Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006038.1 Corchorus capsularis cultivar CVL-1 contig06056, whole genome shotgun sequence
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: 31821
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:6198 original size:7 final size:7
Alignment explanation
Indices: 6186--6387 Score: 53
Period size: 7 Copynumber: 28.7 Consensus size: 7
6176 TGAATACCAA
6186 TTACTCT
1 TTACTCT
6193 TTACTCT
1 TTACTCT
6200 TTAC-CATT
1 TTACTC--T
**
6208 TTACTAA
1 TTACTCT
6215 TTACTCT
1 TTACTCT
* *
6222 TCATTCT
1 TTACTCT
6229 TTAC-CAT
1 TTACTC-T
*
6236 TT-TTCCT
1 TTACT-CT
**
6243 TTACTGA
1 TTACTCT
*
6250 TTACTTT
1 TTACTCT
6257 TTACTCT
1 TTACTCT
6264 TTAC-CAT
1 TTACTC-T
*
6271 TT-TTCT
1 TTACTCT
* **
6277 TCACTGA
1 TTACTCT
6284 TTACTCT
1 TTACTCT
6291 ATTACTCT
1 -TTACTCT
6299 TTAC-CAT
1 TTACTC-T
6306 TT-CTCT
1 TTACTCT
**
6312 TTACTGA
1 TTACTCT
*
6319 TTACTTT
1 TTACTCT
6326 TTACTCT
1 TTACTCT
* *
6333 TCACTATT
1 TTACT-CT
*
6341 TTACTGT
1 TTACTCT
**
6348 TTACTGA
1 TTACTCT
*
6355 TTAC-CA
1 TTACTCT
*
6361 TTACTTT
1 TTACTCT
6368 TTAC-CATT
1 TTACTC--T
6376 TTACTCT
1 TTACTCT
6383 TTACT
1 TTACT
6388 GATTGCCTTT
Statistics
Matches: 139, Mismatches: 37, Indels: 38
0.65 0.17 0.18
Matches are distributed among these distances:
6 15 0.11
7 99 0.71
8 24 0.17
9 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (7 bp):
TTACTCT
Found at i:6253 original size:35 final size:35
Alignment explanation
Indices: 6185--6391 Score: 198
Period size: 35 Copynumber: 6.1 Consensus size: 35
6175 CTGAATACCA
*
6185 ATTACTCTTTACTCTTTACCA----T--TTTACTA
1 ATTACTCTTTACTCTTTACCATTTTTCCTTTACTG
* *
6214 ATTACTCTTCATTCTTTACCATTTTTCCTTTACTG
1 ATTACTCTTTACTCTTTACCATTTTTCCTTTACTG
* *
6249 ATTACTTTTTACTCTTTACCATTTTT-CTTCACTG
1 ATTACTCTTTACTCTTTACCATTTTTCCTTTACTG
*
6283 ATTACTCTATTACTCTTTACCATTTCT-CTTTACTG
1 ATTACTCT-TTACTCTTTACCATTTTTCCTTTACTG
* * * * *
6318 ATTACTTTTTACTCTTCACTATTTTACTGTTTACTG
1 ATTACTCTTTACTCTTTACCATTTTTC-CTTTACTG
* * *
6354 ATTAC-CATTACTTTTTACCATTTTACTCTTTACTG
1 ATTACTCTTTACTCTTTACCATTTTTC-CTTTACTG
6389 ATT
1 ATT
6392 GCCTTTTCAA
Statistics
Matches: 147, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
29 19 0.13
33 1 0.01
34 28 0.19
35 87 0.59
36 12 0.08
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (35 bp):
ATTACTCTTTACTCTTTACCATTTTTCCTTTACTG
Found at i:6319 original size:69 final size:67
Alignment explanation
Indices: 6185--6391 Score: 219
Period size: 69 Copynumber: 3.0 Consensus size: 67
6175 CTGAATACCA
* * * * *
6185 ATTACTCTTTACTCTTTACCA---TTTTACTAATTACTCT-TCATTCTTTACCATTTTTCCTTTA
1 ATTACTTTTTACTCTTTACCATTTTTTTACTGATTACTCTATTACTCTTTACCATTTCT-CTTTA
6246 CTG
65 CTG
6249 ATTACTTTTTACTCTTTACCATTTTTCTTCACTGATTACTCTATTACTCTTTACCATTTCTCTTT
1 ATTACTTTTTACTCTTTACCATTTTT-TT-ACTGATTACTCTATTACTCTTTACCATTTCTCTTT
6314 ACTG
64 ACTG
* * *
6318 ATTACTTTTTACTCTTCACTATTTTACTGTTTACTGATTAC-C-ATTACTTTTTACCATTTTACT
1 ATTACTTTTTACTCTTTACCA-TTT--T-TTTACTGATTACTCTATTACTCTTTACCA-TTT-CT
6381 CTTTACTG
60 CTTTACTG
6389 ATT
1 ATT
6392 GCCTTTTCAA
Statistics
Matches: 123, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
64 20 0.16
67 2 0.02
68 2 0.02
69 51 0.41
70 22 0.18
71 22 0.18
72 3 0.02
73 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.03, T:0.54
Consensus pattern (67 bp):
ATTACTTTTTACTCTTTACCATTTTTTTACTGATTACTCTATTACTCTTTACCATTTCTCTTTAC
TG
Found at i:6371 original size:13 final size:14
Alignment explanation
Indices: 6284--6375 Score: 57
Period size: 13 Copynumber: 6.6 Consensus size: 14
6274 TCTTCACTGA
*
6284 TTACTCTATTACTCT
1 TTACTC-ATTACTTT
* *
6299 TTAC-CATTTCTCT
1 TTACTCATTACTTT
*
6312 TTACTGATTACTTT
1 TTACTCATTACTTT
6326 TTACTC-TTCACTATT
1 TTACTCATT-ACT-TT
** **
6341 TTACTGTTTACTGA
1 TTACTCATTACTTT
6355 TTAC-CATTACTTT
1 TTACTCATTACTTT
6368 TTAC-CATT
1 TTACTCATT
6376 TTACTCTTTA
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
13 26 0.43
14 19 0.31
15 14 0.23
16 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.03, T:0.53
Consensus pattern (14 bp):
TTACTCATTACTTT
Found at i:6521 original size:16 final size:16
Alignment explanation
Indices: 6500--6549 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
6490 TTATTTCCTG
6500 CTCTTTTTACTGATGA
1 CTCTTTTTACTGATGA
6516 CTC-TTTT-CT--T-A
1 CTCTTTTTACTGATGA
*
6527 CTCTTTTTACTGATGG
1 CTCTTTTTACTGATGA
6543 CTCTTTT
1 CTCTTTT
6550 CTTACTCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 10
0.72 0.03 0.26
Matches are distributed among these distances:
11 4 0.14
12 5 0.18
13 2 0.07
14 2 0.07
15 5 0.18
16 10 0.36
ACGTcount: A:0.12, C:0.22, G:0.10, T:0.56
Consensus pattern (16 bp):
CTCTTTTTACTGATGA
Found at i:6523 original size:27 final size:27
Alignment explanation
Indices: 6463--6593 Score: 157
Period size: 27 Copynumber: 4.9 Consensus size: 27
6453 ACTACTATTG
6463 CTCTTTTCTTACTCTTTTTACTGAAT-A
1 CTCTTTTCTTACTCTTTTTACTG-ATGA
* *
6490 -T-TATTTCCTGCTCTTTTTACTGATGA
1 CTCT-TTTCTTACTCTTTTTACTGATGA
*
6516 CTCTTTTCTTACTCTTTTTACTGATGG
1 CTCTTTTCTTACTCTTTTTACTGATGA
6543 CTCTTTTCTTACTCTTTTTACTGAAT-A
1 CTCTTTTCTTACTCTTTTTACTG-ATGA
6570 -T-TGTTTCTTACTCTTTTTACTGAT
1 CTCT-TTTCTTACTCTTTTTACTGAT
6594 TACTGATTAC
Statistics
Matches: 92, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
25 6 0.07
26 39 0.42
27 44 0.48
28 3 0.03
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (27 bp):
CTCTTTTCTTACTCTTTTTACTGATGA
Found at i:10012 original size:25 final size:26
Alignment explanation
Indices: 9984--10033 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
9974 ATATATGACT
9984 AATA-GACCAATGAGAAAATGAAAAA
1 AATAGGACCAATGAGAAAATGAAAAA
*
10009 AATAGGACTAATGAGAAAATGAAAA
1 AATAGGACCAATGAGAAAATGAAAA
10034 TGGATGGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.14
Consensus pattern (26 bp):
AATAGGACCAATGAGAAAATGAAAAA
Found at i:11141 original size:69 final size:69
Alignment explanation
Indices: 10922--11347 Score: 639
Period size: 69 Copynumber: 6.2 Consensus size: 69
10912 TCATATGAAC
* * * *
10922 TTGGCTTATGGAAAAG-CCC--CTGCTTGGATGGAACCAAGG-TTAAACTAACTCATATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
10983 GAGT
66 GAGT
* * * * *
10987 TTGGCTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGC-TAAATTGAGTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
11051 GAGT
66 GAGT
11055 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
11120 GAGT
66 GAGT
*
11124 TTGGCTTGTGGAAAAGCCCCTGAAC-GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAA
1 TTGGCTTGTGGAAAAGCCCCTG--CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAA
*
11188 ATGAGT
64 ACGAGT
* * *
11194 TTGACTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
11259 GAGT
66 GAGT
*
11263 TTGGCTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
1 TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
11328 GAGT
66 GAGT
* *
11332 TTGACTTATGGAAAAG
1 TTGGCTTGTGGAAAAG
11348 TCGAAGCATT
Statistics
Matches: 332, Mismatches: 21, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
65 14 0.04
66 2 0.01
68 83 0.25
69 169 0.51
70 63 0.19
71 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (69 bp):
TTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAAC
GAGT
Found at i:11210 original size:139 final size:138
Alignment explanation
Indices: 10930--11347 Score: 641
Period size: 139 Copynumber: 3.1 Consensus size: 138
10920 ACTTGGCTTA
* * *
10930 TGGAAAAG-CCC--CTGCTTGGATGGAACCAAGG-TTAAACTAACTCATATGGAAACGAGTTTGG
1 TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
* * * * *
10991 CTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGC-TAAATTGAGTCGTATGGAAACGAGT
66 CTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGT
*
11055 TTGGCTTG
131 TTGACTTG
11063 TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
1 TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
* *
11128 CTTGTGGAAAAGCCCCTGAAC-GCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAATGA
66 CTTGTGGAAAAGCCCCTG--CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGA
11192 GTTTGACTTG
129 GTTTGACTTG
* *
11202 TGGAAAAGCCGCTGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGTTTGG
1 TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
*
11267 CTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGT
66 CTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGT
*
11332 TTGACTTA
131 TTGACTTG
11340 TGGAAAAG
1 TGGAAAAG
11348 TCGAAGCATT
Statistics
Matches: 260, Mismatches: 17, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
133 8 0.03
134 3 0.01
136 20 0.08
137 44 0.17
138 76 0.29
139 109 0.42
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (138 bp):
TGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTGG
CTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGT
TTGACTTG
Found at i:11293 original size:208 final size:202
Alignment explanation
Indices: 10922--11347 Score: 656
Period size: 208 Copynumber: 2.1 Consensus size: 202
10912 TCATATGAAC
*
10922 TTGGCTTATGGAAAAGCCCCTGCTTGGATGGAACCAAGGTTAAACTAACTCATATGGAAACGAGT
1 TTGGCTTATGGAAAAGCCCCTGCTTGGATGGAACCAAGCTTAAACTAACTCATATGGAAACGAGT
* * * *
10987 TTGGCTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGCTAAATTGAGTCGTATGGAAACG
66 TTGACTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAAGCTAAACTGACTCGTATGGAAACG
11052 AGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
131 AGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
11117 AACGAGT
196 AACGAGT
* * * *
11124 TTGGCTTGTGGAAAAGCCCCTGAACGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAA
1 TTGGCTTATGGAAAAGCCCCT----GCTTGGATGGAACC-AAGCTTAAACTAACTCATATGGAAA
* * *
11189 TGAGTTTGACTTGTGGAAAAGCCGC-TGCTGCTTGGATGGAACCAAAGCTTGAACTGACTCGTAT
61 CGAGTTTGACTAGTGGAAAAGCC-CTTGCTGCTTGGATGGAACCAAAGC-TAAACTGACTCGTAT
*
11253 GGAAACGAGTTTGGCTTGTGGAAAAGCCGCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTC
124 GGAAACGAGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTC
11318 GTATGGAAACGAGT
189 GTATGGAAACGAGT
*
11332 TTGACTTATGGAAAAG
1 TTGGCTTATGGAAAAG
11348 TCGAAGCATT
Statistics
Matches: 202, Mismatches: 15, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
202 20 0.10
206 14 0.07
207 63 0.31
208 105 0.52
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (202 bp):
TTGGCTTATGGAAAAGCCCCTGCTTGGATGGAACCAAGCTTAAACTAACTCATATGGAAACGAGT
TTGACTAGTGGAAAAGCCCTTGCTGCTTGGATGGAACCAAAGCTAAACTGACTCGTATGGAAACG
AGTTTGGCTTGTGGAAAAGCCCCTGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGA
AACGAGT
Found at i:11944 original size:51 final size:51
Alignment explanation
Indices: 11862--11965 Score: 145
Period size: 51 Copynumber: 2.0 Consensus size: 51
11852 TGCCATTTTG
* * *
11862 AAAAGCGAATTTCGATCTTGGACTCACAAATGGAATGCAATCTTATTTTAA
1 AAAAGCGAATTTCGATATTGAACTCACAAATGGAATGCAATCTTATTATAA
* * **
11913 AAAATCGAATTTTGATATTGAACTCGTAAATGGAATGCAATCTTATTATAA
1 AAAAGCGAATTTCGATATTGAACTCACAAATGGAATGCAATCTTATTATAA
11964 AA
1 AA
11966 CTTCTTGTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (51 bp):
AAAAGCGAATTTCGATATTGAACTCACAAATGGAATGCAATCTTATTATAA
Found at i:12845 original size:12 final size:12
Alignment explanation
Indices: 12830--12854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12820 TTTTCTTTTC
12830 TCTTTTTTTCTT
1 TCTTTTTTTCTT
12842 TCTTTTTTTCTT
1 TCTTTTTTTCTT
12854 T
1 T
12855 GGGTTGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TCTTTTTTTCTT
Found at i:16046 original size:35 final size:36
Alignment explanation
Indices: 15992--16059 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
15982 GACAATACTT
* * *
15992 TTTACTGATTAGTATTTTACTCTTTACCATTTTTCC
1 TTTACTGATTACTACTTTACTCTGTACCATTTTTCC
16028 TTTACTGATTACT-CTTTACTCTGTACCATTTT
1 TTTACTGATTACTACTTTACTCTGTACCATTTT
16060 ATTGATTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 17 0.59
36 12 0.41
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (36 bp):
TTTACTGATTACTACTTTACTCTGTACCATTTTTCC
Found at i:16110 original size:7 final size:7
Alignment explanation
Indices: 16090--16175 Score: 64
Period size: 7 Copynumber: 12.1 Consensus size: 7
16080 TACTATTTTT
16090 TCTTTAC
1 TCTTTAC
**
16097 TGATTAC
1 TCTTTAC
16104 TCTTTAC
1 TCTTTAC
16111 TCTTTAC
1 TCTTTAC
16118 TCTTTAC
1 TCTTTAC
** *
16125 TGATCAC
1 TCTTTAC
16132 TCTTTAC
1 TCTTTAC
* **
16139 TATTTTTT
1 T-CTTTAC
16147 TCTTTAC
1 TCTTTAC
**
16154 TGATTAC
1 TCTTTAC
16161 TCTTTAC
1 TCTTTAC
*
16168 TTTTTAC
1 TCTTTAC
16175 T
1 T
16176 AATTACCATT
Statistics
Matches: 57, Mismatches: 21, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
7 53 0.93
8 4 0.07
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.57
Consensus pattern (7 bp):
TCTTTAC
Found at i:16175 original size:14 final size:14
Alignment explanation
Indices: 16090--16168 Score: 88
Period size: 14 Copynumber: 5.6 Consensus size: 14
16080 TACTATTTTT
16090 TCTTTACTGATTAC
1 TCTTTACTGATTAC
**
16104 TCTTTACTCTTTAC
1 TCTTTACTGATTAC
*
16118 TCTTTACTGATCAC
1 TCTTTACTGATTAC
**
16132 TCTTTACT-ATTTTTT
1 TCTTTACTGA--TTAC
16147 TCTTTACTGATTAC
1 TCTTTACTGATTAC
16161 TCTTTACT
1 TCTTTACT
16169 TTTTACTAAT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 41 0.79
15 9 0.17
16 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.04, T:0.56
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:16189 original size:22 final size:22
Alignment explanation
Indices: 16163--16295 Score: 155
Period size: 22 Copynumber: 6.1 Consensus size: 22
16153 CTGATTACTC
16163 TTTACTTTTTACTAATTACCAT
1 TTTACTTTTTACTAATTACCAT
* *
16185 TTTACTTTTTACTGATTACCCT
1 TTTACTTTTTACTAATTACCAT
* *
16207 TTTTCTCTTTT-CTAATTACTAT
1 TTTACT-TTTTACTAATTACCAT
* *
16229 TTTACTTTTCACTGATTACC--
1 TTTACTTTTTACTAATTACCAT
16249 TTTACTTTTTACTAATTACCAT
1 TTTACTTTTTACTAATTACCAT
* * *
16271 TTTACTTTTTATTGATTACCTT
1 TTTACTTTTTACTAATTACCAT
16293 TTT
1 TTT
16296 TCCTTACTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.20
21 3 0.03
22 67 0.73
23 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTACTTTTTACTAATTACCAT
Found at i:16255 original size:86 final size:85
Alignment explanation
Indices: 16135--16310 Score: 266
Period size: 86 Copynumber: 2.1 Consensus size: 85
16125 TGATCACTCT
* *
16135 TTACTATTTTTTTCTTTACTGATTACTCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGA
1 TTACTATTTTCTTCTTCACTGATTACTCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGA
* *
16200 TTACCCTTTTTCTCTTTTCTAA
66 TTA-CCTTTTT-TCCTTACTAA
*
16222 TTACTATTTTACTT-TTCACTGATTAC-CTTTACTTTTTACTAATTACCATTTTACTTTTTATTG
1 TTACTATTTT-CTTCTTCACTGATTACTCTTTACTTTTTACTAATTACCATTTTACTTTTTACTG
16285 ATTACCTTTTTTCCTTACTAA
65 ATTACCTTTTTTCCTTACTAA
16306 TTACT
1 TTACT
16311 CTTTACTCTT
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
84 13 0.16
85 7 0.08
86 40 0.48
87 21 0.25
88 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.02, T:0.57
Consensus pattern (85 bp):
TTACTATTTTCTTCTTCACTGATTACTCTTTACTTTTTACTAATTACCATTTTACTTTTTACTGA
TTACCTTTTTTCCTTACTAA
Found at i:16352 original size:35 final size:35
Alignment explanation
Indices: 16286--16447 Score: 152
Period size: 35 Copynumber: 4.6 Consensus size: 35
16276 TTTTTATTGA
* * *
16286 TTACCTTTTTTCCTTACTAATTACTCT-TTACTCT
1 TTACCATTTTTCTTTACTGATTACTCTATTACTCT
*
16320 TTACCATTTTTCTTCACTGATTACTCTATTACTCT
1 TTACCATTTTTCTTTACTGATTACTCTATTACTCT
* * *
16355 TTACCATTTCTCTTTACTGATTACT-TTTTAGTCT
1 TTACCATTTTTCTTTACTGATTACTCTATTACTCT
* * * *
16389 TCACTATTTTACTGTTTACTGATTAC-C-ATTACTTT
1 TTACCATTTT--TCTTTACTGATTACTCTATTACTCT
*
16424 TTACCATTTTACTCTTTACAGATT
1 TTACCATTTT--TCTTTACTGATT
16448 GCCTTTTCAT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
34 37 0.35
35 55 0.52
36 13 0.12
ACGTcount: A:0.20, C:0.23, G:0.04, T:0.53
Consensus pattern (35 bp):
TTACCATTTTTCTTTACTGATTACTCTATTACTCT
Found at i:16540 original size:26 final size:27
Alignment explanation
Indices: 16511--16650 Score: 114
Period size: 26 Copynumber: 5.3 Consensus size: 27
16501 CTTTGTTGAC
16511 TACT-ATTGCGCTTTTCTTACTCTTTT
1 TACTGATTGCGCTTTTCTTACTCTTTT
* ** * *
16537 TACTGAAT--ATTATTTCCTGCTCTTTT
1 TACTGATTGCGCT-TTTCTTACTCTTTT
*
16563 TACTGA-TGACTCTTTTCTTACTCTTTT
1 TACTGATTG-CGCTTTTCTTACTCTTTT
*
16590 TACTGAATAT-TG--TTTCTTACTCTTTT
1 TACTG-AT-TGCGCTTTTCTTACTCTTTT
* *
16616 TACTGATGGCTCTTTTCTTACTCTTTT
1 TACTGATTGCGCTTTTCTTACTCTTTT
16643 TACTGATT
1 TACTGATT
16651 ACTGATTACT
Statistics
Matches: 88, Mismatches: 15, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
25 4 0.05
26 41 0.47
27 40 0.45
28 2 0.02
30 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.09, T:0.56
Consensus pattern (27 bp):
TACTGATTGCGCTTTTCTTACTCTTTT
Found at i:16578 original size:53 final size:53
Alignment explanation
Indices: 16521--16648 Score: 220
Period size: 53 Copynumber: 2.4 Consensus size: 53
16511 TACTATTGCG
*
16521 CTTTTCTTACTCTTTTTACTGAATATTATTTCCTGCTCTTTTTACTGATGACT
1 CTTTTCTTACTCTTTTTACTGAATATTATTTCCTACTCTTTTTACTGATGACT
* * *
16574 CTTTTCTTACTCTTTTTACTGAATATTGTTTCTTACTCTTTTTACTGATGGCT
1 CTTTTCTTACTCTTTTTACTGAATATTATTTCCTACTCTTTTTACTGATGACT
16627 CTTTTCTTACTCTTTTTACTGA
1 CTTTTCTTACTCTTTTTACTGA
16649 TTACTGATTA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 71 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (53 bp):
CTTTTCTTACTCTTTTTACTGAATATTATTTCCTACTCTTTTTACTGATGACT
Found at i:16579 original size:27 final size:27
Alignment explanation
Indices: 16521--16649 Score: 153
Period size: 27 Copynumber: 4.9 Consensus size: 27
16511 TACTATTGCG
16521 CTTTTCTTACTCTTTTTACTGAAT-A-T
1 CTTTTCTTACTCTTTTTACTG-ATGACT
* *
16547 -TATTTCCTGCTCTTTTTACTGATGACT
1 CT-TTTCTTACTCTTTTTACTGATGACT
16574 CTTTTCTTACTCTTTTTACTGAAT-A-T
1 CTTTTCTTACTCTTTTTACTG-ATGACT
*
16600 -TGTTTCTTACTCTTTTTACTGATGGCT
1 CT-TTTCTTACTCTTTTTACTGATGACT
16627 CTTTTCTTACTCTTTTTACTGAT
1 CTTTTCTTACTCTTTTTACTGAT
16650 TACTGATTAC
Statistics
Matches: 89, Mismatches: 5, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
25 6 0.07
26 38 0.43
27 41 0.46
28 4 0.04
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.57
Consensus pattern (27 bp):
CTTTTCTTACTCTTTTTACTGATGACT
Found at i:20720 original size:12 final size:12
Alignment explanation
Indices: 20705--20746 Score: 56
Period size: 10 Copynumber: 3.8 Consensus size: 12
20695 AAATTATGCA
20705 TATTTTTATAGC
1 TATTTTTATAGC
20717 TATTTTTATA--
1 TATTTTTATAGC
20727 TATTTTT-T-GC
1 TATTTTTATAGC
20737 TATTTTTATA
1 TATTTTTATA
20747 TGTGTTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 1 0.04
10 14 0.54
11 1 0.04
12 10 0.38
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.67
Consensus pattern (12 bp):
TATTTTTATAGC
Found at i:20738 original size:20 final size:22
Alignment explanation
Indices: 20704--20747 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
20694 CAAATTATGC
20704 ATATTTTTATAGCTATTTTTAT
1 ATATTTTTATAGCTATTTTTAT
20726 ATATTTTT-T-GCTATTTTTAT
1 ATATTTTTATAGCTATTTTTAT
20746 AT
1 AT
20748 GTGTTTTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (22 bp):
ATATTTTTATAGCTATTTTTAT
Found at i:20754 original size:20 final size:20
Alignment explanation
Indices: 20715--20754 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20705 TATTTTTATA
*
20715 GCTATTTTTATATATTTTTT
1 GCTATTTTTATATATGTTTT
*
20735 GCTATTTTTATATGTGTTTT
1 GCTATTTTTATATATGTTTT
20755 TACCCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.10, T:0.68
Consensus pattern (20 bp):
GCTATTTTTATATATGTTTT
Found at i:22300 original size:6 final size:6
Alignment explanation
Indices: 22289--22315 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
22279 ATTAATCTGC
22289 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
22316 GCTTTGCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:22610 original size:57 final size:57
Alignment explanation
Indices: 22522--22667 Score: 274
Period size: 57 Copynumber: 2.6 Consensus size: 57
22512 GACACGATCA
* *
22522 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCATTCCAAATCTATTTTCATTTCC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCATTCCAAATCTAGTCTCATTTCC
22579 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCATTCCAAATCTAGTCTCATTTCC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCATTCCAAATCTAGTCTCATTTCC
22636 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTT
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTT
22668 CTTGTTTCAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 87 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (57 bp):
AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTTCATTCCAAATCTAGTCTCATTTCC
Found at i:22709 original size:63 final size:62
Alignment explanation
Indices: 22522--23056 Score: 533
Period size: 63 Copynumber: 8.7 Consensus size: 62
22512 GACACGATCA
* *
22522 AAATCCTAATCGAGGTCTCTAGTCGAGAG-----T-TTTCATTCC-AAATCTATTTTCATTTCC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCT-TGTTCATTT-C
* *
22579 AAATCCTAATCGAGGTCTCTAGTCGAGAG-----T-TTTCATTCC-AAATCTAGTCTCATTTCC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTTGT-TCATTT-C
* * * *
22636 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCTTGCTTCGTTTA
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTTG-TTCATTTC
* *
22699 AAATCCTAATCGAAGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTGTTCATTAC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCCAAAATCTTGTTCATTTC
** * * *
22762 AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGTTCATTTT
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCCAAAATCTTGTTCATTTC
** * * * **
22825 AAATCCTGTTTGAGGTCTCTAGTCGGGATTTTCTTGTTTCAATCCAAAAGTCTTGTTTTGTTTTC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAA-TCTTG--TTCATTTC
** * * *
22890 AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTTTTTCAATTCCAAAATCATGTTCATTTC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA-TCCAAAATCTTGTTCATTTC
** * * * *
22953 AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGCTCCAAT-CTAAATCTTGTTTCATTTCC
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTTG-TTCATTT-C
* *
23016 AAATCCTAATCGAGGTCTCTAGTCAAGAGTCTCTTGTTTCA
1 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCA
23057 TTTCAAATCC
Statistics
Matches: 415, Mismatches: 47, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
56 1 0.00
57 82 0.20
61 8 0.02
62 16 0.04
63 232 0.56
64 21 0.05
65 48 0.12
66 7 0.02
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (62 bp):
AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCCAAAATCTTGTTCATTTC
Found at i:23053 original size:191 final size:186
Alignment explanation
Indices: 22522--23281 Score: 670
Period size: 191 Copynumber: 4.2 Consensus size: 186
22512 GACACGATCA
** *
22522 AAATCCTAATCGAGGTCTCTAGTCGAGAG-----T-TTTC-ATTCC-AAATCTATTTTCATTTCC
1 AAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATC-ATGTTCATTTCC
* * * *
22579 AAATCCTAATCGAGGTCTCTAGTCGAGAG--T-TT-TCATTCCAAATCTAGTCTCATTTCCAAAT
65 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTCAATCAAAATCTTGTTTCATTT-CAAAT
* * * *
22640 CCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCTAAAGTCTTGCTTCGTTTA
129 CCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATC-AAAATCTTGTTTTGTTTC
** * * *
22699 AAATCCTAATCGAAGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCTTGTTCA-TTACA
1 AAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGTTCATTTCCA
** * * *
22763 AATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATG-TTCATTTTAA
66 AATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTG--TCAA-T-CAAAATCTTGTTTCATTTCAA
** * * *
22827 ATCCTGTTTGAGGTCTCTAGTCGGGATTTTCTTGTTTCAATCCAAAAGTCTTGTTTTGTTTTC
127 ATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT-CAAAA-TCTTGTTTTG-TTTC
* *
22890 AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTTTTTCAATTCCAAAATCATGTTCATTT-CA
1 AAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGTTCATTTCCA
** * *
22954 AATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGCTCCAATCTAAATCTTGTTTCATTTCCAAA
66 AATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTG-T-CAATCAAAATCTTGTTTCATTT-CAAA
* *
23019 TCCTAATCGAGGTCTCTAGTCAAGAGTCTCTTG-TT---TC---A----------TTTC
128 TCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCAAAATCTTGTTTTGTTTC
* * * *
23061 AAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAA-T-CTAAATCTTGTTTCATTTCC
1 AAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATG-TTCATTTCC
* *
23124 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGT--TTCAAAATCTTGTTTCATTTTAAATC
65 AAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTCAATCAAAATCTTGTTTCATTTCAAATC
**
23187 CTGCTCGAGGTCTCTAGTCGAGAG-----T-TTTCAATCCAAAATCTTGTTTTGTTTTC
130 CTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT-CAAAATCTTGTTTTG-TTTC
* * *
23240 AAATCCTGCTCAAGGTCTCTAGCCAAGAGTTTC-TGTTTCAAT
1 AAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAT
23282 CTAAAATTTT
Statistics
Matches: 481, Mismatches: 57, Indels: 88
0.77 0.09 0.14
Matches are distributed among these distances:
161 3 0.01
164 1 0.00
165 1 0.00
166 26 0.05
167 18 0.04
168 1 0.00
169 8 0.02
170 9 0.02
171 78 0.16
177 28 0.06
178 7 0.01
179 33 0.07
182 1 0.00
183 34 0.07
184 10 0.02
185 6 0.01
186 3 0.01
187 1 0.00
189 52 0.11
190 27 0.06
191 132 0.27
192 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.40
Consensus pattern (186 bp):
AAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATTCCAAAATCATGTTCATTTCCA
AATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTCAATCAAAATCTTGTTTCATTTCAAATCC
TAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAATCAAAATCTTGTTTTGTTTC
Found at i:23077 original size:45 final size:46
Alignment explanation
Indices: 23001--23098 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 46
22991 CCAATCTAAA
23001 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTC
1 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTC
** * * *
23047 TCTTGTTTCATTT-CAAATCCTGCTTGAGGTCTCTAGTCGAGAGTT
1 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTC
23092 TCTTGTT
1 TCTTGTT
23099 CCAATCTAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 34 0.72
46 13 0.28
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.42
Consensus pattern (46 bp):
TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTC
Found at i:23080 original size:108 final size:108
Alignment explanation
Indices: 22945--23164 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 108
22935 CAAAATCATG
22945 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGCTCCAATCTAAATCTTGTTTC
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGCTCCAATCTAAATCTTGTTTC
23010 ATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTCTCTTGT
66 ATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTCTCTTGT
*
23053 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCTAAATCTTGTTTC
1 TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGCTCCAATCTAAATCTTGTTTC
* *
23118 ATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGT
66 ATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTCTCTTGT
23161 TTCA
1 TTCA
23165 AAATCTTGTT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (108 bp):
TTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGCTCCAATCTAAATCTTGTTTC
ATTTCCAAATCCTAATCGAGGTCTCTAGTCAAGAGTCTCTTGT
Found at i:23210 original size:58 final size:58
Alignment explanation
Indices: 23047--23280 Score: 274
Period size: 58 Copynumber: 4.0 Consensus size: 58
23037 GTCAAGAGTC
* *
23047 TCTTGTTTCATTTCAAATCCTGCTTGAGGTCTCTAGTCGAGAGTTTCTTGTTCCAATCTAAA
1 TCTTGTTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTT----TCAAAA
**
23109 TCTTGTTTCATTTCCAAATCCTAATCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAAA
1 TCTTGTTTCATTT-CAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAAA
* *** *
23168 TCTTGTTTCATTTTAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTT-TCAATCCAAAA
1 TCTTGTTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAAA
** * * *
23225 TCTTGTTTTGTTTTCAAATCCTGCTCAAGGTCTCTAGCCAAGAGTTTC-TGTTTCAA
1 TCTTG-TTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAA
23281 TCTAAAATTT
Statistics
Matches: 148, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
57 12 0.08
58 69 0.47
59 18 0.12
62 13 0.09
63 36 0.24
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (58 bp):
TCTTGTTTCATTTCAAATCCTGCTCGAGGTCTCTAGTCGAGAGTTTCTTGTTTCAAAA
Found at i:23543 original size:26 final size:26
Alignment explanation
Indices: 23514--23587 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 26
23504 TAGGGTCACC
*
23514 TAGGGTCATTTTGGTCATTTTACATT
1 TAGGGGCATTTTGGTCATTTTACATT
*
23540 TAGGGGCATTTTGGTCATTTCCACATT
1 TAGGGGCATTTTGGTCATTT-TACATT
*
23567 CAGGGGCATTTTGGTCATTTT
1 TAGGGGCATTTTGGTCATTTT
23588 TGTATTTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.44
27 24 0.56
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.45
Consensus pattern (26 bp):
TAGGGGCATTTTGGTCATTTTACATT
Found at i:23963 original size:14 final size:14
Alignment explanation
Indices: 23944--23977 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
23934 GCATATTAAC
23944 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
23958 TTTAGTCCATTTAG
1 TTTAGTCCATTTAG
*
23972 ATTAGT
1 TTTAGT
23978 ATCATAGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.50
Consensus pattern (14 bp):
TTTAGTCCATTTAG
Found at i:24154 original size:20 final size:20
Alignment explanation
Indices: 24118--24156 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24108 AAATACAAGG
*
24118 CATTTGATTTACGAATTGGA
1 CATTTGATTTACAAATTGGA
*
24138 CATTTGATTTGCAAATTGG
1 CATTTGATTTACAAATTGG
24157 TGCTCTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (20 bp):
CATTTGATTTACAAATTGGA
Found at i:29281 original size:19 final size:18
Alignment explanation
Indices: 29257--29293 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29247 TTGAAGATTT
29257 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
29276 CTTGAAGATTATTGAAGA
1 CTTGAAGATAATTGAAGA
29294 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.