Mismatches: 26, Indels: 46
0.79 0.08 0.14
Matches are distributed among these distances:
26 20 0.08
27 24 0.09
28 1 0.00
29 5 0.02
31 1 0.00
32 34 0.13
33 70 0.27
34 89 0.34
35 17 0.06
36 3 0.01
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:29520 original size:59 final size:62
Alignment explanation
Indices: 29385--29673 Score: 266
Period size: 66 Copynumber: 4.5 Consensus size: 62
29375 TCTGTGGCAC
* * *
29385 CCTTTTAAGTCCACAACTCCGTGGCACATTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAGTCCACAACTCCGTGGCAC----CTCCTTTT-AAGTCCACAACTCCGTGGCA-TCTT
29450 TTT
60 TTT
29453 CCTTTTAAGTCCACAACTCC-TGGCA-C-CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* *
29512 CCTTTTAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCTGTGGCA-CCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACC----TCCTTTTAAGTCCACAACTCCGTGGCATCTTTT
29576 T
62 T
* ** * *
29577 CTTTTTAAGTCCATGACTCTGTGGCACCATTTTCCCTTTTAAG-CTCACACCTCCGTGGCATACC
1 CCTTTTAAGTCCACAACTCCGTGGCACC----T-CCTTTTAAGTC-CACAACTCCGTGGCAT--C
29641 TTTTT
58 TTTTT
* *
29646 CC-TATAAGTCCACAACTCCGTGGAACCT
1 CCTTTTAAGTCCACAACTCCGTGGCACCT
29674 TTAATTCCAA
Statistics
Matches: 189, Mismatches: 20, Indels: 28
0.80 0.08 0.12
Matches are distributed among these distances:
59 27 0.14
60 24 0.13
61 6 0.03
64 1 0.01
65 33 0.17
66 47 0.25
67 5 0.03
68 40 0.21
69 6 0.03
ACGTcount: A:0.20, C:0.32, G:0.13, T:0.35
Consensus pattern (62 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTCCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
Found at i:29782 original size:39 final size:39
Alignment explanation
Indices: 29728--30062 Score: 211
Period size: 39 Copynumber: 7.9 Consensus size: 39
29718 ATCTTTAAGA
* *
29728 CCAATGTCACTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * * *
29767 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAGGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
*
29815 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * * *
29854 CTAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA------C---AAGC
* *
29902 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * * * **
29941 CCAATATTGCTGACCTTGGATCAGCATATTGGCACCTTGTCTCTAAAA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA--------C-AAGC
* *
29989 CCAATGTCGCTGGCCTTGAATCAACACATTGGCACAAGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
* * *
30028 CTAATATCGTTGGCCTTGAATCAGCATATTGGCAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
30063 CTTCATCTTT
Statistics
Matches: 226, Mismatches: 43, Indels: 54
0.70 0.13 0.17
Matches are distributed among these distances:
39 126 0.56
40 1 0.00
42 1 0.00
45 2 0.01
48 96 0.42
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (39 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGC
Found at i:29828 original size:87 final size:87
Alignment explanation
Indices: 29680--30111 Score: 675
Period size: 87 Copynumber: 5.0 Consensus size: 87
29670 ACCTTTAATT
* * * *
29680 CCAATATCGCTAGCCTTGAATTAGCATATTGGCACCTTATCTTTAAGACCAATGTCACTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
29745 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* *
29767 CCAATATCGCTGGCCTTAAATCAGCATATTGGCACCTTGTCTTTAGGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
29832 GAATCAGCACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* *
29854 CTAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
*
29919 GAATCAGCACATTGGCATAAGC
66 GAATCAGCACATTGGCACAAGC
* * * * *
29941 CCAATATTGCTGACCTTGGATCAGCATATTGGCACCTTGTCTCTAAAACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
*
30006 GAATCAACACATTGGCACAAGC
66 GAATCAGCACATTGGCACAAGC
* * * * *
30028 CTAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-GTCTTTAAGACCAATGTCGCTGGCCT
30093 TGAATCAGCACATTGGCAC
65 TGAATCAGCACATTGGCAC
30112 CTTAACCATC
Statistics
Matches: 313, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
87 274 0.88
88 39 0.12
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCACATTGGCACAAGC
Found at i:30108 original size:49 final size:49
Alignment explanation
Indices: 30038--30457 Score: 392
Period size: 49 Copynumber: 8.4 Consensus size: 49
30028 CTAATATCGT
* * * *
30038 TGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGT
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGC
30087 TGGCCTTGAATCAGCACATTGGCACCTTAACCATCTTTAAGTCCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTT---CATCTTTAAGTCCAATGTCGC
* * * * * * *
30139 CGACCTTGAATCGGCATATTGGCATCTTCATCTTTAAGTCCGATATCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGC
* * * **
30188 TGGCCTTAAATCAGCATATTGGCACCTTTATCTTTAAAACCAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGC
* * * * * * **
30237 TGGCTTTAAATCAGTACATTGGGACCTTCATCTTTAAGTCCGATATCAT
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGC
* * * * *
30286 TGGCCTTGAATCAGCACATTGGCACCTTTATCTTTAAATCCGATATCGT
1 TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGC
* * * *
30335 TGGCCTTGAGTCAGCACATTGGCATCTTTAACATTCCTAAG-CCAAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCATC-TT--TAAGTCC-AATGTCGC
* ** * * * *
30387 TAGCCTTGTCTCAGCACATTGGCATTCTTCTTCTTCAAGTCTAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCA-CCTTCATCTTTAAGTCCAATGTCGC
*
30437 TGGCCATGAATCAGCACATTG
1 TGGCCTTGAATCAGCACATTG
30458 TCATTCTTCG
Statistics
Matches: 304, Mismatches: 58, Indels: 17
0.80 0.15 0.04
Matches are distributed among these distances:
49 194 0.64
50 30 0.10
51 3 0.01
52 72 0.24
53 5 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (49 bp):
TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTCGC
Found at i:33502 original size:21 final size:20
Alignment explanation
Indices: 33478--33530 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
33468 TACAGGCCAA
*
33478 TGTATCGATACAATTTTTTTG
1 TGTATCGATACAA-TATTTTG
33499 TGTATCGATAC-ATATTTTG
1 TGTATCGATACAATATTTTG
33518 TGTATCGATACAA
1 TGTATCGATACAA
33531 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
20 2 0.07
21 11 0.37
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATATTTTG
Found at i:34698 original size:27 final size:27
Alignment explanation
Indices: 34666--34717 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
34656 AAAATTTTTT
34666 GGGGATACTCCAACCCCATTCTTTTGA
1 GGGGATACTCCAACCCCATTCTTTTGA
*
34693 GGGGATACTCCAACCCCGTTCTTTT
1 GGGGATACTCCAACCCCATTCTTTT
34718 AAACTTATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.31
Consensus pattern (27 bp):
GGGGATACTCCAACCCCATTCTTTTGA
Found at i:34808 original size:27 final size:27
Alignment explanation
Indices: 34778--34845 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
34768 CATTATTGGA
34778 GACACTCCAACCCCATGTC-TCCGAGAG
1 GACACTCCAACCCCAT-TCTTCCGAGAG
* * * *
34805 GACACTCCAACTCTATTCTTCTGAGGG
1 GACACTCCAACCCCATTCTTCCGAGAG
34832 GACACTCCAACCCC
1 GACACTCCAACCCC
34846 GTTTTCAACC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 2 0.06
27 32 0.94
ACGTcount: A:0.25, C:0.40, G:0.16, T:0.19
Consensus pattern (27 bp):
GACACTCCAACCCCATTCTTCCGAGAG
Found at i:40314 original size:20 final size:19
Alignment explanation
Indices: 40289--40361 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
40279 CTGTCAGTTT
**
40289 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
40309 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
40328 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
40349 -ATGTATCGATACA
1 CATGTATCGATACA
40362 TCTGGATGTG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 18 0.38
20 29 0.60
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:43783 original size:25 final size:25
Alignment explanation
Indices: 43753--43830 Score: 147
Period size: 25 Copynumber: 3.1 Consensus size: 25
43743 TAGTTCAAAG
43753 TAAGAACTCTTTCTTGTAGGTCTTC
1 TAAGAACTCTTTCTTGTAGGTCTTC
*
43778 TAAGAACTCTTTCTTATAGGTCTTC
1 TAAGAACTCTTTCTTGTAGGTCTTC
43803 TAAGAACTCTTTCTTGTAGGTCTTC
1 TAAGAACTCTTTCTTGTAGGTCTTC
43828 TAA
1 TAA
43831 TTCTTCAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (25 bp):
TAAGAACTCTTTCTTGTAGGTCTTC
Found at i:45938 original size:20 final size:20
Alignment explanation
Indices: 45913--45987 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
45903 TTTTACCCAG
45913 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
45933 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
45953 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
45973 ATGTATCAATACATT
1 ATGTATCGATACATT
45988 CTGTCTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:50180 original size:452 final size:455
Alignment explanation
Indices: 49264--50303 Score: 1357
Period size: 452 Copynumber: 2.3 Consensus size: 455
49254 AGGCAAATGC
* * * * *
49264 TTTAGAATCATGAAGCTTCATGCTTCAATTTAAAGAAGGGACAGAAATAAACATCTAGGATGCAT
1 TTTAGAATCATGAAGCTTCATGCTTCAATTTAAAGAAGGAAAAGAAACAAATATCT-GGAAGCAT
* * *
49329 AAACAATGCATGGCAAATAATGACAATAAGCCTCATATGCACGAAAAAAGTTTAAAATGGATGAG
65 AAACAATGCATGGCAAATAATGACAATAAGCCTTATATGCACGAAAAAAGTTTAAAATGCATAAG
* * *
49394 AAAGTTTTTTTTTTTCATTTTCAAAACATGAAGAAGTTTATGCATGCTATGTGAGTGCATGGAAA
130 AAAGGTTTTTTTTTTCATTTTCAAAACATGAAGAAGTTCATGCATGCAATGTGAGTGCATGG--A
*
49459 ACTAAAAAAATAAGTAAAAAAAGTAATATACCTAAATAAGGATGAAAGGTAAACTTTTTTTTTCT
193 AC-AAAAAAATAAG-AAAAAAAGTAATATACCTAAATAAGGATGAAAGATAAACTTTTTTTTTCT
* *
49524 TTTACTTTTCTTTTCTCTCTTTCTCTTACTTTTTTTTTTGTTATAATTTTTACTCTAAGAGATGA
256 TTTACTTTTCTTTTCTCTCTTTCTC-TACTTTTTTTTTTGTTATAATTTTTACTCTAAAAAATGA
* * **
49589 TAAGAATGATGGAAGATATCAAAAAAATAAATTTCCAAGCCATAACGTTTGGCCAAAATCTTGTC
320 TAAGAATGATAGAAGATATCAAAAAAATAAATTTCCAAACCATAACGCCTGGCCAAAATCTTGTC
*
49654 AAAAAAATAAATTTCCAAGCTAAAAGGTTTAGCCAAAACCCTTTTTTAGAAGGAAAAAAAGAAAT
385 AAAAAAATAAATTTCCAAGCCAAAA-GTTTAGCCAAAACCCTTTTTTAGAAGGAAAAAAAGAAAT
49719 CGCCATT
449 CGCCATT
* * *
49726 TTTAGAATCATGAAGCTTCATGCTTTAATTTAAAGAAGGAAAAGAAACAAATATTTGGGAAGTAT
1 TTTAGAATCATGAAGCTTCATGCTTCAATTTAAAGAAGGAAAAGAAACAAATATCT-GGAAGCAT
* * *
49791 AAATAATGTATGGCAAATAATGACAATAAGCCTTATATGCACGGAAAAAGTTT-AAATGCATAAG
65 AAACAATGCATGGCAAATAATGACAATAAGCCTTATATGCACGAAAAAAGTTTAAAATGCATAAG
* * * *
49855 AAAGGTTTTTTTTTTCATTTTTAAACCATGAAGGAGTTCATGGATGCAATGTGAGTGCAT-G-A-
130 AAAGGTTTTTTTTTTCATTTTCAAAACATGAAGAAGTTCATGCATGCAATGTGAGTGCATGGAAC
*** *
49917 AAAATTTTAA-AAAAAAAGTAATATACTTAAATAAGGATGAAAGATAAA-TTTCTTTTTTCTTTT
195 AAAAAAATAAGAAAAAAAGTAATATACCTAAATAAGGATGAAAGATAAACTTT-TTTTTTCTTTT
* * *
49980 ACTTTT-TTCTCTTTCTCTTTCTC-A-TTTTTTTTTTGTTATAATTTTTGCTCTAAAAAATGATG
259 ACTTTTCTT-T-TCTCTCTTTCTCTACTTTTTTTTTTGTTATAATTTTTACTCTAAAAAATGATA
* *
50042 AGAATGATAGAAGATGTCAAAAAAAATAAATTTCCAAACCATAACGCCTGGTCAAAATCTTGTCA
322 AGAATGATAGAAGATATC-AAAAAAATAAATTTCCAAACCATAACGCCTGGCCAAAATCTTGTCA
* * ***
50107 AAAAAATAAATTTCTAAGCCAGAAA-TCTTAGCCAAAA-CCTTTCTTTAGGAGGAAAAGGGGAAA
386 AAAAAATAAATTTCCAAGCCA-AAAGT-TTAGCCAAAACCCTTT-TTTAGAAGGAAAAAAAGAAA
* *
50170 TGGTCATT
448 TCGCCATT
* * * **
50178 TTTAGAACCATGAAGCTTCATGCTTCAATTTAAAAAAAGAAAAGAAACAAATATCTATAACGCAT
1 TTTAGAATCATGAAGCTTCATGCTTCAATTTAAAGAAGGAAAAGAAACAAATATCTGGAA-GCAT
* ** *
50243 AAACAATGCATGGCGAATAATGGTAAT-AGACCTTATATGCATGAAAAAAGTTTAAAATGCA
65 AAACAATGCATGGCAAATAATGACAATAAG-CCTTATATGCACGAAAAAAGTTTAAAATGCA
50304 CGAGAAATTT
Statistics
Matches: 507, Mismatches: 61, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
451 60 0.12
452 196 0.39
453 64 0.13
454 11 0.02
455 7 0.01
457 1 0.00
460 1 0.00
461 62 0.12
462 105 0.21
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.33
Consensus pattern (455 bp):
TTTAGAATCATGAAGCTTCATGCTTCAATTTAAAGAAGGAAAAGAAACAAATATCTGGAAGCATA
AACAATGCATGGCAAATAATGACAATAAGCCTTATATGCACGAAAAAAGTTTAAAATGCATAAGA
AAGGTTTTTTTTTTCATTTTCAAAACATGAAGAAGTTCATGCATGCAATGTGAGTGCATGGAACA
AAAAAATAAGAAAAAAAGTAATATACCTAAATAAGGATGAAAGATAAACTTTTTTTTTCTTTTAC
TTTTCTTTTCTCTCTTTCTCTACTTTTTTTTTTGTTATAATTTTTACTCTAAAAAATGATAAGAA
TGATAGAAGATATCAAAAAAATAAATTTCCAAACCATAACGCCTGGCCAAAATCTTGTCAAAAAA
ATAAATTTCCAAGCCAAAAGTTTAGCCAAAACCCTTTTTTAGAAGGAAAAAAAGAAATCGCCATT
Found at i:53400 original size:2 final size:2
Alignment explanation
Indices: 53393--53432 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
53383 CATGATTATC
*
53393 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA -A TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53433 GTAAAACAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54285 original size:2 final size:2
Alignment explanation
Indices: 54278--54305 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54268 TTTTACTATG
54278 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
54306 TTTATTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54577 original size:2 final size:2
Alignment explanation
Indices: 54570--54600 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
54560 TAATTCTGAT
54570 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
54601 TTCTTTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:58549 original size:2 final size:2
Alignment explanation
Indices: 58542--58575 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
58532 GATTAGTTTA
58542 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
58576 GTGTCAGACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:60441 original size:11 final size:12
Alignment explanation
Indices: 60416--60441 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
60406 ATTGAGTAAA
60416 TTTCCTTCTTTT
1 TTTCCTTCTTTT
60428 TTTCCTTCTTTT
1 TTTCCTTCTTTT
60440 TT
1 TT
60442 AACGTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTCCTTCTTTT
Found at i:69226 original size:18 final size:17
Alignment explanation
Indices: 69186--69228 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
69176 TATTATGTAT
* *
69186 TTTTTATATTTAATACT
1 TTTTAATATTTAATACG
69203 TATTTAATATTTACATACG
1 T-TTTAATATTTA-ATACG
69222 TTTTAAT
1 TTTTAAT
69229 TTAATTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 16 0.73
19 5 0.23
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTTAATATTTAATACG
Found at i:72927 original size:20 final size:22
Alignment explanation
Indices: 72899--72941 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
72889 TGTATCATTG
72899 TATCAATACATTA-A-TTAAAA
1 TATCAATACATTATATTTAAAA
*
72919 TATCGATACATTATATTTAAAA
1 TATCAATACATTATATTTAAAA
72941 T
1 T
72942 TATAGCCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 12 0.60
21 1 0.05
22 7 0.35
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (22 bp):
TATCAATACATTATATTTAAAA
Found at i:72985 original size:20 final size:20
Alignment explanation
Indices: 72960--73034 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
72950 TTGGCCTAAT
72960 TGTATCGATACAATTCTGAA
1 TGTATCGATACAATTCTGAA
72980 TGTATCGATAC-ATTCTGGAA
1 TGTATCGATACAATTCT-GAA
* * *
73000 TTGTATCGACACAATCTTATGTA
1 -TGTATCGATACAA--TTCTGAA
73023 TGTATCGATACA
1 TGTATCGATACA
73035 TTTGAGGGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 5 0.11
20 14 0.30
21 10 0.22
22 12 0.26
23 2 0.04
24 3 0.07
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (20 bp):
TGTATCGATACAATTCTGAA
Found at i:73006 original size:21 final size:21
Alignment explanation
Indices: 72957--73014 Score: 84
Period size: 20 Copynumber: 2.8 Consensus size: 21
72947 CCGTTGGCCT
72957 AATTGTATCGATACAATTCTG
1 AATTGTATCGATACAATTCTG
72978 AA-TGTATCGATAC-ATTCTGG
1 AATTGTATCGATACAATTCT-G
*
72998 AATTGTATCGACACAAT
1 AATTGTATCGATACAAT
73015 CTTATGTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 12 0.36
22 2 0.06
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (21 bp):
AATTGTATCGATACAATTCTG
Found at i:73007 original size:41 final size:42
Alignment explanation
Indices: 72957--73036 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
72947 CCGTTGGCCT
* *
72957 AATTGTATCGATACAA-TTCTGAATGTATCGATACATTCTGG
1 AATTGTATCGACACAACTTATGAATGTATCGATACATTCTGG
*
72998 AATTGTATCGACACAATCTTATGTATGTATCGATACATT
1 AATTGTATCGACACAA-CTTATGAATGTATCGATACATT
73037 TGAGGGGTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 15 0.44
43 19 0.56
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (42 bp):
AATTGTATCGACACAACTTATGAATGTATCGATACATTCTGG
Found at i:74506 original size:16 final size:16
Alignment explanation
Indices: 74482--74524 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
74472 TCTGGTCATA
*
74482 TTAATTTTAAATTTTT
1 TTAAATTTAAATTTTT
*
74498 TTAAGTTT-AATTTTT
1 TTAAATTTAAATTTTT
74513 TTAAATTTAAAT
1 TTAAATTTAAAT
74525 ATTTAACTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTAAATTTAAATTTTT
Found at i:87585 original size:8 final size:7
Alignment explanation
Indices: 87539--87589 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
87529 CGGATTTTAT
87539 TTTTAAA
1 TTTTAAA
87546 CTTTTAGAA
1 -TTTTA-AA
*
87555 -TCTAAA
1 TTTTAAA
87561 TTTTAAA
1 TTTTAAA
87568 TTTTAAA
1 TTTTAAA
87575 TTTTAAA
1 TTTTAAA
*
87582 ATTTAAA
1 TTTTAAA
87589 T
1 T
87590 AGATTTGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 2 0.05
7 28 0.76
8 5 0.14
9 2 0.05
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (7 bp):
TTTTAAA
Done.