Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1162
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: 25233
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Found at i:4195 original size:1 final size:1
Alignment explanation
Indices: 4191--4267 Score: 64
Period size: 1 Copynumber: 77.0 Consensus size: 1
4181 CATCCTCCAC
* * * * * * * * *
4191 AAAAAAAAACAGAAGAAAAAAAGAAAAAAAACAAAACAAAAAACAAAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
4256 AAAACAAAAAAA
1 AAAAAAAAAAAA
4268 CAACAACAAC
Statistics
Matches: 56, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:4211 original size:17 final size:16
Alignment explanation
Indices: 4191--4270 Score: 90
Period size: 17 Copynumber: 4.8 Consensus size: 16
4181 CATCCTCCAC
4191 AAAAAAAAACAGAAGAAA
1 AAAAAAAAACA-AA-AAA
*
4209 AAAAGAAAAA-AAACAA
1 AAAA-AAAAACAAAAAA
*
4225 AACAAAAAACAAAAAA
1 AAAAAAAAACAAAAAA
4241 AACAAAAAAACAAAAAA
1 AA-AAAAAAACAAAAAA
4258 AACAAAAAAACAA
1 AA-AAAAAAACAA
4271 CAACAACAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
15 5 0.09
16 12 0.22
17 28 0.51
18 5 0.09
19 5 0.09
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (16 bp):
AAAAAAAAACAAAAAA
Found at i:4217 original size:5 final size:5
Alignment explanation
Indices: 4209--4293 Score: 63
Period size: 5 Copynumber: 16.8 Consensus size: 5
4199 ACAGAAGAAA
*
4209 AAAAG AAAA- AAAAC AAAAC AAAAAAC AAAA- AAAAC -AAA- AAAAC AAAA-
1 AAAAC AAAAC AAAAC AAAAC --AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
*
4256 AAAAC AAAAA AACAAC AACAAC AACAAC AACAAC AAAA
1 AAAAC AAAAC AA-AAC AA-AAC AA-AAC AA-AAC AAAA
4294 AGGGTCCGGA
Statistics
Matches: 70, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
4 18 0.26
5 25 0.36
6 22 0.31
7 5 0.07
ACGTcount: A:0.82, C:0.16, G:0.01, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:4217 original size:21 final size:18
Alignment explanation
Indices: 4191--4267 Score: 75
Period size: 20 Copynumber: 4.1 Consensus size: 18
4181 CATCCTCCAC
* *
4191 AAAAAAAAACAGAAGAAAA
1 AAAAAAAAAAACAA-AAAA
4210 AAAGAAAAAAAACAAAACAA
1 AAA-AAAAAAAACAAAA-AA
4230 AAAACAAAAAAA-ACAAAAA
1 AAAA-AAAAAAACA-AAAAA
*
4249 AACAAAAAAAACAAAAAA
1 AAAAAAAAAAACAAAAAA
4267 A
1 A
4268 CAACAACAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
18 13 0.26
19 13 0.26
20 24 0.48
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAA
Found at i:4220 original size:9 final size:9
Alignment explanation
Indices: 4206--4294 Score: 83
Period size: 9 Copynumber: 9.8 Consensus size: 9
4196 AAAACAGAAG
*
4206 AAAAAAAGA
1 AAAAAAACA
4215 AAAAAAACAAA
1 AAAAAAAC--A
4226 ACAAAAAACA
1 A-AAAAAACA
4236 AAAAAAAC-
1 AAAAAAACA
4244 AAAAAAACA
1 AAAAAAACA
4253 AAAAAAAC-
1 AAAAAAACA
4261 AAAAAAACA
1 AAAAAAACA
* *
4270 ACAACAACA
1 AAAAAAACA
* *
4279 ACAACAACA
1 AAAAAAACA
*
4288 ACAAAAA
1 AAAAAAA
4295 GGGTCCGGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 10
0.84 0.05 0.12
Matches are distributed among these distances:
8 16 0.23
9 44 0.62
10 2 0.03
11 2 0.03
12 7 0.10
ACGTcount: A:0.83, C:0.16, G:0.01, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:4220 original size:22 final size:19
Alignment explanation
Indices: 4191--4267 Score: 86
Period size: 21 Copynumber: 3.9 Consensus size: 19
4181 CATCCTCCAC
4191 AAAAAAAAACAGAAGAAAAAA
1 AAAAAAAAACA-AA-AAAAAA
4212 AGAAAAAAAACAAAACAAAAA
1 A-AAAAAAAACAAAA-AAAAA
4233 ACAAAAAAAAC--AAAAAAA
1 A-AAAAAAAACAAAAAAAAA
*
4251 CAAAAAAAACAAAAAAA
1 AAAAAAAAACAAAAAAA
4268 CAACAACAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
17 9 0.18
18 5 0.10
19 7 0.14
20 1 0.02
21 18 0.36
22 10 0.20
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAAAAAACAAAAAAAAA
Found at i:4272 original size:3 final size:3
Alignment explanation
Indices: 4220--4291 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
4210 AAAGAAAAAA
* * * * *
4220 AAC AA- AAC AA- AA- AAC AAA AAA AAC AA- AAA AAC AAA AAA AAC AA-
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
*
4263 AAA AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
4292 AAAGGGTCCG
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
2 10 0.17
3 49 0.83
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:5773 original size:29 final size:28
Alignment explanation
Indices: 5734--5925 Score: 208
Period size: 29 Copynumber: 6.8 Consensus size: 28
5724 TTACCCTTCA
*
5734 AAAGCCCACAAGTCAATGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATC-TTTTC
5763 AAAGCCCACAAGTCAGTGGCATCTTTCTC
1 AAAGCCCACAAGTCAGTGGCATCTTT-TC
* * * * *
5792 AAAGTCCACAAGTTAGTGGCAAC-CTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
* *
5819 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTT-C
* * * *
5849 GAAGCCCACAAGTCAGTGGCAACCTTTA
1 AAAGCCCACAAGTCAGTGGCATCTTTTC
*
5877 AAAGCCCACAAGTCAGTGGCAATC-TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTC
5905 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
5926 ACCTTCAAAA
Statistics
Matches: 139, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
27 20 0.14
28 48 0.35
29 51 0.37
30 20 0.14
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTC
Found at i:5860 original size:86 final size:85
Alignment explanation
Indices: 5731--5971 Score: 249
Period size: 85 Copynumber: 2.8 Consensus size: 85
5721 TCCTTACCCT
* * * * * *
5731 TCAAAAGCCCACAAGTCAATGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTCTCAAAG
1 TCAAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTT-TAAAAG
* *
5796 TCCACAAGTTAGTGGCAA-CC
65 CCCACAAGTCAGTGGCAATCC
* * *
5816 TCCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCAGTGGCAACCTTTAAAAG
1 TCAAAAGCCCACAAGTCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAG
*
5881 CCCACAAGTCAGTGGCAATCT
65 CCCACAAGTCAGTGGCAATCC
* * * *
5902 TTAAAAGCCCACAAGTCAGTGGCAACC--TTCAAAAGCACACAAGT-TGAT-GCAAACCTTTTAA
1 TCAAAAGCCCACAAGTCAGTGGC-ACCTTTTCCAAAGCCCACAAGTCAG-TGGC-AACC-TTTAA
5963 AAGCCCACA
62 AAGCCCACA
5972 CAAGTTGGTG
Statistics
Matches: 131, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
83 3 0.02
84 19 0.15
85 56 0.43
86 52 0.40
87 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.20
Consensus pattern (85 bp):
TCAAAAGCCCACAAGTCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGC
CCACAAGTCAGTGGCAATCC
Found at i:5890 original size:28 final size:28
Alignment explanation
Indices: 5728--5971 Score: 224
Period size: 28 Copynumber: 8.6 Consensus size: 28
5718 CATTCCTTAC
* * *
5728 CCTTCAAAAGCCCACAAGTCAATGGCAT
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
* * *
5756 CTTTTTCAAAGCCCACAAGTCAGTGGCAT
1 C-CTTTAAAAGCCCACAAGTCAGTGGCAA
* * * *
5785 CTTTCTCAAAGTCCACAAGTTAGTGGCAA
1 CCTT-TAAAAGCCCACAAGTCAGTGGCAA
** * *
5814 CC-TCCAAAGCCCACAAATCAGTGGCAC
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
**
5841 CCTTTTCCGAAGCCCACAAGTCAGTGGCAA
1 CC-TTT-AAAAGCCCACAAGTCAGTGGCAA
5871 CCTTTAAAAGCCCACAAGTCAGTGGCAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
*
5899 TCTTTAAAAGCCCACAAGTCAGTGGCAA
1 CCTTTAAAAGCCCACAAGTCAGTGGCAA
* * *
5927 CCTTCAAAAGCACACAAGT-TGAT-GCAAA
1 CCTTTAAAAGCCCACAAGTCAG-TGGC-AA
5955 CCTTTTAAAAGCCCACA
1 CC-TTTAAAAGCCCACA
5972 CAAGTTGGTG
Statistics
Matches: 182, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
27 24 0.13
28 74 0.41
29 62 0.34
30 22 0.12
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (28 bp):
CCTTTAAAAGCCCACAAGTCAGTGGCAA
Found at i:6071 original size:52 final size:51
Alignment explanation
Indices: 5993--6234 Score: 277
Period size: 52 Copynumber: 4.8 Consensus size: 51
5983 CATCTTCTTC
5993 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGT-ACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTT-GTCACC-T
* * * *
6045 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC----T--CC-
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCT
* *
6089 -AAGTCCAATATCGCTAGTCTTGAATCAGCATATTGGCGCCTTTGTCATCCT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA-CCT
* * * *
6140 TAAGTCCTATATCGCTGGCCTTGGATCAGCATATTGGCGTCTTTGTCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCA-CCT
* *
6192 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTT
6235 CATCTTTAAC
Statistics
Matches: 160, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
43 34 0.21
46 2 0.01
47 2 0.01
50 2 0.01
52 120 0.75
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (51 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCACCT
Found at i:6157 original size:95 final size:95
Alignment explanation
Indices: 5994--6177 Score: 273
Period size: 95 Copynumber: 1.9 Consensus size: 95
5984 ATCTTCTTCT
* *
5994 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATGTAG
1 AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATATAG
6059 CTGGCCTTGAATCAGCACATTGGCACCTCC
66 CTGGCCTTGAATCAGCACATTGGCACCTCC
* *
6089 AAGTCCAATATCGCTAGTCTTGAATCAGCATATTGGCGCCTTT-GTCATCC-TTAAGTCCTATAT
1 AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGGT-A-CCTTTAAGTCCAATAT
* * *
6152 CGCTGGCCTTGGATCAGCATATTGGC
64 AGCTGGCCTTGAATCAGCACATTGGC
6178 GTCTTTGTCA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 2 0.03
95 76 0.95
96 2 0.03
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (95 bp):
AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGGTACCTTTAAGTCCAATATAG
CTGGCCTTGAATCAGCACATTGGCACCTCC
Found at i:6908 original size:10 final size:10
Alignment explanation
Indices: 6871--6934 Score: 67
Period size: 10 Copynumber: 6.2 Consensus size: 10
6861 TGGGGACGAA
6871 AAATTTTGTT
1 AAATTTTGTT
*
6881 AACTTTT-TAT
1 AAATTTTGT-T
*
6891 AACTTTTTGTT
1 AA-ATTTTGTT
6902 AAATTTTGTT
1 AAATTTTGTT
6912 AAATTTTGTT
1 AAATTTTGTT
*
6922 AACTTTTTGTT
1 AA-ATTTTGTT
6933 AA
1 AA
6935 GCCCGAATCC
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
9 1 0.02
10 28 0.61
11 16 0.35
12 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (10 bp):
AAATTTTGTT
Found at i:6909 original size:31 final size:31
Alignment explanation
Indices: 6871--6934 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
6861 TGGGGACGAA
*
6871 AAATTTTGTTAACTTTT-TATAACTTTTTGTT
1 AAATTTTGTTAAATTTTGT-TAACTTTTTGTT
6902 AAATTTTGTTAAATTTTGTTAACTTTTTGTT
1 AAATTTTGTTAAATTTTGTTAACTTTTTGTT
6933 AA
1 AA
6935 GCCCGAATCC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (31 bp):
AAATTTTGTTAAATTTTGTTAACTTTTTGTT
Found at i:6930 original size:21 final size:21
Alignment explanation
Indices: 6871--6934 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
6861 TGGGGACGAA
*
6871 AAATTTTGTTAACTTTTT-AT
1 AAATTTTGTTAACTTTTTGTT
* *
6891 AACTTTTTGTTAA-ATTTTGTT
1 AA-ATTTTGTTAACTTTTTGTT
6912 AAATTTTGTTAACTTTTTGTT
1 AAATTTTGTTAACTTTTTGTT
6933 AA
1 AA
6935 GCCCGAATCC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.28, C:0.05, G:0.08, T:0.59
Consensus pattern (21 bp):
AAATTTTGTTAACTTTTTGTT
Found at i:7132 original size:33 final size:33
Alignment explanation
Indices: 7089--7155 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
7079 TTCAACGATT
7089 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *** *
7122 TGTATTGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
7155 T
1 T
7156 TTAAGCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:7214 original size:13 final size:13
Alignment explanation
Indices: 7196--7220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7186 ATTACTCAAA
7196 TGTATCGATACAT
1 TGTATCGATACAT
7209 TGTATCGATACA
1 TGTATCGATACA
7221 CTGATCTTTG
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:11018 original size:34 final size:35
Alignment explanation
Indices: 10980--11046 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
10970 CCTTACAACA
10980 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
11014 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
11047 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:11522 original size:13 final size:13
Alignment explanation
Indices: 11504--11529 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11494 CAATTTTTTG
11504 TGTATCGATACAT
1 TGTATCGATACAT
11517 TGTATCGATACAT
1 TGTATCGATACAT
11530 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11541 original size:32 final size:33
Alignment explanation
Indices: 11484--11547 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
11474 TATAAGCCAA
**
11484 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
11517 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
11548 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:12278 original size:21 final size:21
Alignment explanation
Indices: 12237--12280 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12227 CTCCCCTTTA
* *
12237 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
12258 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
12279 TC
1 TC
12281 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:13463 original size:13 final size:13
Alignment explanation
Indices: 13445--13469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13435 ACTGAAGCAA
13445 TGTATCGATACAT
1 TGTATCGATACAT
13458 TGTATCGATACA
1 TGTATCGATACA
13470 ATCTGGAAAA
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:17206 original size:13 final size:13
Alignment explanation
Indices: 17188--17213 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17178 CAATTTTTTG
17188 TGTATCGATACAT
1 TGTATCGATACAT
17201 TGTATCGATACAT
1 TGTATCGATACAT
17214 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17225 original size:32 final size:33
Alignment explanation
Indices: 17168--17231 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
17158 TATAAGCCAA
**
17168 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATCGATACAT
17201 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTGTGTATCGATACA
17232 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATCGATACAT
Found at i:21834 original size:23 final size:22
Alignment explanation
Indices: 21794--21856 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
21784 TCAACTGGAA
*
21794 AAAAAAAAAAG-AGAAAAAAGAG
1 AAAAAAATAAGTA-AAAAAAGAG
* *
21816 AGAAAGAA-AAGTAAGAAAAATAG
1 A-AAAAAATAAGTAA-AAAAAGAG
21839 AAAAAAATAAGTAAAAAA
1 AAAAAAATAAGTAAAAAA
21857 TAATAGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (22 bp):
AAAAAAATAAGTAAAAAAAGAG
Found at i:21866 original size:23 final size:22
Alignment explanation
Indices: 21807--21872 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
21797 AAAAAAAGAG
* * *
21807 AAAAAAGAGAGAAAGAA-AAGT
1 AAAAAAAATAGAAAAAATAAGT
*
21828 AAGAAAAATAGAAAAAAATAAGT
1 AAAAAAAATAG-AAAAAATAAGT
*
21851 AAAAAATAATAGAAAAACTAAG
1 AAAAAA-AATAGAAAAAATAAG
21873 CTAGCTTTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 8 0.22
22 5 0.14
23 18 0.50
24 5 0.14
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.11
Consensus pattern (22 bp):
AAAAAAAATAGAAAAAATAAGT
Done.