Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2485
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: 359192
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 3 of 4
Found at i:204984 original size:16 final size:17
Alignment explanation
Indices: 204958--205000 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
204948 TTAGTTTGTA
204958 TTGTTATAAAATT-TTAT
1 TTGTTA-AAAATTATTAT
204975 TTGTTAAAAATTACTTAT
1 TTGTTAAAAATTA-TTAT
*
204993 TAGTTAAA
1 TTGTTAAA
205001 TTTATTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 6 0.26
18 11 0.48
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (17 bp):
TTGTTAAAAATTATTAT
Found at i:205524 original size:16 final size:16
Alignment explanation
Indices: 205505--205536 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
205495 GTTTGGATTG
*
205505 TTTCAAATTCGGGTCA
1 TTTCAAATTCGAGTCA
205521 TTTCAAATTCGAGTCA
1 TTTCAAATTCGAGTCA
205537 ATCGGGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (16 bp):
TTTCAAATTCGAGTCA
Found at i:205610 original size:53 final size:53
Alignment explanation
Indices: 205512--205612 Score: 123
Period size: 53 Copynumber: 1.9 Consensus size: 53
205502 TTGTTTCAAA
* * *
205512 TTCGGGTCATTTCAAATTCGAGTCAATCGGGTTTAACGCTTGGGTTAATGGGG
1 TTCGGATCATTTCAAATTCGAGTCAATCGGGTTCAACGATTGGGTTAATGGGG
* * * *
205565 TTCGGATCATTTTAAATTCGGGTTAATTGGGTTCAAC-ATTCGGGTTAA
1 TTCGGATCATTTCAAATTCGAGTCAATCGGGTTCAACGATT-GGGTTAA
205613 ATCAAATTTA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
52 2 0.05
53 38 0.95
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.37
Consensus pattern (53 bp):
TTCGGATCATTTCAAATTCGAGTCAATCGGGTTCAACGATTGGGTTAATGGGG
Found at i:206927 original size:20 final size:20
Alignment explanation
Indices: 206899--206937 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
206889 TTTCCTAGTT
*
206899 ATAAGTAAGAAAGAAAGAAG
1 ATAAATAAGAAAGAAAGAAG
*
206919 ATAAATAAGAAAGGAAGAA
1 ATAAATAAGAAAGAAAGAA
206938 AAAAAAAAGA
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:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (20 bp):
ATAAATAAGAAAGAAAGAAG
Found at i:214619 original size:27 final size:27
Alignment explanation
Indices: 214549--214856 Score: 251
Period size: 28 Copynumber: 10.9 Consensus size: 27
214539 TGGTATTTCC
* *
214549 TTTTAAGTTCACAACTCGGTGGCACCTT
1 TTTTAAGTCCACAACTCCGTGGCACC-T
* *
214577 TTTTAAGTCCACAACTCTGTGGCACCG
1 TTTTAAGTCCACAACTCCGTGGCACCT
* * *
214604 TTTTAAGTCCATAACTCAGTGGCTCCGTGGTACCCG
1 TTTTAAGTCC---A--CA---ACTCCGTGGCA-CCT
* *
214640 TTTTAAGTCCACAACTCAGTGACACCT
1 TTTTAAGTCCACAACTCCGTGGCACCT
**
214667 TTTTAAGTCCGTAACTCCGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCT
*
214694 TTTTGAAGTCCACAACTCCATGGCATCC-
1 TTTT-AAGTCCACAACTCCGTGGCA-CCT
*
214722 TTTTAAGTCCACAACTCCGTGGTACCCT
1 TTTTAAGTCCACAACTCCGTGGCA-CCT
* * *
214750 TTTAAAGTCCAAAACACCGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCT
* * **
214777 TTTTAAAATCCATAACTTGGTGGCA-CT
1 TTTT-AAGTCCACAACTCCGTGGCACCT
*
214804 CTTTTAAGTCCACAACTTCGTGGCATCCT
1 -TTTTAAGTCCACAACTCCGTGGCA-CCT
* *
214833 TTTTAAGTCCACAAGTCAGTGGCA
1 TTTTAAGTCCACAACTCCGTGGCA
214857 TTCCCTTCTA
Statistics
Matches: 227, Mismatches: 37, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
27 84 0.37
28 112 0.49
29 4 0.02
30 1 0.00
31 2 0.01
32 2 0.01
33 1 0.00
35 8 0.04
36 13 0.06
ACGTcount: A:0.24, C:0.28, G:0.17, T:0.31
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCT
Found at i:214620 original size:55 final size:55
Alignment explanation
Indices: 214549--214843 Score: 270
Period size: 55 Copynumber: 5.2 Consensus size: 55
214539 TGGTATTTCC
* * * * *
214549 TTTTAAGTTCACAACTCGGTGGCACCTTTTTTAAGTCCACAACTCTGTGGCACCG
1 TTTTAAGTCCATAACTCCGTGGCACCTTTTTTAAGTCCACAACTCCGTGGCACCT
* * * *
214604 TTTTAAGTCCATAACTCAGTGGCTCCGTGGTACCCGTTTTAAGTCCACAACTCAGTGACACCT
1 TTTTAAGTCCATAACTCCGTGGCACC-T--T-----TTTTAAGTCCACAACTCCGTGGCACCT
* * *
214667 TTTTAAGTCCGTAACTCCGTGGCACCTTTTTGAAGTCCACAACTCCATGGCATCC-
1 TTTTAAGTCCATAACTCCGTGGCACCTTTTTTAAGTCCACAACTCCGTGGCA-CCT
* * * * * *
214722 TTTTAAGTCCACAACTCCGTGGTACCCTTTTAAAGTCCAAAACACCGTGGCACCT
1 TTTTAAGTCCATAACTCCGTGGCACCTTTTTTAAGTCCACAACTCCGTGGCACCT
* ** * *
214777 TTTTAAAATCCATAACTTGGTGGCA-CTCTTTTAAGTCCACAACTTCGTGGCATCCT
1 TTTT-AAGTCCATAACTCCGTGGCACCTTTTTTAAGTCCACAACTCCGTGGCA-CCT
214833 TTTTAAGTCCA
1 TTTTAAGTCCA
214844 CAAGTCAGTG
Statistics
Matches: 194, Mismatches: 34, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
54 2 0.01
55 117 0.60
56 25 0.13
58 1 0.01
60 1 0.01
62 1 0.01
63 47 0.24
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (55 bp):
TTTTAAGTCCATAACTCCGTGGCACCTTTTTTAAGTCCACAACTCCGTGGCACCT
Found at i:214855 original size:55 final size:55
Alignment explanation
Indices: 214630--214933 Score: 215
Period size: 55 Copynumber: 5.4 Consensus size: 55
214620 CAGTGGCTCC
* * * *
214630 GTGGTACCCGTTTT-AAGTCCACAAC-TCAGTGACACCTTTTTAAGTCCGTAACTCC
1 GTGGCACCC-TTTTAAAGTCCACAACTTC-GTGGCACCTTTTTAAGTCCATAACTCA
* * * * * *
214685 GTGGCACCTTTTTGAAGTCCACAACTCCATGGCATCC-TTTTAAGTCCACAACTCC
1 GTGGCACCCTTTTAAAGTCCACAACTTCGTGGCA-CCTTTTTAAGTCCATAACTCA
* * ** * **
214740 GTGGTACCCTTTTAAAGTCCAAAACACCGTGGCACCTTTTTAAAATCCATAACTTG
1 GTGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCTTTTT-AAGTCCATAACTCA
* * *
214796 GTGGCACTCTTTT-AAGTCCACAACTTCGTGGCATCCTTTTTAAGTCCACAAGTCA
1 GTGGCACCCTTTTAAAGTCCACAACTTCGTGGCA-CCTTTTTAAGTCCATAACTCA
* * * * * *
214851 GTGGCATTCCCTTCTAGAG-CTCACAAGTTAGTGGCACCCCTTTTAAAG-CCGATAAGTCA
1 GTGGCA--CCCTTTTAAAGTC-CACAACTTCGTGGCA--CCTTTTTAAGTCC-ATAACTCA
*
214910 GTGGCACTCTTTTCAAAGTCCACA
1 GTGGCACCCTTTT-AAAGTCCACA
214934 CAAGTTGGTG
Statistics
Matches: 197, Mismatches: 38, Indels: 25
0.76 0.15 0.10
Matches are distributed among these distances:
54 6 0.03
55 102 0.52
56 31 0.16
57 11 0.06
58 24 0.12
59 23 0.12
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (55 bp):
GTGGCACCCTTTTAAAGTCCACAACTTCGTGGCACCTTTTTAAGTCCATAACTCA
Found at i:214856 original size:83 final size:82
Alignment explanation
Indices: 214640--214843 Score: 241
Period size: 83 Copynumber: 2.5 Consensus size: 82
214630 GTGGTACCCG
* ** * *
214640 TTTTAAGTCCACAAC-TCAGTGACACCTTTTTAAGTCCGTAACTCCGTGGCACCTTTTTGAAGTC
1 TTTTAAGTCCACAACTTC-GTGGCACCTTTTTAAGTCCAAAACTCCGTGGCACCTTTTTAAAATC
214704 CACAACTCCATGGCATCC
65 CACAACTCCATGGCATCC
* * * *
214722 TTTTAAGTCCACAACTCCGTGGTACCCTTTTAAAGTCCAAAACACCGTGGCACCTTTTTAAAATC
1 TTTTAAGTCCACAACTTCGTGGCA-CCTTTTTAAGTCCAAAACTCCGTGGCACCTTTTTAAAATC
* ***
214787 CATAACTTGGTGGCA-CTC
65 CACAACTCCATGGCATC-C
214805 TTTTAAGTCCACAACTTCGTGGCATCCTTTTTAAGTCCA
1 TTTTAAGTCCACAACTTCGTGGCA-CCTTTTTAAGTCCA
214844 CAAGTCAGTG
Statistics
Matches: 102, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
82 20 0.20
83 82 0.80
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (82 bp):
TTTTAAGTCCACAACTTCGTGGCACCTTTTTAAGTCCAAAACTCCGTGGCACCTTTTTAAAATCC
ACAACTCCATGGCATCC
Found at i:214857 original size:28 final size:28
Alignment explanation
Indices: 214640--215266 Score: 312
Period size: 28 Copynumber: 21.9 Consensus size: 28
214630 GTGGTACCCG
* *
214640 TTTT-AAGTCCACAACTCAGTGACA-CC
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* ** * *
214666 TTTTTAAGTCCGTAACTCCGTGGCA-CC
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* *
214693 TTTTTGAAGTCCACAACTCCA-TGGCATCC
1 -TTTTAAAGTCCACAAGT-CAGTGGCATCC
* * * *
214722 TTTT-AAGTCCACAACTCCGTGGTACCC
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* ** *
214749 TTTTAAAGTCCAAAACACCGTGGCA-CC
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* * * **
214776 TTTTTAAAATCCATAACTTGGTGGCA-CTC
1 -TTTTAAAGTCCACAAGTCAGTGGCATC-C
*
214805 TTTT-AAGTCCACAACTTC-GTGGCATCC
1 TTTTAAAGTCCACAA-GTCAGTGGCATCC
*
214832 TTTTTAAGTCCACAAGTCAGTGGCATTCCC
1 TTTTAAAGTCCACAAGTCAGTGGCA-T-CC
* * * *
214862 TTCTAGAG-CTCACAAGTTAGTGGCACCCC
1 TTTTAAAGTC-CACAAGTCAGTGGCA-TCC
*
214891 TTTTAAAG-CCGATAAGTCAGTGGCA-CTC
1 TTTTAAAGTCC-ACAAGTCAGTGGCATC-C
** *
214919 TTTTCAAAGTCCACACAAGTTGGTGGCAACTCA
1 TTTT-AAAGT-C-CACAAGTCAGTGGC-A-TCC
* * * *
214952 TTTCAAAGCCCACAAGTTAGTGGCATCT
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* * * * * *
214980 TTTTAAAGCCCACACAAGTCGGCGGTAACTT
1 TTTTAAAG-TC-CACAAGTCAGTGGCATC-C
*
215011 TTTTCAAAGTCCACAAGTTAGTGGCATCC
1 TTTT-AAAGTCCACAAGTCAGTGGCATCC
* * * * *
215040 TTTCAAAGCCCACAAGTTAGTAGCATCA
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* *
215068 TTTTAAAGCCCACAAGTCAGTGGCAT-A
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
*
215095 TTTTCAAAG-CCTACAAGTTAGTGGCATCC
1 TTTT-AAAGTCC-ACAAGTCAGTGGCATCC
**
215124 TTCCAAAG-CTCACAAGTCAGTGGCATCC
1 TTTTAAAGTC-CACAAGTCAGTGGCATCC
** * *
215152 TTCCAAAGCCCACAAGTCAGTGCCATCC
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
*
215180 TTTTAAAGCCCATAAGTCAAAGTCAGTGGCATCC
1 TTTTAAAGTCC---A--C-AAGTCAGTGGCATCC
* * * *
215214 TTTCAAAGCCCGCAAGTCAGTGCCATCC
1 TTTTAAAGTCCACAAGTCAGTGGCATCC
* *
215242 TTTCAAAGCCCACAAGTCAGTGGCA
1 TTTTAAAGTCCACAAGTCAGTGGCA
215267 CCAGCTCAAA
Statistics
Matches: 486, Mismatches: 76, Indels: 76
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.01
27 71 0.15
28 252 0.52
29 42 0.09
30 58 0.12
31 19 0.04
32 10 0.02
33 4 0.01
34 25 0.05
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (28 bp):
TTTTAAAGTCCACAAGTCAGTGGCATCC
Found at i:215100 original size:56 final size:56
Alignment explanation
Indices: 214796--215427 Score: 421
Period size: 56 Copynumber: 10.7 Consensus size: 56
214786 CCATAACTTG
* * * * *
214796 GTGGCACTCTTTT--AAGTCCACAACTTCGTGGCATCCTTTTTAAGTCCACAAGTCA
1 GTGGCA-TCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCA
** * * * * *
214851 GTGGCATTCCCTTCTAGAGCTCACAAGTTAGTGGCACCCCTTTTAAAGCCGATAAGTCA
1 GTGGCA-TCTTTTC-AAAGCCCACAAGTTAGTGGCA-TCCTTTTAAAGCCCACAAGTCA
* * * *
214910 GTGGCACTCTTTTCAAAGTCCACACAAGTTGGTGGCAACTCATTTCAAAGCCCACAAGTTA
1 GTGGCA-TCTTTTCAAAG-CC-CACAAGTTAGTGGC-A-TCCTTTTAAAGCCCACAAGTCA
* ** * * * * * *
214971 GTGGCATCTTTTTAAAGCCCACACAAGTCGGCGGTAACTTTTTTCAAAGTCCACAAGTTA
1 GTGGCATCTTTTCAAAG-CC-CACAAGTTAGTGGCATC-CTTTT-AAAGCCCACAAGTCA
* * *
215031 GTGGCATCCTTTCAAAGCCCACAAGTTAGTAGCATCATTTTAAAGCCCACAAGTCA
1 GTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * ** *
215087 GTGGCATATTTTCAAAGCCTACAAGTTAGTGGCATCCTTCCAAAGCTCACAAGTCA
1 GTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCA
* * * *
215143 GTGGCATCCTTCCAAAGCCCACAAGTCAGTGCCATCCTTTTAAAGCCCATAAGTCAAAGTCA
1 GTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCC---A--C-AAGTCA
* * * * *
215205 GTGGCATCCTTTCAAAGCCCGCAAGTCAGTGCCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCA
* *** * * * * *
215261 GTGGCACCAGCTCAAAACCCACAAGTCAATGACATACCCTTTCAAAGCTCACACAAGTC-
1 GTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCAT--CCTTTTAAAGC-C-CACAAGTCA
*
215320 GATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCA-CCTTTTTTTAAAGCCCACGCAGTC-
1 G-TGGC-A-TCTTTTCAAAG-CC-CACAAGTTAGTGGCATCC---TTTTAAAGCCCAC-AAGTCA
215383 GATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCA-CCTTTT
1 G-TGGC-A-TCTTTTCAAAG-CC-CACAAGTTAGTGGCATCCTTTT
215428 TTTTAAAGCC
Statistics
Matches: 466, Mismatches: 83, Indels: 51
0.78 0.14 0.09
Matches are distributed among these distances:
55 10 0.02
56 133 0.29
57 5 0.01
58 41 0.09
59 39 0.08
60 82 0.18
61 28 0.06
62 60 0.13
63 48 0.10
64 20 0.04
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (56 bp):
GTGGCATCTTTTCAAAGCCCACAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCA
Found at i:215275 original size:28 final size:28
Alignment explanation
Indices: 214823--215363 Score: 386
Period size: 28 Copynumber: 18.4 Consensus size: 28
214813 CCACAACTTC
** *
214823 GTGGCATCCTTTTTAAGTCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * * *
214851 GTGGCATTCCCTTCTAGAGCTCACAAGTTA
1 GTGGCA-TCCTTTC-AAAGCCCACAAGTCA
* * * *
214881 GTGGCACCCCTTTTAAAGCCGATAAGTCA
1 GTGGCA-TCCTTTCAAAGCCCACAAGTCA
* **
214910 GTGGCACTCTTTTCAAAGTCCACACAAGTTG
1 GTGGCA-TCCTTTCAAAG-CC-CACAAGTCA
* *
214941 GTGGCAACTCATTTCAAAGCCCACAAGTTA
1 GTGGC-A-TCCTTTCAAAGCCCACAAGTCA
* * *
214971 GTGGCATCTTTTTAAAGCCCACACAAGTCG
1 GTGGCATCCTTTCAAAG-CC-CACAAGTCA
* * ** * *
215001 GCGGTAACTTTTTTCAAAGTCCACAAGTTA
1 GTGG-CA-TCCTTTCAAAGCCCACAAGTCA
*
215031 GTGGCATCCTTTCAAAGCCCACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* * *
215059 GTAGCATCATTTTAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
** * *
215087 GTGGCATATTTTCAAAGCCTACAAGTTA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
215115 GTGGCATCCTTCCAAAGCTCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
215143 GTGGCATCCTTCCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
* *
215171 GTGCCATCCTTTTAAAGCCCATAAGTCAAAGTCA
1 GTGGCATCCTTTCAAAGCCC---A--C-AAGTCA
*
215205 GTGGCATCCTTTCAAAGCCCGCAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
*
215233 GTGCCATCCTTTCAAAGCCCACAAGTCA
1 GTGGCATCCTTTCAAAGCCCACAAGTCA
** *
215261 GTGGCA-CCAGCTCAAAACCCACAAGTCA
1 GTGGCATCC-TTTCAAAGCCCACAAGTCA
* *
215289 ATGACATACCCTTTCAAAGCTCACACAAGTC-
1 GTGGCAT--CCTTTCAAAGC-C-CACAAGTCA
* *
215320 GATGGCAACTCTTTTCAAAGCCCACACAAGTTA
1 G-TGGC-A-TCCTTTCAAAG-CC-CACAAGTCA
215353 GTGGCA-CCTTT
1 GTGGCATCCTTT
215364 TTTTAAAGCC
Statistics
Matches: 407, Mismatches: 80, Indels: 51
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.00
28 203 0.50
29 39 0.10
30 61 0.15
31 19 0.05
32 54 0.13
33 4 0.01
34 25 0.06
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
GTGGCATCCTTTCAAAGCCCACAAGTCA
Found at i:215316 original size:32 final size:32
Alignment explanation
Indices: 215280--215413 Score: 110
Period size: 32 Copynumber: 4.2 Consensus size: 32
215270 GCTCAAAACC
*
215280 CACAAGTCAATGACATAC-CCTTTCAAAGCTCA
1 CACAAGTCAATGACA-ACTCCTTTCAAAGCCCA
* * *
215312 CACAAGTCGATGGCAACTCTTTTCAAAGCCCA
1 CACAAGTCAATGACAACTCCTTTCAAAGCCCA
* * * * ** *
215344 CACAAGTTAGTGGCACCTTTTTTTAAAGCCCA
1 CACAAGTCAATGACAACTCCTTTCAAAGCCCA
* * * *
215376 CGC-AGTCGATGGCAACTCTTTTCAAAGCCCA
1 CACAAGTCAATGACAACTCCTTTCAAAGCCCA
215407 CACAAGT
1 CACAAGT
215414 TAGTGGCACC
Statistics
Matches: 82, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
31 26 0.32
32 56 0.68
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (32 bp):
CACAAGTCAATGACAACTCCTTTCAAAGCCCA
Found at i:215336 original size:118 final size:117
Alignment explanation
Indices: 215081--215345 Score: 288
Period size: 118 Copynumber: 2.2 Consensus size: 117
215071 TAAAGCCCAC
* * * * *
215081 AAGTCAGTGGCATATTTTCAAAGCCTACAAGTTAGTGGCATCCTTCCAAAGCTCACAAGTCAGTG
1 AAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGCCATCCTTCCAAAGCCCACAAGTCAGTG
** * * * *
215146 GCATCCTTCCAAAGCCCACAAGTCAGTGCCATCCTTTTAAAGCCCATAAGTCA
66 GCATCCAGCCAAAACCCACAAGTCAATGACATCCTTTCAAAGCCCATAAG-CA
* * *
215199 AAGTCAGTGGCATCCTTTCAAAGCCCGCAAGTCAGTGCCATCCTTTCAAAGCCCACAAGTCAGTG
1 AAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGCCATCCTTCCAAAGCCCACAAGTCAGTG
* *
215264 GCA-CCAGCTCAAAACCCACAAGTCAATGACATACCCTTTCAAAGCTCA-CA-C-
66 GCATCCAGC-CAAAACCCACAAGTCAATGACAT--CCTTTCAAAGCCCATAAGCA
215315 AAGTC-GATGGCAACTCTTTTCAAAGCCCACA
1 AAGTCAG-TGGC-A-TCTTTTCAAAGCCCACA
215346 CAAGTTAGTG
Statistics
Matches: 123, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
115 1 0.01
116 9 0.07
117 5 0.04
118 95 0.77
119 1 0.01
120 12 0.10
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (117 bp):
AAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGCCATCCTTCCAAAGCCCACAAGTCAGTG
GCATCCAGCCAAAACCCACAAGTCAATGACATCCTTTCAAAGCCCATAAGCA
Found at i:215390 original size:63 final size:65
Alignment explanation
Indices: 215304--215466 Score: 258
Period size: 63 Copynumber: 2.5 Consensus size: 65
215294 ATACCCTTTC
* *
215304 AAAGCTCACACAAGTCGATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACC-TTTTTTT
1 AAAGCCCACGCAAGTCGATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTTTTT
215368 AAAGCCCACGC-AGTCGATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTTTTT
1 AAAGCCCACGCAAGTCGATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTTTTT
* * * *
215432 AAAGCCTACGCAAGTCGGTAGCAACCCTTTTCAAA
1 AAAGCCCACGCAAGTCGATGGCAACTCTTTTCAAA
215467 TCACCATTGT
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
63 45 0.49
64 26 0.29
65 20 0.22
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (65 bp):
AAAGCCCACGCAAGTCGATGGCAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACCTTTTTTTT
Found at i:215403 original size:31 final size:32
Alignment explanation
Indices: 215300--215466 Score: 151
Period size: 32 Copynumber: 5.2 Consensus size: 32
215290 TGACATACCC
*
215300 TTTCAAAGCTCACACAAGTCGATGGCAACTCT
1 TTTCAAAGCCCACACAAGTCGATGGCAACTCT
* * *
215332 TTTCAAAGCCCACACAAGT-TAGTGGCACCTTT
1 TTTCAAAGCCCACACAAGTCGA-TGGCAACTCT
* *
215364 TTTTAAAGCCCACGC-AGTCGATGGCAACTCT
1 TTTCAAAGCCCACACAAGTCGATGGCAACTCT
* * *
215395 TTTCAAAGCCCACACAAGT-TAGTGGCACCTTTT
1 TTTCAAAGCCCACACAAGTCGA-TGGCAAC-TCT
* * * * * *
215428 TTTTAAAGCCTACGCAAGTCGGTAGCAACCCT
1 TTTCAAAGCCCACACAAGTCGATGGCAACTCT
215460 TTTCAAA
1 TTTCAAA
215467 TCACCATTGT
Statistics
Matches: 105, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
31 26 0.25
32 56 0.53
33 23 0.22
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGATGGCAACTCT
Found at i:216682 original size:17 final size:16
Alignment explanation
Indices: 216656--216690 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
216646 ATAGGTAAGA
*
216656 AAGAAAGAAGATAAAG
1 AAGAAAGAAGAAAAAG
216672 AAGAAAGGAAGAAAAAG
1 AAGAAA-GAAGAAAAAG
216689 AA
1 AA
216691 AAAAAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (16 bp):
AAGAAAGAAGAAAAAG
Found at i:219430 original size:32 final size:32
Alignment explanation
Indices: 219394--219455 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
219384 CGAATTTAGG
*
219394 TCATTTCGGGTTCAAGTCATTTTGGGTTCGGC
1 TCATTTCAGGTTCAAGTCATTTTGGGTTCGGC
* **
219426 TCATTTTAGGTTCGGGTCATTTTGGGTTCG
1 TCATTTCAGGTTCAAGTCATTTTGGGTTCG
219456 ATTTATTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.11, C:0.16, G:0.29, T:0.44
Consensus pattern (32 bp):
TCATTTCAGGTTCAAGTCATTTTGGGTTCGGC
Found at i:219464 original size:16 final size:16
Alignment explanation
Indices: 219410--219455 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
219400 CGGGTTCAAG
219410 TCATTTTGGGTTCGGC
1 TCATTTTGGGTTCGGC
* *
219426 TCATTTTAGGTTCGGG
1 TCATTTTGGGTTCGGC
219442 TCATTTTGGGTTCG
1 TCATTTTGGGTTCG
219456 ATTTATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.09, C:0.15, G:0.30, T:0.46
Consensus pattern (16 bp):
TCATTTTGGGTTCGGC
Found at i:219482 original size:17 final size:16
Alignment explanation
Indices: 219394--219482 Score: 65
Period size: 16 Copynumber: 5.4 Consensus size: 16
219384 CGAATTTAGG
*
219394 TCATTTCGGGTTCA-A
1 TCATTTTGGGTTCAGA
* *
219409 GTCATTTTGGGTTCGGC
1 -TCATTTTGGGTTCAGA
* * *
219426 TCATTTTAGGTTCGGG
1 TCATTTTGGGTTCAGA
219442 TCATTTTGGGTTC-GA
1 TCATTTTGGGTTCAGA
*
219457 TTTATTTTTGGGTTCAGA
1 -TCA-TTTTGGGTTCAGA
219475 TCAGTTTT
1 TCA-TTTT
219483 CTTTGGGTTG
Statistics
Matches: 59, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
15 1 0.02
16 40 0.68
17 16 0.27
18 2 0.03
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.47
Consensus pattern (16 bp):
TCATTTTGGGTTCAGA
Found at i:219557 original size:28 final size:28
Alignment explanation
Indices: 219524--219585 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
219514 GGTTGGATTG
219524 GGTTCGAGTTAATCAATCAGGTTTTTTA
1 GGTTCGAGTTAATCAATCAGGTTTTTTA
*
219552 GGTTCGAGTTAATCAATCAGGTTTTTTG
1 GGTTCGAGTTAATCAATCAGGTTTTTTA
219580 GGTTCG
1 GGTTCG
219586 TGTCAGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.11, G:0.26, T:0.42
Consensus pattern (28 bp):
GGTTCGAGTTAATCAATCAGGTTTTTTA
Found at i:230343 original size:52 final size:52
Alignment explanation
Indices: 230262--230382 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
230252 GTCCCGAAAT
* *
230262 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGCAAATTTGC
*
230314 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGCAAATTTGC
230366 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
230383 AAGATCAGTG
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGAGCAAATTTGC
Found at i:230395 original size:52 final size:51
Alignment explanation
Indices: 230262--230402 Score: 203
Period size: 52 Copynumber: 2.7 Consensus size: 51
230252 GTCCCGAAAT
*
230262 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGCAAATTTGC
* *
230314 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGAGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGAGCAAATTTGC
*
230366 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
230403 ATGTATCAAT
Statistics
Matches: 81, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 79 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGAGCAAATTTGC
Found at i:230493 original size:33 final size:33
Alignment explanation
Indices: 230456--230522 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
230446 AGTAGCTTAA
230456 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
230489 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
230522 A
1 A
230523 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:230496 original size:13 final size:13
Alignment explanation
Indices: 230478--230502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230468 CAAAAAAATA
230478 TGTATCGATACAT
1 TGTATCGATACAT
230491 TGTATCGATACA
1 TGTATCGATACA
230503 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:233153 original size:13 final size:13
Alignment explanation
Indices: 233135--233159 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233125 TTCAATGATT
233135 TGTATCGATACAA
1 TGTATCGATACAA
233148 TGTATCGATACA
1 TGTATCGATACA
233160 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:233172 original size:19 final size:19
Alignment explanation
Indices: 233148--233229 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
233138 ATCGATACAA
233148 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
233167 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
233186 TGTATCGAT--ATAA----
1 TGTATCGATACATAAGTGT
*
233199 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
233218 TGTATCGATACA
1 TGTATCGATACA
233230 ATATATCGCT
Statistics
Matches: 57, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
13 9 0.16
15 4 0.07
17 4 0.07
19 40 0.70
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:233203 original size:32 final size:32
Alignment explanation
Indices: 233167--233237 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
233157 ACATAAGTGT
*
233167 TGTATCGATACATAAGTGTTGTATCGATATAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
233199 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
233231 TATATCG
1 TGTATCG
233238 CTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:233300 original size:13 final size:13
Alignment explanation
Indices: 233282--233306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
233272 ATTACTCAAA
233282 TGTATCGATACAT
1 TGTATCGATACAT
233295 TGTATCGATACA
1 TGTATCGATACA
233307 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:233359 original size:52 final size:52
Alignment explanation
Indices: 233315--233443 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
233305 CACTGATCTT
*
233315 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
233367 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
233419 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
233444 TCATATTTTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:245307 original size:21 final size:20
Alignment explanation
Indices: 245277--245316 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
245267 ATGACATGAA
245277 AAATAATAAAAATATAAAAT
1 AAATAATAAAAATATAAAAT
*
245297 AAATATATAAACATATAAAA
1 AAATA-ATAAAAATATAAAA
245317 ATTTACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AAATAATAAAAATATAAAAT
Found at i:246050 original size:2 final size:2
Alignment explanation
Indices: 246043--246068 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
246033 GTAACAACTA
246043 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
246069 GCATGTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246066 original size:35 final size:34
Alignment explanation
Indices: 245989--246066 Score: 102
Period size: 35 Copynumber: 2.3 Consensus size: 34
245979 TTATTGTAGG
* * * *
245989 TATAGATATGTAACAACTAATATATATATGTGTG
1 TATATATATGTAACAACTAATATATATATATATA
*
246023 TATGTATATGGTAACAACTAATATATATATATATA
1 TATATATAT-GTAACAACTAATATATATATATATA
246058 TATATATAT
1 TATATATAT
246067 ATGCATGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 7 0.19
35 30 0.81
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (34 bp):
TATATATATGTAACAACTAATATATATATATATA
Found at i:251190 original size:18 final size:18
Alignment explanation
Indices: 251167--251210 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
251157 ATTTTATATT
251167 TTTATAAATT-ATTTAATA
1 TTTATAAATTAATTTAA-A
251185 TTTATAAAATTAATTTAAA
1 TTTAT-AAATTAATTTAAA
251204 -TTATAAA
1 TTTATAAA
251211 ATAAATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 9 0.38
19 6 0.25
20 6 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATAAATTAATTTAAA
Found at i:251211 original size:18 final size:20
Alignment explanation
Indices: 251157--251218 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
251147 TTAATTAAAT
* *
251157 ATTTTATATTTTTATAAATT-
1 ATTTAATATTTATA-AAATTA
251177 ATTTAATATTTATAAAATTA
1 ATTTAATATTTATAAAATTA
*
251197 ATTTAA-A-TTATAAAATAA
1 ATTTAATATTTATAAAATTA
251215 ATTT
1 ATTT
251219 TTATTTATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 14 0.37
19 6 0.16
20 18 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAATATTTATAAAATTA
Found at i:252372 original size:2 final size:2
Alignment explanation
Indices: 252365--252561 Score: 136
Period size: 2 Copynumber: 104.5 Consensus size: 2
252355 GAATTCTGTA
* * *
252365 AT AT AT AT A- AT AT AC AT AT AT A- AT GT AT AT A- AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
252404 AT AT AT A- AT AT -T AT AT AT A- AT AT AC AT AT GT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
252442 AT AT AA AT AT -T AT AT AT A- AT AT AC AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
252481 AT AC AT AT AT AC AT CAA AT AT AT A- AT AT AC AT AT AT A- AT GT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
252522 AT AT AT A- AT AT AT GAT -T TT AGT AT AT AT TT A- AT AT AT AT A
1 AT AT AT AT AT AT AT -AT AT AT A-T AT AT AT AT AT AT AT AT AT A
252562 CTAGACTTTG
Statistics
Matches: 150, Mismatches: 27, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
1 15 0.10
2 130 0.87
3 5 0.03
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:252406 original size:37 final size:35
Alignment explanation
Indices: 252363--252534 Score: 149
Period size: 37 Copynumber: 4.8 Consensus size: 35
252353 TAGAATTCTG
*
252363 TAATATATATAATATACATATATAATGTATATAATA
1 TAATATATATAATAT-CATATATAATATATATAATA
* *
252399 TACATATATATAATATTATATATAATATACATATGTATA
1 TA-ATATATATAATATCATATATAATAT--ATAT-AATA
* *
252438 TAATATATA-AATATTATATATAATATACAT-ATA
1 TAATATATATAATATCATATATAATATATATAATA
*
252471 TATATATAATATACATAT-ATACATCAA-ATATATAATA
1 TA-ATAT-ATATA-ATATCATATAT-AATATATATAATA
* *
252508 T-ACATATATAATGT-ATATATAATATAT
1 TAATATATATAATATCATATATAATATAT
252535 GATTTTAGTA
Statistics
Matches: 116, Mismatches: 9, Indels: 25
0.77 0.06 0.17
Matches are distributed among these distances:
32 2 0.02
33 17 0.15
34 9 0.08
35 9 0.08
36 23 0.20
37 40 0.34
38 11 0.09
39 5 0.04
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (35 bp):
TAATATATATAATATCATATATAATATATATAATA
Found at i:252557 original size:11 final size:11
Alignment explanation
Indices: 252365--252561 Score: 138
Period size: 11 Copynumber: 17.6 Consensus size: 11
252355 GAATTCTGTA
252365 ATATATATAAT
1 ATATATATAAT
*
252376 ATACATAT-AT
1 ATATATATAAT
*
252386 AATGTATATAAT
1 -ATATATATAAT
*
252398 ATACATAT-AT
1 ATATATATAAT
*
252408 ATA-ATATTAT
1 ATATATATAAT
252418 ATATAATATACAT
1 ATAT-ATATA-AT
*
252431 ATGTATATAAT
1 ATATATATAAT
*
252442 ATATAAAT-AT
1 ATATATATAAT
252452 -TATATATAAT
1 ATATATATAAT
*
252462 ATACATATATAT
1 ATATATATA-AT
252474 ATATAATATACAT
1 ATAT-ATATA-AT
*
252487 ATATACATCAA-
1 ATATATAT-AAT
252498 ATATATA-ATAT
1 ATATATATA-AT
*
252509 ACATATATAAT
1 ATATATATAAT
*
252520 GTATATATAAT
1 ATATATATAAT
* *
252531 ATATGATTTTAGT
1 ATAT-A-TATAAT
*
252544 ATATATTTAAT
1 ATATATATAAT
252555 ATATATA
1 ATATATA
252562 CTAGACTTTG
Statistics
Matches: 147, Mismatches: 23, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
9 11 0.07
10 17 0.12
11 71 0.48
12 23 0.16
13 25 0.17
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (11 bp):
ATATATATAAT
Found at i:252559 original size:13 final size:13
Alignment explanation
Indices: 252365--252561 Score: 155
Period size: 13 Copynumber: 15.4 Consensus size: 13
252355 GAATTCTGTA
252365 ATATATATAATAT
1 ATATATATAATAT
* *
252378 ACATATATAATGT
1 ATATATATAATAT
*
252391 ATATA-AT-ATAC
1 ATATATATAATAT
252402 ATATATATAATAT
1 ATATATATAATAT
252415 -TATATATAATAT
1 ATATATATAATAT
252427 ACATATGTATATAATAT
1 --ATA--TATATAATAT
* *
252444 ATAAATATTATAT
1 ATATATATAATAT
252457 ATA-ATATACATAT
1 ATATATATA-ATAT
252470 ATATATATAATAT
1 ATATATATAATAT
*
252483 ACATATATACATCA-
1 ATATATATA-AT-AT
252497 A-ATATATAATAT
1 ATATATATAATAT
*
252509 ACATATAT-A-AT
1 ATATATATAATAT
*
252520 GTATATATAATAT
1 ATATATATAATAT
* *
252533 ATGAT-TTTAGTAT
1 AT-ATATATAATAT
252546 ATAT-T-TAATAT
1 ATATATATAATAT
252557 ATATA
1 ATATA
252562 CTAGACTTTG
Statistics
Matches: 151, Mismatches: 16, Indels: 35
0.75 0.08 0.17
Matches are distributed among these distances:
11 25 0.17
12 28 0.19
13 72 0.48
14 10 0.07
15 6 0.04
17 10 0.07
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (13 bp):
ATATATATAATAT
Found at i:252561 original size:15 final size:15
Alignment explanation
Indices: 252363--252561 Score: 131
Period size: 15 Copynumber: 12.7 Consensus size: 15
252353 TAGAATTCTG
252363 TAATATATATA-ATA
1 TAATATATATATATA
*
252377 TACATATATAATGTATA
1 TA-ATATAT-ATATATA
*
252394 TAATATACATATATA
1 TAATATATATATATA
252409 TAATATTATATATAATA
1 TAATA-TATATAT-ATA
252426 TACATATGTATATAATATA
1 TA-ATA--TATAT-ATATA
252445 TAA-ATAT-TATATA
1 TAATATATATATATA
*
252458 TAATATACATATATA
1 TAATATATATATATA
*
252473 T-ATATA-ATATACA
1 TAATATATATATATA
* *
252486 TATATACATCAAATATA
1 TA-ATATAT-ATATATA
*
252503 TAATATACATATATA
1 TAATATATATATATA
*
252518 -ATGTATATATAATATA
1 TA-ATATATAT-ATATA
* * *
252534 TGATTTTAGTATATATT
1 T-AATATA-TATATATA
252551 TAATATATATA
1 TAATATATATA
252562 CTAGACTTTG
Statistics
Matches: 146, Mismatches: 20, Indels: 37
0.72 0.10 0.18
Matches are distributed among these distances:
13 15 0.10
14 12 0.08
15 47 0.32
16 26 0.18
17 26 0.18
18 8 0.05
19 10 0.07
20 2 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:253212 original size:15 final size:15
Alignment explanation
Indices: 253192--253230 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
253182 TGAATGAAAT
253192 ATAATTAAATTTAAA
1 ATAATTAAATTTAAA
253207 ATAATTTAAA-TTAAA
1 ATAA-TTAAATTTAAA
253222 A-AATTAAAT
1 ATAATTAAAT
253231 CTAATACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.23
14 2 0.09
15 10 0.45
16 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAATTAAATTTAAA
Found at i:253217 original size:16 final size:16
Alignment explanation
Indices: 253151--253230 Score: 55
Period size: 16 Copynumber: 5.3 Consensus size: 16
253141 TAAATTAACC
* *
253151 TAAATTCAAAATATTT
1 TAAATTTAAAATAATT
* *
253167 TAAACTTAAAA-AATA
1 TAAATTTAAAATAATT
* *
253182 TGAA-TGAAATATAA-T
1 TAAATTTAAA-ATAATT
253197 TAAATTTAAAATAATT
1 TAAATTTAAAATAATT
253213 TAAA-TTAAAA-AA-T
1 TAAATTTAAAATAATT
253226 TAAAT
1 TAAAT
253231 CTAATACATC
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 19 0.38
16 20 0.40
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (16 bp):
TAAATTTAAAATAATT
Found at i:254658 original size:27 final size:28
Alignment explanation
Indices: 254628--254688 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
254618 TTATGGTATA
*
254628 ATTATATTTAAAGTATATT-AT-ATTTAT
1 ATTATATTT-AAGTATATTAATAATTCAT
* *
254655 ATTA-ATTTTAGTATGTTAATAATTCAT
1 ATTATATTTAAGTATATTAATAATTCAT
254682 ATTATAT
1 ATTATAT
254689 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 7 0.25
26 6 0.21
27 13 0.46
28 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (28 bp):
ATTATATTTAAGTATATTAATAATTCAT
Found at i:255513 original size:2 final size:2
Alignment explanation
Indices: 255506--255560 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
255496 TCCAAACTAT
255506 TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
255548 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
255561 TCCCATAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:256097 original size:35 final size:35
Alignment explanation
Indices: 256058--256124 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
256048 TTTATATATT
256058 AATATTTATATATT-TTATAAT-TAAATTTAAATAAA
1 AATATTT-TATATTATTA-AATATAAATTTAAATAAA
*
256093 AATATTTTTTATTATTAAATATAAATTTAAAT
1 AATATTTTATATTATTAAATATAAATTTAAAT
256125 TAAATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (35 bp):
AATATTTTATATTATTAAATATAAATTTAAATAAA
Found at i:256374 original size:20 final size:19
Alignment explanation
Indices: 256328--256375 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
256318 AAAAATCCCA
256328 AAATAAA-AATAAGAAAAT
1 AAATAAATAATAAGAAAAT
256346 AAA-AGAATAATAAAGAAAAT
1 AAATA-AATAAT-AAGAAAAT
256366 AAATAAATAA
1 AAATAAATAA
256376 GCAAAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.04
18 5 0.19
19 3 0.12
20 16 0.62
21 1 0.04
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
AAATAAATAATAAGAAAAT
Found at i:256827 original size:17 final size:17
Alignment explanation
Indices: 256797--256829 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
256787 ACTCGTCTAC
256797 GGTTTAGATCAAGTTTG
1 GGTTTAGATCAAGTTTG
256814 GGTTTGAGAT-AAGTTT
1 GGTTT-AGATCAAGTTT
256830 AAATATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.42
Consensus pattern (17 bp):
GGTTTAGATCAAGTTTG
Found at i:259898 original size:19 final size:20
Alignment explanation
Indices: 259857--259898 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
259847 ATTTTTTTAA
* **
259857 AATATTTAAATATTATATTT
1 AATATTTAAATATAATAAAT
259877 AATA-TTAAATATAATAAAT
1 AATATTTAAATATAATAAAT
259896 AAT
1 AAT
259899 TAATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AATATTTAAATATAATAAAT
Found at i:260283 original size:80 final size:80
Alignment explanation
Indices: 260145--260310 Score: 305
Period size: 80 Copynumber: 2.1 Consensus size: 80
260135 CAATTCAACC
260145 AGTTCAATTAGTCGATTCTATCTTATTTTTTAATTAGATGATTATTCATATACATTTATCATGCC
1 AGTT-AATTAGTCGATTCTATCTTATTTTTTAATTAGATGATTATTCATATACATTTATCATGCC
260210 TATACCATTATAAAAA
65 TATACCATTATAAAAA
* *
260226 AGTTAATTAGTTGATTCTATCTTATTTTTTAATTAGATGATTATTCATGTACATTTATCATGCCT
1 AGTTAATTAGTCGATTCTATCTTATTTTTTAATTAGATGATTATTCATATACATTTATCATGCCT
260291 ATACCATTATAAAAA
66 ATACCATTATAAAAA
260306 AGTTA
1 AGTTA
260311 GTTGAGTTTG
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
80 79 0.95
81 4 0.05
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.45
Consensus pattern (80 bp):
AGTTAATTAGTCGATTCTATCTTATTTTTTAATTAGATGATTATTCATATACATTTATCATGCCT
ATACCATTATAAAAA
Found at i:260567 original size:21 final size:22
Alignment explanation
Indices: 260528--260568 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
260518 ACATTATTAT
*
260528 TATTATTATTATTCTTCCACTC
1 TATTATTATTATTCATCCACTC
*
260550 TATTA-TATTTTTCATCCAC
1 TATTATTATTATTCATCCAC
260569 ATACATGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATTATTATTCATCCACTC
Found at i:260827 original size:22 final size:22
Alignment explanation
Indices: 260783--260826 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
260773 TTAGTAACTT
260783 TAAAAAAATTATAATTTAAAAA
1 TAAAAAAATTATAATTTAAAAA
260805 TAAAAAATATTA-AATATTAAAA
1 TAAAAAA-ATTATAAT-TTAAAA
260827 TTTTTAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAAAAATTATAATTTAAAAA
Found at i:261190 original size:19 final size:20
Alignment explanation
Indices: 261166--261204 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
261156 TCCTAATGTT
*
261166 ATTT-AAATATGATATAAAA
1 ATTTAAAATATAATATAAAA
261185 ATTTAAAATATAATATAAAA
1 ATTTAAAATATAATATAAAA
261205 TATAATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTTAAAATATAATATAAAA
Found at i:261236 original size:25 final size:27
Alignment explanation
Indices: 261177--261237 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
261167 TTTAAATATG
* * *
261177 ATATAAAAATTTAAAATATAATATAAA
1 ATATAATATTTTAAAATATAAAATAAA
261204 ATATAATATTTTAAAAT-TAAAAT-AA
1 ATATAATATTTTAAAATATAAAATAAA
261229 ATATAATAT
1 ATATAATAT
261238 GAAAATATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 11 0.35
26 5 0.16
27 15 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (27 bp):
ATATAATATTTTAAAATATAAAATAAA
Found at i:263048 original size:16 final size:16
Alignment explanation
Indices: 263027--263076 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
263017 TATGATAGAA
263027 TATATAATTTAAATTT
1 TATATAATTTAAATTT
*
263043 TATATAATATAAATTAT
1 TATATAATTTAAATT-T
*
263060 TA-AT-ATTTAAAATT
1 TATATAATTTAAATTT
263074 TAT
1 TAT
263077 TTAAATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 3 0.10
15 7 0.24
16 16 0.55
17 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATAATTTAAATTT
Found at i:263070 original size:31 final size:30
Alignment explanation
Indices: 263033--263115 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 30
263023 AGAATATATA
*
263033 ATTTAAATTTTATAT-AATATAAATTATTAAT
1 ATTTAAAATTTATATAAATAT-AATTA-TAAT
*
263064 ATTTAAAATTTATTTAAATATAATTATAAT
1 ATTTAAAATTTATATAAATATAATTATAAT
*
263094 ATAATAAAA--TATATAAATATAA
1 AT-TTAAAATTTATATAAATATAA
263116 CTTTATTATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 12 0.26
30 6 0.13
31 23 0.50
32 5 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTTAAAATTTATATAAATATAATTATAAT
Found at i:264266 original size:3 final size:3
Alignment explanation
Indices: 264258--264288 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
264248 AATAAAAACA
264258 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
264289 CAACCATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:265401 original size:2 final size:2
Alignment explanation
Indices: 265396--265420 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
265386 AAAATTGCCC
265396 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
265421 TCCCTACATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:266588 original size:18 final size:17
Alignment explanation
Indices: 266555--266595 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
266545 ATGATATAAT
266555 TTAATAAATTAAAAAAA
1 TTAATAAATTAAAAAAA
266572 TTAA-AAATTATATAAAAA
1 TTAATAAATTA-A-AAAAA
266590 TTAATA
1 TTAATA
266596 TTAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 5 0.24
18 9 0.43
19 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAATAAATTAAAAAAA
Found at i:267194 original size:22 final size:23
Alignment explanation
Indices: 267139--267195 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 23
267129 TAGCTCATAA
*
267139 AATTAATCGATTTTTTTTAATTTTT
1 AATTAAT--ATTTTTATTAATTTTT
267164 AA-TATATATTTTTATT-ATTTTT
1 AATTA-ATATTTTTATTAATTTTT
267186 AATTAATATT
1 AATTAATATT
267196 AAAAGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 13 0.45
23 10 0.34
24 2 0.07
25 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
AATTAATATTTTTATTAATTTTT
Found at i:268435 original size:101 final size:100
Alignment explanation
Indices: 268288--268470 Score: 305
Period size: 101 Copynumber: 1.8 Consensus size: 100
268278 ATGGCCACAT
* * *
268288 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGT
1 TTGTCAAAGGTTGGTGAAAAATCGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGT
268353 GAAGAATCAGTCAACAATAATGGCCACCTCTCTCTA
66 GAAGAAT-AGTCAACAATAATGGCCACCTCTCTCTA
268389 TTGTCAAAGGTTGGT-AAAATATCGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGG
1 TTGTCAAAGGTTGGTGAAAA-ATCGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGG
*
268453 TGAAGGATAGTCAACAAT
65 TGAAGAATAGTCAACAAT
268471 GACAACAACT
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 13 0.17
101 64 0.83
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (100 bp):
TTGTCAAAGGTTGGTGAAAAATCGTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGT
GAAGAATAGTCAACAATAATGGCCACCTCTCTCTA
Found at i:268437 original size:50 final size:50
Alignment explanation
Indices: 268288--268470 Score: 287
Period size: 50 Copynumber: 3.6 Consensus size: 50
268278 ATGGCCACAT
268288 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
*
268338 TTGTCAAAGGTTGGTGAAGAATCAGTCAACAATAATGGCCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATC-GTCAACAATTATGGCCACCTCTCTCTA
* * *
268389 TTGTCAAAGGTTGGT-AAAATATCGTCAACAATTACGACCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGA-ATCGTCAACAATTATGGCCACCTCTCTCTA
* *
268439 TTGTCAAAGGTTGGTGAAGGATAGTCAACAAT
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAAT
268471 GACAACAACT
Statistics
Matches: 122, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 76 0.62
51 46 0.38
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
Found at i:273066 original size:50 final size:50
Alignment explanation
Indices: 272886--273053 Score: 275
Period size: 50 Copynumber: 3.4 Consensus size: 50
272876 ATGGTCACAT
*
272886 TTGTCAAAGGTT-GTGAAGAATCGTCAACAATTATGGCCACCTCTTTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
* *
272935 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATAATGGCCACCTCCCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
* **
272985 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTACGATCACCTCTCTCTA
1 TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
273035 TTGTCAAAGGTTGGTGAAG
1 TTGTCAAAGGTTGGTGAAG
273054 CATAATCAAC
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 12 0.11
50 98 0.89
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (50 bp):
TTGTCAAAGGTTGGTGAAGAATCGTCAACAATTATGGCCACCTCTCTCTA
Found at i:274541 original size:25 final size:25
Alignment explanation
Indices: 274513--274562 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
274503 CCATCTGCCT
274513 GATTCTTATGTTTTAAAAATTATCA
1 GATTCTTATGTTTTAAAAATTATCA
*
274538 GATTCTTATTTTTTAAAAATTATCA
1 GATTCTTATGTTTTAAAAATTATCA
274563 TAAATATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (25 bp):
GATTCTTATGTTTTAAAAATTATCA
Found at i:274834 original size:15 final size:16
Alignment explanation
Indices: 274811--274841 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
274801 ACTTATTTTT
274811 AAAT-TTTTTAATAAA
1 AAATATTTTTAATAAA
274826 AAATATTTTTAATAAA
1 AAATATTTTTAATAAA
274842 CGGAGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTTTTAATAAA
Found at i:276063 original size:19 final size:20
Alignment explanation
Indices: 276030--276067 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
276020 TCTAAGAGAA
276030 AAAAATTCACTAATTATAAC
1 AAAAATTCACTAATTATAAC
*
276050 AAAAATTTAC-AATTATAA
1 AAAAATTCACTAATTATAA
276068 ATACGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCACTAATTATAAC
Found at i:276472 original size:15 final size:15
Alignment explanation
Indices: 276444--276486 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
276434 TACTTAATAA
* *
276444 TTTATGTATTTATTT
1 TTTATTTATATATTT
276459 TTTATTTATATATTT
1 TTTATTTATATATTT
276474 TATTATATTATAT
1 T-TTAT-TTATAT
276487 TATATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 4 0.17
17 6 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTATTTATATATTT
Found at i:276481 original size:12 final size:13
Alignment explanation
Indices: 276450--276505 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
276440 ATAATTTATG
276450 TATTTAT-T-TTT
1 TATTTATATATTT
276461 TATTTATATATTT
1 TATTTATATATTT
*
276474 TATTATATTATATTA
1 TATT-TA-TATATTT
*
276489 TATTTAAAATATTT
1 TATTT-ATATATTT
276503 TAT
1 TAT
276506 ATTTATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
11 7 0.19
12 1 0.03
13 7 0.19
14 11 0.30
15 11 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTATATATTT
Found at i:276487 original size:15 final size:15
Alignment explanation
Indices: 276444--276513 Score: 53
Period size: 13 Copynumber: 5.0 Consensus size: 15
276434 TACTTAATAA
*
276444 TTTATGTAT-TTATTT
1 TTTAT-TATATTATAT
276459 TTTATT-TA-TATAT
1 TTTATTATATTATAT
276472 TTTATTATATTATAT
1 TTTATTATATTATAT
* **
276487 TATATT-TAAAATAT
1 TTTATTATATTATAT
276501 TTTA-TAT-TTATAT
1 TTTATTATATTATAT
276514 AAATTCACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
13 16 0.36
14 13 0.30
15 15 0.34
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (15 bp):
TTTATTATATTATAT
Found at i:276541 original size:12 final size:12
Alignment explanation
Indices: 276524--276549 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
276514 AAATTCACAT
276524 TCACTCATTAAC
1 TCACTCATTAAC
276536 TCACTCATTAAC
1 TCACTCATTAAC
276548 TC
1 TC
276550 TTCGTATAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (12 bp):
TCACTCATTAAC
Found at i:276987 original size:30 final size:30
Alignment explanation
Indices: 276940--276996 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
276930 AATAATAATA
276940 TTTATTAATATAAAAATAA-AATATTAATTT
1 TTTATTAATATAAAAATAATAAT-TTAATTT
**
276970 TTTATTAATATTTAAATAATAATTTAA
1 TTTATTAATATAAAAATAATAATTTAA
276997 AACTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTATTAATATAAAAATAATAATTTAATTT
Found at i:277695 original size:18 final size:17
Alignment explanation
Indices: 277658--277722 Score: 59
Period size: 16 Copynumber: 4.0 Consensus size: 17
277648 TGTCATAATC
* *
277658 ATATTTATAT-TATTAT
1 ATATTTATATAAATTTT
277674 ATATTTATATAAATTTT
1 ATATTTATATAAATTTT
277691 GATATGTTA-AT-AA-TTT
1 -ATAT-TTATATAAATTTT
277707 ATA-TTATATAAATTTT
1 ATATTTATATAAATTTT
277723 CAAACATTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 3 0.07
14 2 0.05
15 5 0.12
16 16 0.39
17 6 0.15
18 6 0.15
19 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATATTTATATAAATTTT
Found at i:278270 original size:23 final size:22
Alignment explanation
Indices: 278222--278278 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
278212 ATATATTTAT
**
278222 ATTATTAAAT-TTAATTATTAA
1 ATTATTAAATATTAATTAAAAA
*
278243 TTTATTAAAATATTAATTAAAAA
1 ATTATT-AAATATTAATTAAAAA
278266 ATTATTTAAATAT
1 ATTA-TTAAATAT
278279 ATAAAATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 5 0.17
22 4 0.14
23 18 0.62
24 2 0.07
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATTAAATATTAATTAAAAA
Found at i:278708 original size:20 final size:20
Alignment explanation
Indices: 278663--278744 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
278653 TTTAAATAAG
*
278663 TATTTATTTTAAATTT-AAT
1 TATTTATTTTTAATTTAAAT
*
278682 TCGATTTATTTTTATTTTAAAT
1 T--ATTTATTTTTAATTTAAAT
* *
278704 TATTTATTATTAATATAAAT
1 TATTTATTTTTAATTTAAAT
* *
278724 TTTTTA-TTTAAATTT-AAT
1 TATTTATTTTTAATTTAAAT
278742 TAT
1 TAT
278745 AAAATATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
18 5 0.10
19 7 0.14
20 21 0.42
21 13 0.26
22 4 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (20 bp):
TATTTATTTTTAATTTAAAT
Found at i:278770 original size:22 final size:22
Alignment explanation
Indices: 278728--278781 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
278718 ATAAATTTTT
278728 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATTAATTATAAAA
278749 TATTTAAATATTAA-TATAAAA
1 TATTTAAATATTAATTATAAAA
* *
278770 AATTTTAATATT
1 TATTTAAATATT
278782 TTTTAAACAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTAAATATTAATTATAAAA
Found at i:280666 original size:9 final size:9
Alignment explanation
Indices: 280631--280672 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
280621 TGAAATTTAA
280631 TATTAATTT
1 TATTAATTT
280640 TAATATAA-TT
1 T-AT-TAATTT
280650 TA-TAATTT
1 TATTAATTT
280658 TATTAATTT
1 TATTAATTT
280667 TATTAA
1 TATTAA
280673 ATTAAATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.10
8 4 0.14
9 14 0.48
10 5 0.17
11 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTAATTT
Found at i:280698 original size:22 final size:22
Alignment explanation
Indices: 280657--280716 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
280647 ATTTATAATT
280657 TTATT-AA-TTTTATTAAATTAAA
1 TTATTAAATTTTTATT-AATT-AA
280679 TTATTAAATTTTTATT-ATTAA
1 TTATTAAATTTTTATTAATTAA
*
280700 TAAATTAAATTATTTAT
1 T-TATTAAATT-TTTAT
280717 GTTAATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
21 3 0.09
22 16 0.48
23 7 0.21
24 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTAAATTTTTATTAATTAA
Found at i:281418 original size:13 final size:14
Alignment explanation
Indices: 281400--281430 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
281390 TCTAAATGCT
281400 AATTAATTATA-TA
1 AATTAATTATATTA
281413 AATTAATTATATTA
1 AATTAATTATATTA
281427 AATT
1 AATT
281431 TCATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTAATTATATTA
Found at i:283163 original size:17 final size:19
Alignment explanation
Indices: 283131--283166 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
283121 TTAATAAAAA
283131 TATTATTTTAAATATATTT
1 TATTATTTTAAATATATTT
283150 TATTA-TTT-AATATATTT
1 TATTATTTTAAATATATTT
283167 AATTTATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATTTTAAATATATTT
Found at i:283249 original size:25 final size:25
Alignment explanation
Indices: 283185--283249 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
283175 CAAAATTTTA
*
283185 TTTATATAAT-TAAATAAATATAAAT
1 TTTATA-AATATAATTAAATATAAAT
*
283210 TTT-TAATATAAAATTAAAT-TAATAT
1 TTTATAA-ATATAATTAAATATAA-AT
283235 TTTATAAATATAATT
1 TTTATAAATATAATT
283250 TTCTAAAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 1 0.03
24 7 0.21
25 22 0.67
26 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTATAAATATAATTAAATATAAAT
Found at i:283548 original size:2 final size:2
Alignment explanation
Indices: 283541--283575 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
283531 CCTTTCTACG
283541 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
283576 GTTTGGCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:289823 original size:142 final size:142
Alignment explanation
Indices: 289562--289824 Score: 382
Period size: 142 Copynumber: 1.9 Consensus size: 142
289552 TGCATAACTT
* * * * * * * * *
289562 AAAATTTTATTTTATAATATGTATTTAACAGTCGAAAGTTTTTATGTTAAAAATTAGTTAAAAAT
1 AAAAATTTATTTTACAATATATATTTAAAAGTCAAAAATTTTTATATTAAAAAATAGCTAAAAAT
* *
289627 TTTTAATTTATTAAAAATTCGACATACATAACTTAAGTGAATTAAAGATAAAATACATACAACAA
66 TTTTAATTTATTAAAAACTCGACATACATAACTTAAGTGAATAAAAGATAAAATACATACAACAA
289692 TAATATATTGAA
131 TAATATATTGAA
* *
289704 AAAAATTTATTTTACAATATATATTTAAAATTCAAAAATTTTTATATTAAAAAATAGCTAGAAAT
1 AAAAATTTATTTTACAATATATATTTAAAAGTCAAAAATTTTTATATTAAAAAATAGCTAAAAAT
* **
289769 TTTTAATTTATTAAAAACTCGATATGTATAACTTAAGTGAATAAAAGATAAAATAC
66 TTTTAATTTATTAAAAACTCGACATACATAACTTAAGTGAATAAAAGATAAAATAC
289825 GACAGTTAAA
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
142 105 1.00
ACGTcount: A:0.49, C:0.06, G:0.07, T:0.38
Consensus pattern (142 bp):
AAAAATTTATTTTACAATATATATTTAAAAGTCAAAAATTTTTATATTAAAAAATAGCTAAAAAT
TTTTAATTTATTAAAAACTCGACATACATAACTTAAGTGAATAAAAGATAAAATACATACAACAA
TAATATATTGAA
Found at i:292424 original size:13 final size:12
Alignment explanation
Indices: 292402--292456 Score: 65
Period size: 13 Copynumber: 4.4 Consensus size: 12
292392 AATATAAAAA
292402 ATAAATATTATT
1 ATAAATATTATT
* *
292414 ATAATTAATTATG
1 ATAAAT-ATTATT
292427 ATAAATATTAATT
1 ATAAATATT-ATT
*
292440 ATAAATATTAAT
1 ATAAATATTATT
292452 ATAAA
1 ATAAA
292457 AAATTAAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 15 0.42
13 21 0.58
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (12 bp):
ATAAATATTATT
Found at i:292462 original size:13 final size:14
Alignment explanation
Indices: 292392--292473 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 14
292382 CTATCGTATG
*
292392 AATATA-AAAAATA
1 AATATATAAAAATT
* *
292405 AATATTATTATAATT
1 AATA-TATAAAAATT
*
292420 AATTATGATAAATATT
1 AA-TAT-ATAAAAATT
*
292436 AAT-TATAAATATT
1 AATATATAAAAATT
292449 AATATA-AAAAATT
1 AATATATAAAAATT
*
292462 AAATTTATAAAA
1 -AATATATAAAA
292474 TAATACTCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
13 22 0.41
14 10 0.19
15 12 0.22
16 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (14 bp):
AATATATAAAAATT
Found at i:292462 original size:26 final size:27
Alignment explanation
Indices: 292433--292503 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 27
292423 TATGATAAAT
292433 ATTAATTATAAATATTAATA-TAAAAA
1 ATTAATTATAAATATTAATACTAAAAA
**
292459 ATTAAATTTATAAA-A-TAATACTCTAAA
1 ATT-AA-TTATAAATATTAATACTAAAAA
*
292486 ATTACATTATAATTATTA
1 ATTA-ATTATAAATATTA
292504 TTTACATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
26 15 0.42
27 12 0.33
28 9 0.25
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTAATTATAAATATTAATACTAAAAA
Found at i:292510 original size:18 final size:19
Alignment explanation
Indices: 292487--292526 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
292477 TACTCTAAAA
292487 TTACATTATAATTAT-TAT
1 TTACATTATAATTATATAT
*
292505 TTACATTATTATTATATAT
1 TTACATTATAATTATATAT
292524 TTA
1 TTA
292527 AAAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TTACATTATAATTATATAT
Found at i:293242 original size:22 final size:22
Alignment explanation
Indices: 293210--293266 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
293200 AATTTAAAAG
293210 TTTTTAATTATATTTA-ATTAAT
1 TTTTTAATTAT-TTTATATTAAT
*
293232 TTTTTATTTATTTTATATTAAT
1 TTTTTAATTATTTTATATTAAT
*
293254 CTTATTAA-TATTT
1 -TTTTTAATTATTT
293267 AAATTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 21 0.70
23 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTTAATTATTTTATATTAAT
Found at i:294138 original size:3 final size:3
Alignment explanation
Indices: 294132--294187 Score: 85
Period size: 3 Copynumber: 17.7 Consensus size: 3
294122 TTCTTCTTAT
294132 TTA TTA TTTA CTTCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA -TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
294180 TTA TTA TT
1 TTA TTA TT
294188 TAGTTTTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
3 42 0.84
4 7 0.14
5 1 0.02
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:296407 original size:8 final size:8
Alignment explanation
Indices: 296394--296418 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
296384 CTTTTTCAAA
296394 ATAAAAAT
1 ATAAAAAT
296402 ATAAAAAT
1 ATAAAAAT
296410 ATAAAAAT
1 ATAAAAAT
296418 A
1 A
296419 AATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:296416 original size:22 final size:21
Alignment explanation
Indices: 296393--296449 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 21
296383 TCTTTTTCAA
296393 AATAAAAATATAAA-AATATAAA
1 AATAAAAA-ATAAATAA-ATAAA
296415 AATAAATAAATAAATAAATAAA
1 AATAAA-AAATAAATAAATAAA
296437 AGATAAAATAATA
1 A-ATAAAA-AATA
296450 CACAGCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
22 18 0.58
23 13 0.42
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAAAAAATAAATAAATAAA
Found at i:296425 original size:16 final size:15
Alignment explanation
Indices: 296394--296437 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
296384 CTTTTTCAAA
296394 ATAAAAATATAAAAAT
1 ATAAAAATA-AAAAAT
296410 ATAAAAATAAATAAAT
1 ATAAAAATAAA-AAAT
296426 A-AATAAATAAAA
1 ATAA-AAATAAAA
296438 GATAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAAATAAAAAAT
Found at i:296445 original size:12 final size:12
Alignment explanation
Indices: 296391--296447 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 12
296381 GATCTTTTTC
296391 AAAATAAAAATAT
1 AAAATAAAAA-AT
296404 AAAAATATAAAAAT
1 -AAAATA-AAAAAT
296418 -AAATAAATAAAT
1 AAAATAAA-AAAT
*
296430 -AAATAAAAGAT
1 AAAATAAAAAAT
296441 AAAATAA
1 AAAATAA
296448 TACACAGCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 5 0.13
12 22 0.56
14 8 0.21
15 4 0.10
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:296589 original size:2 final size:2
Alignment explanation
Indices: 296582--296617 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
296572 ATAAATTTAT
296582 TA TA TA TA TA TA 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 TA TA TA
296618 GATTAATGGA
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):
TA
Found at i:296907 original size:18 final size:19
Alignment explanation
Indices: 296874--296913 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
296864 AGATCTGATA
296874 ATTTATATATTTTTATTAT
1 ATTTATATATTTTTATTAT
296893 ATTTATATA-TTTTATTAT
1 ATTTATATATTTTTATTAT
296911 ATT
1 ATT
296914 ATAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTATATATTTTTATTAT
Found at i:296920 original size:29 final size:29
Alignment explanation
Indices: 296875--296935 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
296865 GATCTGATAA
* * *
296875 TTTATATATTTTTATTATATTT-ATATAT
1 TTTATATATTATAATTATATTTAAAATAT
296903 TTTATTATATTATAATTATATTTAAAATAT
1 TTTA-TATATTATAATTATATTTAAAATAT
296933 TTT
1 TTT
296936 TTAGTGACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.14
29 16 0.57
30 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTATATATTATAATTATATTTAAAATAT
Found at i:296921 original size:23 final size:21
Alignment explanation
Indices: 296871--296923 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
296861 GATAGATCTG
296871 ATAATT-TATATATTTTTATT
1 ATAATTATATATATTTTTATT
* *
296891 ATATTTATATATTTTATTATATT
1 ATAATTATATATATT-TT-TATT
296914 ATAATTATAT
1 ATAATTATAT
296924 TTAAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.19
21 7 0.26
22 2 0.07
23 13 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATAATTATATATATTTTTATT
Found at i:297460 original size:14 final size:14
Alignment explanation
Indices: 297441--297470 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
297431 CATTCTTAGC
297441 CATTAACATAATCA
1 CATTAACATAATCA
*
297455 CATTAACCTAATCA
1 CATTAACATAATCA
297469 CA
1 CA
297471 ATTCGTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
CATTAACATAATCA
Found at i:297748 original size:26 final size:26
Alignment explanation
Indices: 297718--297769 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
297708 CAAATGTTAA
*
297718 AATTAAT-ATTAAATAATATTAAATAT
1 AATTAATAATT-AATAAAATTAAATAT
*
297744 AATTAATAATTAATAAAATTACATAT
1 AATTAATAATTAATAAAATTAAATAT
297770 TTGTCTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 20 0.87
27 3 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
AATTAATAATTAATAAAATTAAATAT
Found at i:303109 original size:13 final size:13
Alignment explanation
Indices: 303091--303115 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303081 TAACATGATT
303091 AACTTTTAATCTC
1 AACTTTTAATCTC
303104 AACTTTTAATCT
1 AACTTTTAATCT
303116 TGTTTACAAG
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:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
AACTTTTAATCTC
Found at i:303535 original size:19 final size:19
Alignment explanation
Indices: 303511--303550 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
303501 ACGATCAACT
* *
303511 AAGAAATCAGAGTAACTGA
1 AAGAAATCAAAATAACTGA
303530 AAGAAATCAAAATAACTGA
1 AAGAAATCAAAATAACTGA
303549 AA
1 AA
303551 TATAAAAGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (19 bp):
AAGAAATCAAAATAACTGA
Found at i:304711 original size:17 final size:17
Alignment explanation
Indices: 304675--304708 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
304665 TTTTGCTATA
*
304675 TATTTTTTAATTTTTAT
1 TATTTTTTAATGTTTAT
304692 TATTTTTT-ATGTTTAT
1 TATTTTTTAATGTTTAT
304708 T
1 T
304709 TATCTCTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTTTAATGTTTAT
Found at i:305047 original size:24 final size:25
Alignment explanation
Indices: 305002--305055 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
304992 TTTAAATAAT
305002 AATTTAAATTATTAAATTAAATT-A
1 AATTTAAATTATTAAATTAAATTCA
305026 AATTTAAA-T-TTAAACTTAAAATTCA
1 AATTTAAATTATTAAA-TT-AAATTCA
305051 AATTT
1 AATTT
305056 TAATAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 5 0.19
23 3 0.11
24 13 0.48
25 6 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
AATTTAAATTATTAAATTAAATTCA
Found at i:306711 original size:2 final size:2
Alignment explanation
Indices: 306706--306736 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
306696 TCTCACGTGC
306706 AT AT AT 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 AT AT AT A
306737 ACTATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:307666 original size:18 final size:17
Alignment explanation
Indices: 307625--307696 Score: 62
Period size: 16 Copynumber: 4.4 Consensus size: 17
307615 TTTTTTATAA
*
307625 TTATATTT-AATATATT
1 TTATATTTAAATAAATT
*
307641 ATATATTTAAATAAATT
1 TTATATTTAAATAAATT
*
307658 TTAATATTTTAAT-AA-T
1 TT-ATATTTAAATAAATT
*
307674 TTAT-TTTATATAAATT
1 TTATATTTAAATAAATT
307690 TTGATAT
1 TT-ATAT
307697 ATTATTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 5 0.11
15 4 0.09
16 13 0.30
17 12 0.27
18 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TTATATTTAAATAAATT
Found at i:307689 original size:32 final size:32
Alignment explanation
Indices: 307630--307714 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
307620 TATAATTATA
*
307630 TTTAATATATTATATATTTAAATAAATTTTAATAT
1 TTTAATA-ATT-TAT-TTTATATAAATTTTAATAT
*
307665 TTTAATAATTTATTTTATATAAATTTTGATAT
1 TTTAATAATTTATTTTATATAAATTTTAATAT
* * * *
307697 ATTATTTATTTATGTTAT
1 TTTAATAATTTATTTTAT
307715 GTTTATTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 31 0.70
33 3 0.07
34 3 0.07
35 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
TTTAATAATTTATTTTATATAAATTTTAATAT
Found at i:307740 original size:19 final size:19
Alignment explanation
Indices: 307718--307773 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
307708 ATGTTATGTT
307718 TATTTTATTTTTTATATTA
1 TATTTTATTTTTTATATTA
*
307737 TA--TTATATTTTA-ATTA
1 TATTTTATTTTTTATATTA
* *
307753 TTTTTTTATTATTTATATTA
1 -TATTTTATTTTTTATATTA
307773 T
1 T
307774 TGACATGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
16 4 0.14
17 10 0.34
19 11 0.38
20 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTATTTTTTATATTA
Found at i:308328 original size:46 final size:46
Alignment explanation
Indices: 308277--308405 Score: 121
Period size: 46 Copynumber: 2.8 Consensus size: 46
308267 ATATATTTTA
308277 TTATATGATAATTATATTTAAATTAT-TTATATATATATATAAATTT
1 TTATATGATAATTATATTTAAATTATATTATATATATATA-AAATTT
*
308323 TTATAT-ATTAA-TA-ATTTATATTATATTA-AT-T-T-TAAAATTT
1 TTATATGA-TAATTATATTTAAATTATATTATATATATATAAAATTT
* *
308363 TTATCTGTTCATATTATATTTATATATTATATTATATATATAT
1 TTATATGAT-A-ATTATATTTA-A-ATTATATTATATATATAT
308406 TTTAGTATTA
Statistics
Matches: 66, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
40 12 0.18
41 3 0.05
42 2 0.03
43 3 0.05
44 17 0.26
45 6 0.09
46 18 0.27
47 2 0.03
48 1 0.02
49 1 0.02
50 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (46 bp):
TTATATGATAATTATATTTAAATTATATTATATATATATAAAATTT
Found at i:308336 original size:18 final size:18
Alignment explanation
Indices: 308295--308352 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
308285 TAATTATATT
308295 TAAATTATTTATATATATATA
1 TAAATT-TTTATATAT-TA-A
308316 TAAATTTTTATATATTAA
1 TAAATTTTTATATATTAA
*
308334 T-AATTTATATTATATTAA
1 TAAATTTTTA-TATATTAA
308352 T
1 T
308353 TTTAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
17 7 0.20
18 11 0.31
19 2 0.06
20 9 0.26
21 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TAAATTTTTATATATTAA
Found at i:308389 original size:13 final size:13
Alignment explanation
Indices: 308373--308416 Score: 58
Period size: 12 Copynumber: 3.5 Consensus size: 13
308363 TTATCTGTTC
308373 ATATTATATTTAT
1 ATATTATATTTAT
308386 ATATTATA-TTAT
1 ATATTATATTTAT
308398 ATA-TATATTT-T
1 ATATTATATTTAT
308409 AGTATTAT
1 A-TATTAT
308417 GTAATCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.21
12 11 0.39
13 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
ATATTATATTTAT
Found at i:308655 original size:17 final size:17
Alignment explanation
Indices: 308633--308693 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 17
308623 GGTGCAGCCG
308633 AAAAAGAGAGAAAGAAA
1 AAAAAGAGAGAAAGAAA
308650 AAAAAGAAAGAGAAAAAAAGAAA
1 AAAAAG--AGAG----AAAGAAA
*
308673 AAAAAGAAAGAAAGAAA
1 AAAAAGAGAGAAAGAAA
308690 AAAA
1 AAAA
308694 TTTATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
17 17 0.46
19 4 0.11
21 3 0.08
23 13 0.35
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAGAAAGAAA
Found at i:308669 original size:23 final size:24
Alignment explanation
Indices: 308643--308693 Score: 86
Period size: 23 Copynumber: 2.1 Consensus size: 24
308633 AAAAAGAGAG
308643 AAAGAAAAAAAAGAAAG-AGAAAA
1 AAAGAAAAAAAAGAAAGAAGAAAA
308666 AAAGAAAAAAAAGAAAGAAAGAAAA
1 AAAGAAAAAAAAGAAAG-AAGAAAA
308691 AAA
1 AAA
308694 TTTATATCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.65
25 9 0.35
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (24 bp):
AAAGAAAAAAAAGAAAGAAGAAAA
Found at i:308820 original size:3 final size:3
Alignment explanation
Indices: 308814--308860 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
308804 AAAAAAAAGG
308814 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
308861 CTATCTATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 41 0.95
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:308922 original size:4 final size:4
Alignment explanation
Indices: 308913--308984 Score: 71
Period size: 4 Copynumber: 19.0 Consensus size: 4
308903 CTTTGGCTGG
* * * *
308913 GAAA GAAA GAAA GAAA GTAA GAAA -AAA AAAA GAAT GAAT GAAA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
*
308959 GAAA AAAA GAAA -AAA -AAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
308985 AAAATTATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
3 12 0.21
4 46 0.79
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (4 bp):
GAAA
Found at i:308934 original size:12 final size:12
Alignment explanation
Indices: 308913--308984 Score: 71
Period size: 11 Copynumber: 6.3 Consensus size: 12
308903 CTTTGGCTGG
308913 GAAAGAAAGAAA
1 GAAAGAAAGAAA
*
308925 GAAAGTAAGAAA
1 GAAAGAAAGAAA
* *
308937 -AAAAAAAGAAT
1 GAAAGAAAGAAA
*
308948 GAATGAAAG-AA
1 GAAAGAAAGAAA
*
308959 GAAAAAAAGAAA
1 GAAAGAAAGAAA
308971 -AAA-AAAGAAA
1 GAAAGAAAGAAA
308981 GAAA
1 GAAA
308985 AAAATTATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
10 7 0.15
11 22 0.46
12 19 0.40
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (12 bp):
GAAAGAAAGAAA
Found at i:308944 original size:23 final size:23
Alignment explanation
Indices: 308918--308988 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
308908 GCTGGGAAAG
*
308918 AAAGAAAGAAAGTAAGAAAAAAA
1 AAAGAAAGAAAGAAAGAAAAAAA
* * *
308941 AAAGAATGAATGAAAGAAGAAAA
1 AAAGAAAGAAAGAAAGAAAAAAA
308964 AAAGAAA-AAA-AAAGAAAGAAAA
1 AAAGAAAGAAAGAAAGAAA-AAAA
308986 AAA
1 AAA
308989 TTATATGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 6 0.15
22 9 0.22
23 25 0.62
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (23 bp):
AAAGAAAGAAAGAAAGAAAAAAA
Found at i:309751 original size:16 final size:16
Alignment explanation
Indices: 309712--309752 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
309702 TTTTTATTAA
309712 AAATAATTAAAAATAT
1 AAATAATTAAAAATAT
* *
309728 AAAAAATTAAAAATGT
1 AAATAATTAAAAATAT
*
309744 AATTAATTA
1 AAATAATTA
309753 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (16 bp):
AAATAATTAAAAATAT
Found at i:310521 original size:19 final size:18
Alignment explanation
Indices: 310497--310545 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 18
310487 TACTCAGGTG
310497 AAAAAGAAAAAAAGAAACA
1 AAAAAGAAAAAAAGAAA-A
*
310516 AAAAAGCAAAAAAGAAAA
1 AAAAAGAAAAAAAGAAAA
*
310534 AAAAGGAAAAAA
1 AAAAAGAAAAAA
310546 TTTATGTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.84, C:0.04, G:0.12, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAAAGAAAA
Found at i:310652 original size:14 final size:15
Alignment explanation
Indices: 310628--310669 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
310618 TTTATTTGAT
*
310628 TTTATTTTATATATA
1 TTTATTATATATATA
310643 TTT-TTATATATA-A
1 TTTATTATATATATA
*
310656 TTTATTTTATATAT
1 TTTATTATATATAT
310670 GGGAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTATATATATA
Found at i:311858 original size:22 final size:24
Alignment explanation
Indices: 311833--311876 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
311823 CGTGATGGAA
311833 AAGAAAG-A-AAAAAAAAGAAAGG
1 AAGAAAGAAGAAAAAAAAGAAAGG
311855 AAGAAAGAAGAAAAAAAAGAAA
1 AAGAAAGAAGAAAAAAAAGAAA
311877 AAAATTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (24 bp):
AAGAAAGAAGAAAAAAAAGAAAGG
Found at i:311943 original size:24 final size:25
Alignment explanation
Indices: 311916--311980 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 25
311906 TATTTGTATC
311916 TATATTTTTTTATA-CTTAAAATAT
1 TATATTTTTTTATATCTTAAAATAT
* * *
311940 TATATTTTTATATATTTTAACATAT
1 TATATTTTTTTATATCTTAAAATAT
311965 TAATAATTTATTTTAT
1 T-AT-ATTT-TTTTAT
311981 TTTATGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 13 0.39
25 9 0.27
26 2 0.06
27 4 0.12
28 5 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (25 bp):
TATATTTTTTTATATCTTAAAATAT
Found at i:320564 original size:2 final size:2
Alignment explanation
Indices: 320559--320598 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
320549 AAAAAGAAAT
320559 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA
320599 AATGGAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:321313 original size:25 final size:24
Alignment explanation
Indices: 321283--321345 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
321273 ATAAATAAAT
**
321283 AATATTTTATTTAAATCAAAATTTA
1 AATATTTTATAAAAAT-AAAATTTA
*
321308 AATATTATTATAAAAATAAATTTTA
1 AATATT-TTATAAAAATAAAATTTA
321333 ATATTATTTTATA
1 A-A-TATTTTATA
321346 TAATAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 14 0.44
26 14 0.44
27 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
AATATTTTATAAAAATAAAATTTA
Done.