Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold577_ERROPOS16399646
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: 99999
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7776 original size:38 final size:39
Alignment explanation
Indices: 7733--7815 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 39
7723 CTCTTCATGC
7733 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
1 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
7772 -CTATAGAAAAATGATACATTTATAACATTAACAAACTT
1 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
7810 ACTATA
1 ACTATA
7816 TGACCGTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 38 0.88
39 5 0.12
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (39 bp):
ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
Found at i:9364 original size:14 final size:15
Alignment explanation
Indices: 9321--9365 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
9311 AAGCTTCTAA
9321 AGTGCTAAATACCCT
1 AGTGCTAAATACCCT
*
9336 AGTGCTAAATTCCCT
1 AGTGCTAAATACCCT
*
9351 AG-GCTAAGTACCCT
1 AGTGCTAAATACCCT
9365 A
1 A
9366 AACCCTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (15 bp):
AGTGCTAAATACCCT
Found at i:12257 original size:15 final size:15
Alignment explanation
Indices: 12237--12267 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12227 TTCACTATTA
*
12237 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
12252 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
12267 T
1 T
12268 CATTAATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:14199 original size:44 final size:42
Alignment explanation
Indices: 14058--14211 Score: 161
Period size: 44 Copynumber: 3.6 Consensus size: 42
14048 GTACAATGAA
* * * *
14058 AACGTCCCAGACGTGGTCTTACATGTAATTAAATATCGATGCC
1 AACGTCCCAGATGTGGTCTTACACGTAAATCAA-ATCGATGCC
* *
14101 -ACTGTCCCAAACAG-GGTCTTACACG-AAATCAAATACGATGCC
1 AAC-GTCCCAGA-TGTGGTCTTACACGTAAATCAAAT-CGATGCC
* *
14143 AACATCCTAGATGTGGTCTTACACGTAAATCATAAGTCGATGCC
1 AACGTCCCAGATGTGGTCTTACACGTAAATCA-AA-TCGATGCC
14187 AACGTCCCAGATGTGGTCTTACACG
1 AACGTCCCAGATGTGGTCTTACACG
14212 ATAACACATA
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
41 3 0.03
42 30 0.33
43 25 0.27
44 33 0.36
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
AACGTCCCAGATGTGGTCTTACACGTAAATCAAATCGATGCC
Found at i:20548 original size:40 final size:40
Alignment explanation
Indices: 20437--20656 Score: 313
Period size: 40 Copynumber: 5.6 Consensus size: 40
20427 AAACCAAGTA
** * * *
20437 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAATTG
20476 CCTTCGGGACTTAGCCC-GTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
* *
20515 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAATTA
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
*
20555 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
* *
20595 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
20635 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
20657 CAATCGAATA
Statistics
Matches: 166, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
38 1 0.01
39 58 0.35
40 107 0.64
ACGTcount: A:0.21, C:0.28, G:0.24, T:0.27
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
Found at i:28281 original size:40 final size:40
Alignment explanation
Indices: 28210--28430 Score: 268
Period size: 40 Copynumber: 5.6 Consensus size: 40
28200 AAACCAAGTA
** * *
28210 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
* * ** *
28249 CCTTTGGGACTTAGCCTGGTTACGGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
* * * *
28289 CCTTTGGCACTTAGCCCGGTTATAGTAACTCGCACAATTT
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
28329 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
**
28369 CCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
28409 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
28431 CAATCCGAAT
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 24 0.15
40 132 0.85
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:34194 original size:21 final size:23
Alignment explanation
Indices: 34173--34223 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
34163 ATGTTTTTAC
34173 TTTTATTTTT-TTTAAGACTACT
1 TTTTATTTTTCTTTAAGACTACT
34195 TTTTATTTTTCTTTAAG-CTTA-T
1 TTTTATTTTTCTTTAAGAC-TACT
34217 TTTTATT
1 TTTTATT
34224 AGGATTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTTATTTTTCTTTAAGACTACT
Found at i:44353 original size:28 final size:27
Alignment explanation
Indices: 44286--44387 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
44276 TTAGTTTACC
* * *
44286 AAATTACCAAAATACCCTTGATTAGCA
1 AAATTACCAAAATACCCCTGATTTGTA
*
44313 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
44340 AAATTACCAAAAATATCCCTAATTTGTA
1 AAATTACC-AAAATACCCCTGATTTGTA
**
44368 AAATTACTGAAATACCCCTG
1 AAATTACCAAAATACCCCTG
44388 TAGGGTAGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 40 0.63
28 23 0.37
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:44399 original size:27 final size:27
Alignment explanation
Indices: 44369--44590 Score: 284
Period size: 27 Copynumber: 8.2 Consensus size: 27
44359 TAATTTGTAA
44369 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * *
44396 AATTATTGAAATACCTCTGCAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
44423 AATTA-TCGAAATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
*
44450 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
44477 AATTATTGAAATACCCCTATAAGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
** *
44504 AATTACCAAAATAACCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
*
44531 AATTACTGAAATACCCTTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
44558 AAATACTAAAATACCCCTGGAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
44585 AATTAC
1 AATTAC
44591 CGAGGTACCC
Statistics
Matches: 164, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 163 0.99
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:44600 original size:54 final size:54
Alignment explanation
Indices: 44369--44619 Score: 270
Period size: 54 Copynumber: 4.6 Consensus size: 54
44359 TAATTTGTAA
* * *** * * *
44369 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCTCTGCAAGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* *
44423 AATTATCGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
** * * * *
44477 AATTATTGAAATACCCCTATAAGGTAGAATTACCAAAATAACCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
* * * *
44531 AATTACTGAAATACCCTTGTAGGGTAGAAATACTAAAATACCCCTGGAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
** * *
44585 AATTACCGAGGTACCCTCGTGGGGT-GAAATTACCA
1 AATTACCGAAATACCCTTGTAGGGTAG-AATTACCA
44620 TTTTGCCCCT
Statistics
Matches: 167, Mismatches: 29, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 1 0.01
54 166 0.99
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.25
Consensus pattern (54 bp):
AATTACCGAAATACCCTTGTAGGGTAGAATTACCAAAATACCCCTGTAGGGTAG
Found at i:44617 original size:81 final size:80
Alignment explanation
Indices: 44369--44593 Score: 324
Period size: 81 Copynumber: 2.8 Consensus size: 80
44359 TAATTTGTAA
* *
44369 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCTCTGCAAGGTAGAATTATCGAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGCAAGGTAGAATTACCGAAA
44434 TACCCTTGTAGGGTAG
66 TACCC-TGTAGGGTAG
* ** *
44450 AATTACCGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTATAAGGTAGAATTACCAAAA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGCAAGGTAGAATTACCGAAA
44515 TAACCCTGTAGGGTAG
66 T-ACCCTGTAGGGTAG
* * * * * *
44531 AATTACTGAAATACCCTTGTAGGGTAGAAATACTAAAATACCCCTGGAGGGTAGAATTACCGA
1 AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGCAAGGTAGAATTACCGA
44594 GGTACCCTCG
Statistics
Matches: 128, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
81 124 0.97
82 4 0.03
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (80 bp):
AATTACTGAAATACCCCTGTAGGGTAGAATTATTGAAATACCCCTGCAAGGTAGAATTACCGAAA
TACCCTGTAGGGTAG
Found at i:50246 original size:29 final size:29
Alignment explanation
Indices: 50211--50284 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
50201 GTTGTGAGAT
* *
50211 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
50240 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
50269 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
50285 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:58336 original size:29 final size:29
Alignment explanation
Indices: 58301--58374 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
58291 GTTGTGAGAT
* *
58301 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
58330 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
58359 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
58375 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:60604 original size:20 final size:19
Alignment explanation
Indices: 60568--60618 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
60558 AATGGTTATT
*
60568 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
60587 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
60607 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
60619 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:70680 original size:24 final size:24
Alignment explanation
Indices: 70648--70710 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
70638 ATAGATGAAT
* * **
70648 GCTCACACGAGCTGTAATTGGTAA
1 GCTCTCACGAGCTATAATCAGTAA
*
70672 GCTCTCACGAGCTATAATCAGTAT
1 GCTCTCACGAGCTATAATCAGTAA
*
70696 GCTCTCACAAGCTAT
1 GCTCTCACGAGCTAT
70711 GGGTTGGAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (24 bp):
GCTCTCACGAGCTATAATCAGTAA
Found at i:72815 original size:44 final size:44
Alignment explanation
Indices: 72708--72834 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 44
72698 GTAATTCTAT
* * * *
72708 ATCGATGCCTCTGTCCCAGACAAGGTCTTATAC-AAAA--TCAG
1 ATCGATGCCTATGTCCCAGACACGGTCTTACACGAAAATTTCAA
*
72749 ATACGATACCTATGTCCCAGACACGGTCTTACACGAAAATTTCAA
1 AT-CGATGCCTATGTCCCAGACACGGTCTTACACGAAAATTTCAA
* *
72794 ATCGATGCCTATGTCCTAGACACGGTCTAACACGAAAATTT
1 ATCGATGCCTATGTCCCAGACACGGTCTTACACGAAAATTT
72835 AGATTAATAC
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.03
42 27 0.36
43 4 0.05
44 36 0.49
45 5 0.07
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (44 bp):
ATCGATGCCTATGTCCCAGACACGGTCTTACACGAAAATTTCAA
Found at i:79357 original size:31 final size:31
Alignment explanation
Indices: 79297--79357 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
79287 ATTACCGAAG
*
79297 TTTTCAAATCAAACGAATATAAATTTTAAAC
1 TTTTCAAATCAAACGAATATAAATATTAAAC
79328 TTTTCAAATCAAATC-AATA-AACATATTAAA
1 TTTTCAAATCAAA-CGAATATAA-ATATTAAA
79358 ACCGATACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 2 0.07
31 24 0.89
32 1 0.04
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (31 bp):
TTTTCAAATCAAACGAATATAAATATTAAAC
Found at i:82089 original size:79 final size:81
Alignment explanation
Indices: 81978--82161 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
81968 GCTACTCGTT
* * *
81978 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCTCAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC--GATCTTAACCC
* *
82041 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
82058 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGATCTTAACCCGG
* *
82121 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
82137 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
82162 CATCATTCAA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 24 0.27
79 49 0.54
80 15 0.17
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:82161 original size:40 final size:40
Alignment explanation
Indices: 81959--82161 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
81949 CGGAATTTAA
** *
81959 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
81999 CCGGTTATAGTAACTCGCTCAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
82039 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
82078 CCGGA-ATTAGTATCTCGCACAAATGCCTTC--GATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
82117 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
82157 CCGGA
1 CCGGA
82162 CATCATTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
37 1 0.01
39 53 0.38
40 83 0.60
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:90206 original size:44 final size:41
Alignment explanation
Indices: 90132--90254 Score: 133
Period size: 41 Copynumber: 2.9 Consensus size: 41
90122 ACCTTCGGAA
* *
90132 TTAA-CCGGATATAGCT-ACTCGTTCACAATGCCTTCGGGGAC
1 TTAACCCGGATTTAG-TAACTCGCTCA-AATGCCTTCGGGGAC
* * *
90173 TATAGCCCGGTTTATAGTACACTCGCTCAAATGCCTTCAGGGAC
1 T-TAACCCGGATT-TAGTA-ACTCGCTCAAATGCCTTCGGGGAC
*
90217 TTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG
1 TTAACCCGGATTTAGTAACTCGCTCAAATGCCTTCGGG
90255 TTAGCCCGGA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
41 20 0.29
42 7 0.10
43 15 0.22
44 18 0.26
45 8 0.12
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (41 bp):
TTAACCCGGATTTAGTAACTCGCTCAAATGCCTTCGGGGAC
Found at i:90249 original size:41 final size:40
Alignment explanation
Indices: 90158--90345 Score: 152
Period size: 41 Copynumber: 4.6 Consensus size: 40
90148 ACTCGTTCAC
* *
90158 AATGCCTTCGGGGACTATAGCCCGGTTTATAGTACACTCGCTCA
1 AATGCCTTC-GGGACT-TAGCCCGGATT-TAGTA-ACTCGCACA
*
90202 AATGCCTTCAGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTC-GGGACTTAGCCCGGATTTAGTAACTCGCACA
* *
90243 AATGCCTTCGGG--TTAGCCCGGAATTAAGTATCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGG-ATTTAGTAACTCGCACA
* * * * * *
90282 AATG-CTTC-TGATCTTTAGTCCGGATATGGTCACTTAGCACA
1 AATGCCTTCGGGA-C-TTAGCCCGGATTTAGTAAC-TCGCACA
*
90323 AA-GCCTTCGGGACTTTGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
90346 CATCAATTCA
Statistics
Matches: 118, Mismatches: 18, Indels: 20
0.76 0.12 0.13
Matches are distributed among these distances:
37 1 0.01
38 12 0.10
39 19 0.16
40 17 0.14
41 38 0.32
42 7 0.06
43 9 0.08
44 15 0.13
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACA
Found at i:90284 original size:39 final size:40
Alignment explanation
Indices: 90158--90286 Score: 127
Period size: 39 Copynumber: 3.1 Consensus size: 40
90148 ACTCGTTCAC
* * * *
90158 AATGCCTTCGGGGACTATAGCCCGGTTTATAGTACACTCGCTCA
1 AATGCCTTCAGGGA-T-TAACCCGGATTA-AGTA-ACTCGCACA
*
90202 AATGCCTTCAGGGACTTAACCCGGATTTAGTAACTCGCACA
1 AATGCCTTCAGGGA-TTAACCCGGATTAAGTAACTCGCACA
* *
90243 AATGCCTTC-GGG-TTAGCCCGGAATTAAGTATCTCGCACA
1 AATGCCTTCAGGGATTAACCCGG-ATTAAGTAACTCGCACA
90282 AATGC
1 AATGC
90287 TTCTGATCTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
38 8 0.11
39 20 0.26
40 3 0.04
41 17 0.22
42 4 0.05
43 9 0.12
44 15 0.20
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
AATGCCTTCAGGGATTAACCCGGATTAAGTAACTCGCACA
Found at i:93506 original size:38 final size:39
Alignment explanation
Indices: 93463--93545 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 39
93453 CTCTTCATGC
93463 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
1 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
93502 -CTATAGAAAAATGATACATTTATAACATTAACAAACTT
1 ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
93540 ACTATA
1 ACTATA
93546 TGACCGTACC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
38 38 0.88
39 5 0.12
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (39 bp):
ACTATAGAAAAATGATACATTTATAACATTAACAAACTT
Found at i:95093 original size:14 final size:15
Alignment explanation
Indices: 95050--95094 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
95040 AAGCTTCTAA
95050 AGTGCTAAATACCCT
1 AGTGCTAAATACCCT
*
95065 AGTGCTAAATTCCCT
1 AGTGCTAAATACCCT
*
95080 AG-GCTAAGTACCCT
1 AGTGCTAAATACCCT
95094 A
1 A
95095 AACCCTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (15 bp):
AGTGCTAAATACCCT
Found at i:97984 original size:15 final size:15
Alignment explanation
Indices: 97964--97994 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
97954 TTCACTATTA
*
97964 TGTCTTTTATATTTT
1 TGTCTTTCATATTTT
97979 TGTCTTTCATATTTT
1 TGTCTTTCATATTTT
97994 T
1 T
97995 CATTAATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (15 bp):
TGTCTTTCATATTTT
Found at i:99924 original size:44 final size:42
Alignment explanation
Indices: 99783--99936 Score: 161
Period size: 44 Copynumber: 3.6 Consensus size: 42
99773 GTACAATGAA
* * * *
99783 AACGTCCCAGACGTGGTCTTACATGTAATTAAATATCGATGCC
1 AACGTCCCAGATGTGGTCTTACACGTAAATCAA-ATCGATGCC
* *
99826 -ACTGTCCCAAACAG-GGTCTTACACG-AAATCAAATACGATGCC
1 AAC-GTCCCAGA-TGTGGTCTTACACGTAAATCAAAT-CGATGCC
* *
99868 AACATCCTAGATGTGGTCTTACACGTAAATCATAAGTCGATGCC
1 AACGTCCCAGATGTGGTCTTACACGTAAATCA-AA-TCGATGCC
99912 AACGTCCCAGATGTGGTCTTACACG
1 AACGTCCCAGATGTGGTCTTACACG
99937 ATAACACATA
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
41 3 0.03
42 30 0.33
43 25 0.27
44 33 0.36
45 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
AACGTCCCAGATGTGGTCTTACACGTAAATCAAATCGATGCC
Done.