Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2366
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: 75091
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Found at i:9842 original size:50 final size:50
Alignment explanation
Indices: 9767--9998 Score: 356
Period size: 50 Copynumber: 4.6 Consensus size: 50
9757 ATGGCCACAT
9767 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
*
9817 TTGTCAAATGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
* **
9867 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTTTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
* * * * * *
9917 TTGTTAAAGGTTGGTAAAGAATCGTCAATAATTACGACCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
* *
9967 TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
9999 GGCAATAACT
Statistics
Matches: 165, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 165 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCACTCTCTA
Found at i:11965 original size:50 final size:49
Alignment explanation
Indices: 11890--12055 Score: 280
Period size: 50 Copynumber: 3.4 Consensus size: 49
11880 ATGGCCACAT
11890 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCATCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCA-CTCTCTCTA
*
11940 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCA-CTCTCTCTA
* *
11990 TTGTCAAAGGTTGGTAAAGAATCGTCAACAATTACGGCCAC-CTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACTCTCTCTA
12038 TTGTCAAAGGTTGGTGAA
1 TTGTCAAAGGTTGGTGAA
12056 AGATAGTCAA
Statistics
Matches: 110, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
48 24 0.22
49 1 0.01
50 85 0.77
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (49 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACTCTCTCTA
Found at i:12428 original size:18 final size:16
Alignment explanation
Indices: 12401--12435 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
12391 AGAAAATAAC
12401 AAAATATTTTTTTAAAA
1 AAAATA-TTTTTTAAAA
12418 AAAATTATTTTTTAAAA
1 AAAA-TATTTTTTAAAA
12435 A
1 A
12436 TTAATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.88
18 2 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
AAAATATTTTTTAAAA
Found at i:13867 original size:95 final size:95
Alignment explanation
Indices: 13756--13945 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
13746 ACAATTGATC
13756 TCAAAATAATATTTATTACATTTGTAATTATAATAAATATAAAAAAATTAAAAATAAATTCGTGA
1 TCAAAATAATATTTATTACATTTGTAATTATAATAAATATAAAAAAATTAAAAATAAATTCGTGA
13821 CTGTAATTTAAATATTTCTTCCCAAGAATT
66 CTGTAATTTAAATATTTCTTCCCAAGAATT
*
13851 TCAAAATAATATTTATTACATTTGTAATTATAATAAATATAAAACAATTAAAAATAAATTCGTGA
1 TCAAAATAATATTTATTACATTTGTAATTATAATAAATATAAAAAAATTAAAAATAAATTCGTGA
13916 CTGTAATTTAAATATTTCTTCCCAAGAATT
66 CTGTAATTTAAATATTTCTTCCCAAGAATT
13946 CTATGTATTT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (95 bp):
TCAAAATAATATTTATTACATTTGTAATTATAATAAATATAAAAAAATTAAAAATAAATTCGTGA
CTGTAATTTAAATATTTCTTCCCAAGAATT
Found at i:18682 original size:16 final size:18
Alignment explanation
Indices: 18657--18691 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
18647 TGAAAATAAC
18657 AAAATATATTTT-TAAAA
1 AAAATATATTTTCTAAAA
18674 AAAAT-TATTTTCTAAAA
1 AAAATATATTTTCTAAAA
18691 A
1 A
18692 TTAAATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATATTTTCTAAAA
Found at i:18982 original size:21 final size:23
Alignment explanation
Indices: 18958--19009 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
18948 ATTAATATTT
18958 ATAATTAAATT-TTAAAT-AAAA
1 ATAATTAAATTATTAAATAAAAA
* *
18979 ATAATT-ATTTATTATATAAAAA
1 ATAATTAAATTATTAAATAAAAA
19001 ATAATTAAA
1 ATAATTAAA
19010 ATAAAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 3 0.12
21 11 0.44
22 10 0.40
23 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAATTAAATTATTAAATAAAAA
Found at i:19636 original size:24 final size:24
Alignment explanation
Indices: 19607--19652 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
19597 AATAAAAATT
19607 AGCTACCAATT-TTGACAAACAACA
1 AGCTA-CAATTCTTGACAAACAACA
*
19631 AGCTACTATTCTTGACAAACAA
1 AGCTACAATTCTTGACAAACAA
19653 AAAGGAACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (24 bp):
AGCTACAATTCTTGACAAACAACA
Found at i:19676 original size:27 final size:27
Alignment explanation
Indices: 19645--19738 Score: 152
Period size: 27 Copynumber: 3.5 Consensus size: 27
19635 ACTATTCTTG
* *
19645 ACAAACAAAAAGGAACCACCATTTTTT
1 ACAAACACAAAGGAACCACCATTTTTA
* *
19672 ACAAACACAAAGGAACTACCATTTTTG
1 ACAAACACAAAGGAACCACCATTTTTA
19699 ACAAACACAAAGGAACCACCATTTTTA
1 ACAAACACAAAGGAACCACCATTTTTA
19726 ACAAACACAAAGG
1 ACAAACACAAAGG
19739 GTGGCTTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.49, C:0.23, G:0.10, T:0.18
Consensus pattern (27 bp):
ACAAACACAAAGGAACCACCATTTTTA
Found at i:19676 original size:51 final size:54
Alignment explanation
Indices: 19611--19738 Score: 158
Period size: 54 Copynumber: 2.4 Consensus size: 54
19601 AAAATTAGCT
* * *
19611 ACCAATTTTGACAAACAAC-AA-G-CTACTATTCTTGACAAACAAAAAGGAACC
1 ACCATTTTTAACAAACAACAAAGGACTACCATTCTTGACAAACAAAAAGGAACC
* * *
19662 ACCATTTTTTACAAAC-ACAAAGGAACTACCATTTTTGACAAACACAAAGGAACC
1 ACCATTTTTAACAAACAACAAAGG-ACTACCATTCTTGACAAACAAAAAGGAACC
19716 ACCATTTTTAACAAAC-ACAAAGG
1 ACCATTTTTAACAAACAACAAAGG
19739 GTGGCTTTTG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
50 2 0.03
51 16 0.24
52 1 0.01
54 48 0.72
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.21
Consensus pattern (54 bp):
ACCATTTTTAACAAACAACAAAGGACTACCATTCTTGACAAACAAAAAGGAACC
Found at i:19711 original size:54 final size:54
Alignment explanation
Indices: 19633--19738 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
19623 AAACAACAAG
* *
19633 CTACTATTCTTGACAAACAAAAAGGAACCACCATTTTTTACAAACACAAAGGAA
1 CTACCATTCTTGACAAACAAAAAGGAACCACCATTTTTAACAAACACAAAGGAA
* *
19687 CTACCATTTTTGACAAACACAAAGGAACCACCATTTTTAACAAACACAAAGG
1 CTACCATTCTTGACAAACAAAAAGGAACCACCATTTTTAACAAACACAAAGG
19739 GTGGCTTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (54 bp):
CTACCATTCTTGACAAACAAAAAGGAACCACCATTTTTAACAAACACAAAGGAA
Found at i:24476 original size:2 final size:2
Alignment explanation
Indices: 24469--24504 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24459 CCAATCTTTC
24469 AT AT AT AT 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 AT AT AT AT
24505 GTATTTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25041 original size:23 final size:23
Alignment explanation
Indices: 24989--25041 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
24979 TATTTTATAC
24989 TTAAAT-TTAAATAAAAATATTT
1 TTAAATATTAAATAAAAATATTT
* * *
25011 GTATATATTAAATATAAATATTT
1 TTAAATATTAAATAAAAATATTT
25034 TTAAATAT
1 TTAAATAT
25042 AATTTAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAAATATTAAATAAAAATATTT
Found at i:25983 original size:2 final size:2
Alignment explanation
Indices: 25976--26000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25966 TTATTAAGGA
25976 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
26001 ATTAATGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27160 original size:61 final size:61
Alignment explanation
Indices: 27065--27187 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
27055 TAAATTAAAA
27065 TATACATAGATGAGAATTTGGTAATCATTTATTTAG-TTATTTTTTTCATATTCTCATTCTT
1 TATACATAGATGAGAATTTGGTAATCATTTATTTAGTTTA-TTTTTTCATATTCTCATTCTT
27126 TATACATAGATGAGAATTTGGTAATCATTTATTTAGTTTATTTTTTCATATTCTCATTCTT
1 TATACATAGATGAGAATTTGGTAATCATTTATTTAGTTTATTTTTTCATATTCTCATTCTT
27187 T
1 T
27188 CTTTAGCTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 58 0.95
62 3 0.05
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.53
Consensus pattern (61 bp):
TATACATAGATGAGAATTTGGTAATCATTTATTTAGTTTATTTTTTCATATTCTCATTCTT
Found at i:30098 original size:13 final size:13
Alignment explanation
Indices: 30080--30127 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
30070 AATATTAGAG
30080 ATAATTTTTAAAA
1 ATAATTTTTAAAA
*
30093 ATAATTTTAAAAA
1 ATAATTTTTAAAA
**
30106 ATAATTAATAAAA
1 ATAATTTTTAAAA
30119 ATAATTTTT
1 ATAATTTTT
30128 TATTTTTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTTTTAAAA
Found at i:32626 original size:24 final size:25
Alignment explanation
Indices: 32569--32635 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 25
32559 GATTTAAAAT
32569 TTTAT-ATTATTTTTTAAAATAATA
1 TTTATAATTATTTTTTAAAATAATA
* * *
32593 -TTAAATATTA-TTTTTATATTAATA
1 TTTATA-ATTATTTTTTAAAATAATA
**
32617 TTTATAATTAAATTTTAAA
1 TTTATAATTATTTTTTAAA
32636 TAAAAATAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
23 3 0.09
24 16 0.48
25 14 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTATAATTATTTTTTAAAATAATA
Found at i:34853 original size:2 final size:2
Alignment explanation
Indices: 34846--34888 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
34836 AGTGCGTTGA
*
34846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34888 A
1 A
34889 ATCCATTTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:36103 original size:28 final size:28
Alignment explanation
Indices: 36052--36105 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
36042 ATATTTACTA
** *
36052 TATTTAATATTTTTAATATTAAAAATTT
1 TATTTAATATTTAAAATATCAAAAATTT
*
36080 TATTTAATATTTAAAATCTCAAAAAT
1 TATTTAATATTTAAAATATCAAAAAT
36106 CTCATCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTAATATTTAAAATATCAAAAATTT
Found at i:37486 original size:8 final size:8
Alignment explanation
Indices: 37467--37500 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
37457 TATTATTTAA
37467 AATAATATT
1 AATAA-ATT
37476 AATAAATT
1 AATAAATT
37484 AATAAATT
1 AATAAATT
*
37492 AAAAAATT
1 AATAAATT
37500 A
1 A
37501 TTTTATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
8 19 0.79
9 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AATAAATT
Found at i:38429 original size:27 final size:26
Alignment explanation
Indices: 38364--38429 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
38354 TAGTCACTAA
* *
38364 TTTTGACAAAC-AACA-AGCCGCCAT
1 TTTTGACAAACAAAAAGAGCCACCAT
*
38388 TTTTGATAAACAAAAAGAGCCACCAT
1 TTTTGACAAACAAAAAGAGCCACCAT
*
38414 TTTTTACAAACAAAAA
1 TTTTGACAAACAAAAA
38430 TGATAGCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 10 0.29
25 3 0.09
26 22 0.63
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.24
Consensus pattern (26 bp):
TTTTGACAAACAAAAAGAGCCACCAT
Found at i:43358 original size:2 final size:2
Alignment explanation
Indices: 43351--43409 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
43341 TATGACTGTA
43351 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
43393 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
43410 AATTGTGAAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44205 original size:2 final size:2
Alignment explanation
Indices: 44198--44230 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
44188 AAAATTATCT
*
44198 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44231 GTCATGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44459 original size:10 final size:10
Alignment explanation
Indices: 44369--44466 Score: 73
Period size: 10 Copynumber: 10.1 Consensus size: 10
44359 TAAAAAAATT
44369 AATT-TAAAA
1 AATTATAAAA
*
44378 AAATATAAAA
1 AATTATAAAA
44388 AATTATAAAA
1 AATTATAAAA
44398 AATTCA-AAAA
1 AATT-ATAAAA
*
44408 AATTATTAAA
1 AATTATAAAA
*
44418 AA-TAAAAATA
1 AATTATAAA-A
* *
44428 CAAAT-TCAAA
1 -AATTATAAAA
44438 AA-TATAAAA
1 AATTATAAAA
*
44447 AATTATATAA
1 AATTATAAAA
44457 AATT-TAAAA
1 AATTATAAAA
44466 A
1 A
44467 TAAAAATAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
8 1 0.01
9 21 0.30
10 43 0.61
11 5 0.07
12 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (10 bp):
AATTATAAAA
Found at i:44466 original size:20 final size:20
Alignment explanation
Indices: 44355--44466 Score: 72
Period size: 20 Copynumber: 5.5 Consensus size: 20
44345 CATCAACAAT
*
44355 AATATAAAAAAATTAATTTAAA
1 AATATAAAAAAATT-ATAT-AA
* *
44377 AAAATATAAAAAATTATAAAA
1 AATATA-AAAAAATTATATAA
44398 AAT-TCAAAAAAATTAT-TAAA
1 AATAT-AAAAAAATTATAT-AA
* *
44418 AATAAAAATACAAATT-CA-AA
1 AATATAAA-A-AAATTATATAA
44438 AATAT-AAAAAATTATATAA
1 AATATAAAAAAATTATATAA
*
44457 AATTTAAAAA
1 AATATAAAAA
44467 TAAAAATAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 22
0.69 0.10 0.22
Matches are distributed among these distances:
17 5 0.07
18 2 0.03
19 8 0.11
20 29 0.41
21 6 0.09
22 12 0.17
23 8 0.11
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AATATAAAAAAATTATATAA
Found at i:44495 original size:49 final size:50
Alignment explanation
Indices: 44378--44474 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 50
44368 TAATTTAAAA
44378 AAATATAAAAAATTATAAAAAATTCAAAAAAATTATTAAAAATAAAAATAC
1 AAAT-TAAAAAATTATAAAAAATTCAAAAAAATTATTAAAAATAAAAATAC
* *
44429 AAATTCAAAAA-TATAAAAAATT-ATATAAAA-T-TTAAAAATAAAAATA
1 AAATTAAAAAATTATAAAAAATTCA-AAAAAATTATTAAAAATAAAAATA
44475 ATGTTGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 15 0.35
48 2 0.05
49 16 0.37
50 6 0.14
51 4 0.09
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (50 bp):
AAATTAAAAAATTATAAAAAATTCAAAAAAATTATTAAAAATAAAAATAC
Found at i:44558 original size:6 final size:6
Alignment explanation
Indices: 44547--44590 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
44537 ATAAAATTAC
44547 AAAAAT AAAAAT AAAAAT -AAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
44591 TTTTCATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.14
6 32 0.86
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:44570 original size:17 final size:18
Alignment explanation
Indices: 44547--44590 Score: 81
Period size: 17 Copynumber: 2.5 Consensus size: 18
44537 ATAAAATTAC
44547 AAAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAT
44565 -AAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAT
44582 AAAAATAAA
1 AAAAATAAA
44591 TTTTCATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAATAAAAATAAAAAT
Found at i:44576 original size:23 final size:23
Alignment explanation
Indices: 44547--44590 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
44537 ATAAAATTAC
44547 AAAAATAAAAATAAAAATAAAAT
1 AAAAATAAAAATAAAAATAAAAT
44570 AAAAATAAAAATAAAAATAAA
1 AAAAATAAAAATAAAAATAAA
44591 TTTTCATTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (23 bp):
AAAAATAAAAATAAAAATAAAAT
Found at i:44663 original size:20 final size:18
Alignment explanation
Indices: 44645--44724 Score: 80
Period size: 18 Copynumber: 4.7 Consensus size: 18
44635 TTCATAAATT
44645 TTAAAAAAATATATAAAA
1 TTAAAAAAATATATAAAA
*
44663 TTATAAAAATATATAAAA
1 TTAAAAAAATATATAAAA
* *
44681 --AGAAAAA-A-AGAAAA
1 TTAAAAAAATATATAAAA
*
44695 TT-ATAAAATATATAAAA
1 TTAAAAAAATATATAAAA
*
44712 TTAAAAAATTATA
1 TTAAAAAAATATA
44725 ATTTTTTAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
14 5 0.10
15 5 0.10
16 7 0.14
17 7 0.14
18 25 0.51
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAAAAAAATATATAAAA
Found at i:44667 original size:10 final size:9
Alignment explanation
Indices: 44650--44725 Score: 60
Period size: 8 Copynumber: 9.2 Consensus size: 9
44640 AAATTTTAAA
44650 AAAATATAT
1 AAAATATAT
44659 AAAAT-TAT
1 AAAATATAT
44667 AAAAATATAT
1 -AAAATATAT
*
44677 AAAA-AGA-
1 AAAATATAT
*
44684 AAAA-A-AG
1 AAAATATAT
44691 AAAAT-TAT
1 AAAATATAT
44699 AAAATATAT
1 AAAATATAT
*
44708 AAAAT-TAA
1 AAAATATAT
44716 AAAAT-TAT
1 AAAATATAT
44724 AA
1 AA
44726 TTTTTTAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
6 1 0.02
7 9 0.16
8 22 0.39
9 22 0.39
10 3 0.05
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (9 bp):
AAAATATAT
Found at i:44740 original size:18 final size:18
Alignment explanation
Indices: 44719--44786 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
44709 AAATTAAAAA
44719 ATTATAATTTTTTAATTT
1 ATTATAATTTTTTAATTT
44737 ATTAT-ATTTTTATAATTT
1 ATTATAATTTTT-TAATTT
*
44755 -TT-TGAATTTTATTTTTATTT
1 ATTAT-AA--TT-TTTTAATTT
44775 ATTATAATTTTT
1 ATTATAATTTTT
44787 ATTTTTTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 16
0.71 0.02 0.28
Matches are distributed among these distances:
16 1 0.02
17 8 0.20
18 15 0.37
19 2 0.05
20 7 0.17
21 7 0.17
22 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (18 bp):
ATTATAATTTTTTAATTT
Found at i:44776 original size:38 final size:39
Alignment explanation
Indices: 44727--44804 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 39
44717 AAATTATAAT
44727 TTTTTAATTTATTAT-ATTTTTATAATTTTTTGA-ATTTTA
1 TTTTTAATTTATTATAATTTTTAT--TTTTTTGACATTTTA
*
44766 TTTTT-ATTTATTATAATTTTTATTTTTTTTACATTTTA
1 TTTTTAATTTATTATAATTTTTATTTTTTTGACATTTTA
44804 T
1 T
44805 AATTTTTTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
37 7 0.19
38 16 0.44
39 13 0.36
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.72
Consensus pattern (39 bp):
TTTTTAATTTATTATAATTTTTATTTTTTTGACATTTTA
Found at i:47859 original size:26 final size:23
Alignment explanation
Indices: 47818--47864 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
47808 ATTTAAGTTA
47818 TTATTTAATTAATAAAAATATTT
1 TTATTTAATTAATAAAAATATTT
47841 TTATTTAAATTTAATTAAAAATAT
1 TTATTT-AA-TTAA-TAAAAATAT
47865 ATAAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 4 0.19
26 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATTTAATTAATAAAAATATTT
Found at i:49853 original size:31 final size:31
Alignment explanation
Indices: 49806--49882 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
49796 ATTTTAACCA
*
49806 ATATTTTATATTTATAAAAAATTTAAAATA-TT
1 ATATTTT-TA-TTATATAAAATTTAAAATATTT
*
49838 A-ATTTTTATTATATAAATTTTAAAATATTT
1 ATATTTTTATTATATAAAATTTAAAATATTT
*
49868 ATATATTTATTATAT
1 ATATTTTTATTATAT
49883 TATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 17 0.43
30 5 0.12
31 17 0.43
32 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATATTTTTATTATATAAAATTTAAAATATTT
Found at i:50845 original size:19 final size:17
Alignment explanation
Indices: 50805--50837 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
50795 ATATTAATAT
50805 ATATATGATTTTAGTAG
1 ATATATGATTTTAGTAG
50822 ATATATGATTTTAGTA
1 ATATATGATTTTAGTA
50838 TGTGTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATATGATTTTAGTAG
Found at i:53105 original size:11 final size:13
Alignment explanation
Indices: 53075--53118 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
53065 AGGGATACAA
53075 GAGAGAGATGCTT
1 GAGAGAGATGCTT
53088 GAGAGAGATGCTT
1 GAGAGAGATGCTT
* * *
53101 AAGAGGGATACTT
1 GAGAGAGATGCTT
53114 GAGAG
1 GAGAG
53119 GGAGGAGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.39, T:0.20
Consensus pattern (13 bp):
GAGAGAGATGCTT
Found at i:53119 original size:13 final size:13
Alignment explanation
Indices: 53065--53121 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
53055 AGAATTGAAT
**
53065 AGGGATACAAGAG
1 AGGGATACTTGAG
* *
53078 AGAGATGCTTGAG
1 AGGGATACTTGAG
* * *
53091 AGAGATGCTTAAG
1 AGGGATACTTGAG
53104 AGGGATACTTGAG
1 AGGGATACTTGAG
53117 AGGGA
1 AGGGA
53122 GGAGGGAGCC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.37, C:0.07, G:0.39, T:0.18
Consensus pattern (13 bp):
AGGGATACTTGAG
Found at i:55793 original size:31 final size:32
Alignment explanation
Indices: 55758--55817 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
55748 AAGTTCGACA
* *
55758 TATTTTTTAAACAAATCTTTTTA-TCAAAATT
1 TATTTTTAAAACAAATATTTTTATTCAAAATT
*
55789 TATTTTTAAAACTAATATTTTTATTCAAA
1 TATTTTTAAAACAAATATTTTTATTCAAA
55818 TCCTTTTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (32 bp):
TATTTTTAAAACAAATATTTTTATTCAAAATT
Found at i:57927 original size:23 final size:25
Alignment explanation
Indices: 57901--57946 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
57891 ATTTAAGTTA
57901 TTATTT-AA-TTAATAAAAATATTT
1 TTATTTAAATTTAATAAAAATATTT
*
57924 TTATTTAAATTTATTAAAAATAT
1 TTATTTAAATTTAATAAAAATAT
57947 ATAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 2 0.10
25 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATTTAAATTTAATAAAAATATTT
Found at i:58279 original size:65 final size:66
Alignment explanation
Indices: 58175--58303 Score: 233
Period size: 65 Copynumber: 2.0 Consensus size: 66
58165 ATGTTCATCT
58175 ATGTTATTTAGATATAGATATGAGTGCTATACATGAGTATAA-TTTTATGCATTTAGAGAGTTTC
1 ATGTTATTTAGATATAGATATGAGTGCTATACATGAGTATAATTTTTATGCATTTAGAGAGTTTC
58239 A
66 A
* *
58240 ATGTTATTTAGATATAGATATGAGTGCTATATATGAGTATAATTTTTATGTATTTAGAGAGTTT
1 ATGTTATTTAGATATAGATATGAGTGCTATACATGAGTATAATTTTTATGCATTTAGAGAGTTT
58304 TTGAAAGACC
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 41 0.67
66 20 0.33
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (66 bp):
ATGTTATTTAGATATAGATATGAGTGCTATACATGAGTATAATTTTTATGCATTTAGAGAGTTTC
A
Found at i:58705 original size:14 final size:14
Alignment explanation
Indices: 58663--58705 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
58653 TAAAATATAT
58663 TTTATATTATA-T-
1 TTTATATTATATTA
*
58675 TTTA-ATTATTTTA
1 TTTATATTATATTA
58688 TTTATATTATATTA
1 TTTATATTATATTA
58702 TTTA
1 TTTA
58706 ATCATATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 5 0.19
12 5 0.19
13 4 0.15
14 12 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATATTATATTA
Found at i:58715 original size:28 final size:28
Alignment explanation
Indices: 58638--58715 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 28
58628 GTAATAATTC
*
58638 ATATTATATTAATTTTAA-AATATAT-TTT
1 ATATTATATT-A-TTTAATAATATTTATTT
*
58666 ATATTATA-T-TTTAATTAT-TTTATTT
1 ATATTATATTATTTAATAATATTTATTT
*
58691 ATATTATATTATTTAATCATATTTA
1 ATATTATATTATTTAATAATATTTA
58716 AAATTAACGA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
24 7 0.17
25 13 0.31
26 1 0.02
27 9 0.21
28 12 0.29
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
ATATTATATTATTTAATAATATTTATTT
Found at i:59944 original size:31 final size:31
Alignment explanation
Indices: 59897--59973 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
59887 ATTTTAACCA
*
59897 ATATTTTATATTTATAAAAAATTTAAAATA-TT
1 ATATTTT-TA-TTATATAAAATTTAAAATATTT
*
59929 A-ATTTTTATTATATAAATTTTAAAATATTT
1 ATATTTTTATTATATAAAATTTAAAATATTT
*
59959 ATATATTTATTATAT
1 ATATTTTTATTATAT
59974 TATATTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 17 0.43
30 5 0.12
31 17 0.43
32 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
ATATTTTTATTATATAAAATTTAAAATATTT
Found at i:60951 original size:19 final size:17
Alignment explanation
Indices: 60911--60943 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
60901 ATATTAATAT
60911 ATATATGATTTTAGTAG
1 ATATATGATTTTAGTAG
60928 ATATATGATTTTAGTA
1 ATATATGATTTTAGTA
60944 TGTGTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATATGATTTTAGTAG
Found at i:63207 original size:13 final size:13
Alignment explanation
Indices: 63191--63234 Score: 70
Period size: 13 Copynumber: 3.4 Consensus size: 13
63181 AGGGATACAA
63191 GAGAGAGATGCTT
1 GAGAGAGATGCTT
63204 GAGAGAGATGCTT
1 GAGAGAGATGCTT
* *
63217 AAGAGAGATACTT
1 GAGAGAGATGCTT
63230 GAGAG
1 GAGAG
63235 GGAGGAGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.36, T:0.20
Consensus pattern (13 bp):
GAGAGAGATGCTT
Found at i:63348 original size:24 final size:24
Alignment explanation
Indices: 63300--63348 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
63290 TAGTCACCAA
* * *
63300 TTTTGACAAACAATAAGCCATAAT
1 TTTTGACAAACAAAAAGCAACAAT
*
63324 TTTTGACAAACAAAAAGGAACAAT
1 TTTTGACAAACAAAAAGCAACAAT
63348 T
1 T
63349 ATTTTTGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (24 bp):
TTTTGACAAACAAAAAGCAACAAT
Found at i:63360 original size:27 final size:27
Alignment explanation
Indices: 63322--63395 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
63312 ATAAGCCATA
* *
63322 ATTTTTGACAAACAAAAAGGAACAATT
1 ATTTTTGACAAACACAAAGGAACAACT
* * *
63349 ATTTTTGACAAATACAAAGTAACCACT
1 ATTTTTGACAAACACAAAGGAACAACT
*
63376 ACTTTTGACAAACACAAAGG
1 ATTTTTGACAAACACAAAGG
63396 GTGGTTTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAGGAACAACT
Found at i:68377 original size:66 final size:66
Alignment explanation
Indices: 68279--68463 Score: 361
Period size: 66 Copynumber: 2.8 Consensus size: 66
68269 TATTATTTGG
*
68279 ATATAGATATGAGTGCTATACATGAGTATAATTTTTATGCATTTAGAGAGTTTCAATGTTATTTA
1 ATATAGATATGAGTGCTATATATGAGTATAATTTTTATGCATTTAGAGAGTTTCAATGTTATTTA
68344 A
66 A
68345 ATATAGATATGAGTGCTATATATGAGTATAATTTTTATGCATTTAGAGAGTTTCAATGTTATTTA
1 ATATAGATATGAGTGCTATATATGAGTATAATTTTTATGCATTTAGAGAGTTTCAATGTTATTTA
68410 A
66 A
68411 ATATAGATATGAGTGCTATATATGAGTATAATTTTTATGCATTTAGAGAGTTT
1 ATATAGATATGAGTGCTATATATGAGTATAATTTTTATGCATTTAGAGAGTTT
68464 TTGAAAGATC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 118 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (66 bp):
ATATAGATATGAGTGCTATATATGAGTATAATTTTTATGCATTTAGAGAGTTTCAATGTTATTTA
A
Found at i:68504 original size:14 final size:14
Alignment explanation
Indices: 68472--68498 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
68462 TTTTGAAAGA
68472 TCATATTTATATAC
1 TCATATTTATATAC
68486 TCATATTTATATA
1 TCATATTTATATA
68499 TGCATAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
TCATATTTATATAC
Found at i:68875 original size:28 final size:28
Alignment explanation
Indices: 68798--68875 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 28
68788 GTAATAATTC
*
68798 ATATTATATTAATTTTAA-AATATAT-TTT
1 ATATTATATT-A-TTTAATAATATTTATTT
* *
68826 ATATCATA-T-TTTAATTAT-TTTATTT
1 ATATTATATTATTTAATAATATTTATTT
*
68851 ATATTATATTATTTAATCATATTTA
1 ATATTATATTATTTAATAATATTTA
68876 AAATTAACGG
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 7 0.17
25 12 0.30
26 1 0.03
27 9 0.22
28 11 0.28
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (28 bp):
ATATTATATTATTTAATAATATTTATTT
Found at i:70126 original size:31 final size:31
Alignment explanation
Indices: 70050--70128 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
70040 ACATTTTAAC
70050 AAATATTT-TATATTTA-TA-A-AAAATTTA
1 AAATATTTATATATTTATTATATAAAATTTA
* * *
70077 AAAT-TTTA-ATTTTTATTATATGAATTTTA
1 AAATATTTATATATTTATTATATAAAATTTA
70106 AAATATTTATATATTTATTATAT
1 AAATATTTATATATTTATTATAT
70129 TATATTATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 9 0.21
27 6 0.14
28 1 0.02
29 10 0.24
30 4 0.10
31 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (31 bp):
AAATATTTATATATTTATTATATAAAATTTA
Found at i:71108 original size:19 final size:17
Alignment explanation
Indices: 71068--71100 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
71058 ATATTAATAT
71068 ATATATGATTTTAGTAG
1 ATATATGATTTTAGTAG
71085 ATATATGATTTTAGTA
1 ATATATGATTTTAGTA
71101 TGTGTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATATGATTTTAGTAG
Found at i:71116 original size:2 final size:2
Alignment explanation
Indices: 71105--71133 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
71095 TTAGTATGTG
71105 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71134 CTAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:72751 original size:13 final size:13
Alignment explanation
Indices: 72735--72778 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
72725 AGGGATACAA
72735 GAGAGGGATGCTT
1 GAGAGGGATGCTT
*
72748 GAGAGAGATGCTT
1 GAGAGGGATGCTT
* *
72761 AAGAGGGATACTT
1 GAGAGGGATGCTT
72774 GAGAG
1 GAGAG
72779 AGAGGAGGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (13 bp):
GAGAGGGATGCTT
Found at i:72904 original size:27 final size:27
Alignment explanation
Indices: 72866--72939 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
72856 ATAAGCCATA
* *
72866 ATTTTTGACAAACAAAAAGGAACCACT
1 ATTTTTGACAAACACAAAGGAACCACC
* *
72893 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACACAAAGGAACCACC
72920 ATTTTTGACAAACACAAAGG
1 ATTTTTGACAAACACAAAGG
72940 TTGGTTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (27 bp):
ATTTTTGACAAACACAAAGGAACCACC
Found at i:73084 original size:28 final size:27
Alignment explanation
Indices: 73030--73100 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
73020 GCCACCCATT
*
73030 TATTTGTAAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
73057 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
*
73085 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
73101 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 19 0.50
28 18 0.47
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:73220 original size:20 final size:20
Alignment explanation
Indices: 73197--73236 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
73187 AGGCTCCCAA
73197 ATCCATCTCTAGCATCCCTC
1 ATCCATCTCTAGCATCCCTC
* * *
73217 ATCCCTCTCTTGTATCCCTC
1 ATCCATCTCTAGCATCCCTC
73237 TTCAATTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.45, G:0.05, T:0.35
Consensus pattern (20 bp):
ATCCATCTCTAGCATCCCTC
Done.