Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold212
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: 1080337
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 10
Found at i:321428 original size:4 final size:4
Alignment explanation
Indices: 321419--321446 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
321409 CAACTGCACT
321419 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
321447 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:321451 original size:2 final size:2
Alignment explanation
Indices: 321444--321492 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
321434 ACATACATAC
*
321444 AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT GA- 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
321486 AT AT AT A
1 AT AT AT A
321493 AATGTACGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:323694 original size:18 final size:18
Alignment explanation
Indices: 323662--323708 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
323652 ATGTTTTCGT
323662 ATTATTTATAAATAAATTA
1 ATTATTTA-AAATAAATTA
323681 ATTATTTAAAATAAATTA
1 ATTATTTAAAATAAATTA
*
323699 ATTTTTTAAA
1 ATTATTTAAA
323709 CAACTATGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTATTTAAAATAAATTA
Found at i:323845 original size:16 final size:17
Alignment explanation
Indices: 323811--323845 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
323801 AAATATGAAC
323811 TTAATTTTATCTAAAAT
1 TTAATTTTATCTAAAAT
*
323828 TTAATTTT-TCTTAAAT
1 TTAATTTTATCTAAAAT
323844 TT
1 TT
323846 TGAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (17 bp):
TTAATTTTATCTAAAAT
Found at i:324559 original size:2 final size:2
Alignment explanation
Indices: 324554--324586 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
324544 AGCTCTCTTT
*
324554 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
324587 TCAACATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:326161 original size:2 final size:2
Alignment explanation
Indices: 326154--326185 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
326144 CGACCAGAAA
*
326154 AT AT AT AT AT CT 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
326186 TCAACTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:327857 original size:9 final size:9
Alignment explanation
Indices: 327836--327875 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
327826 AATATAAACT
327836 TTTTAAAATA
1 TTTTAAAA-A
327846 TTTTAAAAA
1 TTTTAAAAA
327855 TTTATAAAAA
1 TTT-TAAAAA
*
327865 TTTAAAAAA
1 TTTTAAAAA
327874 TT
1 TT
327876 AAGTATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 11 0.39
10 17 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:330323 original size:2 final size:2
Alignment explanation
Indices: 330316--330348 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
330306 CATCAACATC
330316 AT 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 AT A
330349 CCATTTCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:331565 original size:17 final size:15
Alignment explanation
Indices: 331521--331579 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
331511 TATATTATTC
*
331521 AAATTTATTTAA-AT
1 AAATATATTTAATAT
* *
331535 AAAAATATTAAATAT
1 AAATATATTTAATAT
331550 AAATACGTATTTAATAT
1 AAATA--TATTTAATAT
331567 AAATATATTTAAT
1 AAATATATTTAAT
331580 TTTTTATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
14 9 0.24
15 14 0.38
17 14 0.38
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AAATATATTTAATAT
Found at i:332080 original size:98 final size:98
Alignment explanation
Indices: 331911--332106 Score: 329
Period size: 98 Copynumber: 2.0 Consensus size: 98
331901 CGACCCAAGC
* * *
331911 TTGTTATCTTCATGTAAGATCAACTCAAAGGCAACTTGCACTGGTTCTTTTATGAGCAGATTTTG
1 TTGTTATCTTCACGTAAGATCAACTCAAAGGCAAATTGCAATGGTTCTTTTATGAGCAGATTTTG
331976 GTAAAATAGCAATCATGTCAAAGCCAATTGCTT
66 GTAAAATAGCAATCATGTCAAAGCCAATTGCTT
* *
332009 TTGTTATCTTCACGTAAGATCAACTCAAGGGCAAATTGCAATTGTTCTTTTATGAGCAGATTTTG
1 TTGTTATCTTCACGTAAGATCAACTCAAAGGCAAATTGCAATGGTTCTTTTATGAGCAGATTTTG
* *
332074 GTAAAATGGCAGTCATGTCAAAGCCAATTGCTT
66 GTAAAATAGCAATCATGTCAAAGCCAATTGCTT
332107 GCTAGCTGTG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (98 bp):
TTGTTATCTTCACGTAAGATCAACTCAAAGGCAAATTGCAATGGTTCTTTTATGAGCAGATTTTG
GTAAAATAGCAATCATGTCAAAGCCAATTGCTT
Found at i:332592 original size:24 final size:22
Alignment explanation
Indices: 332542--332592 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 22
332532 CCACTTACGC
332542 TTATAATATTTAAATTTAAATTT
1 TTATAATATTTAAATTT-AATTT
332565 TTATAAATATTTTAAATTT-ATTT
1 TTAT-AATA-TTTAAATTTAATTT
332588 ATTAT
1 -TTAT
332593 TCACATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 8 0.32
24 8 0.32
25 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TTATAATATTTAAATTTAATTT
Found at i:332603 original size:31 final size:30
Alignment explanation
Indices: 332568--332665 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 30
332558 TAAATTTTTA
* *
332568 TAAATATTTTAAATTTATTTATTATTCACAT
1 TAAATATTTTAAATTTATTTA-AATTCAAAT
* *
332599 TAAAT-TTATAAATTATTATTTAAATTTAAAT
1 TAAATATTTTAAA-T-TTATTTAAATTCAAAT
* *
332630 TAAATA-TTTAAATTCATTAAAAATTCAAAT
1 TAAATATTTTAAATTTATT-TAAATTCAAAT
*
332660 TCAATA
1 TAAATA
332666 CTTAATTAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
29 4 0.07
30 21 0.39
31 22 0.41
32 7 0.13
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAATATTTTAAATTTATTTAAATTCAAAT
Found at i:332650 original size:17 final size:17
Alignment explanation
Indices: 332628--332662 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
332618 TTAAATTTAA
* *
332628 ATTAAATATTTAAATTC
1 ATTAAAAATTCAAATTC
332645 ATTAAAAATTCAAATTC
1 ATTAAAAATTCAAATTC
332662 A
1 A
332663 ATACTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTAAAAATTCAAATTC
Found at i:334265 original size:20 final size:20
Alignment explanation
Indices: 334228--334266 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
334218 CTAAGGTTGA
* *
334228 TTATAATAATATTTAATATT
1 TTATAATAATAATAAATATT
*
334248 TTATAATTATAATAAATAT
1 TTATAATAATAATAAATAT
334267 ATAATATGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATAATAATAATAAATATT
Found at i:334269 original size:17 final size:18
Alignment explanation
Indices: 334249--334291 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
334239 TTTAATATTT
334249 TATAATTATAAT-AAATA
1 TATAATTATAATAAAATA
*
334266 TATAA-TATGATAAAATA
1 TATAATTATAATAAAATA
*
334283 TATATTTAT
1 TATAATTAT
334292 GATCGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TATAATTATAATAAAATA
Found at i:334969 original size:7 final size:7
Alignment explanation
Indices: 334957--334983 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
334947 TGTTCTGAAA
334957 AAAAAAT
1 AAAAAAT
334964 AAAAAAT
1 AAAAAAT
334971 AAAAAAT
1 AAAAAAT
334978 AAAAAA
1 AAAAAA
334984 GGGGGCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:336101 original size:14 final size:14
Alignment explanation
Indices: 336082--336115 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
336072 TATTTAATAT
336082 TTAAAAATATTAAA
1 TTAAAAATATTAAA
336096 TT-AAAATATTAAA
1 TTAAAAATATTAAA
336109 TTAAAAA
1 TTAAAAA
336116 ATAAATTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAAAATATTAAA
Found at i:336133 original size:25 final size:27
Alignment explanation
Indices: 336082--336134 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
336072 TATTTAATAT
*
336082 TTAAAAATATTAAATTAAAATATTAAA
1 TTAAAAATATTAAATTAAAATAATAAA
* *
336109 TTAAAAA-A-TAAATTTAGATAATAAA
1 TTAAAAATATTAAATTAAAATAATAAA
336134 T
1 T
336135 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 1 0.04
27 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TTAAAAATATTAAATTAAAATAATAAA
Found at i:336905 original size:22 final size:23
Alignment explanation
Indices: 336840--336970 Score: 88
Period size: 28 Copynumber: 5.3 Consensus size: 23
336830 CTCATAAAAA
* * *
336840 AATATAATATAATATAATTATAT
1 AATATATTAAAATATAAATATAT
336863 GAATATATTAAAATTTTTATAAATATAT
1 -AATATATTAAAA----TATAAATATAT
*
336891 AATA-ATTTAAATAT-AAT-TAT
1 AATATATTAAAATATAAATATAT
*
336911 AATATATTAAAATAAAATATATAT
1 AATATATTAAAATATAA-ATATAT
336935 ATATATATATAAAAGATATAAATATAAT
1 A-ATATAT-T-AAA-ATATAAATAT-AT
*
336963 AAAATATT
1 AATATATT
336971 TCATTTAAGA
Statistics
Matches: 86, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
20 7 0.08
21 11 0.13
22 4 0.05
23 2 0.02
24 14 0.16
25 6 0.07
26 8 0.09
27 16 0.19
28 18 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
AATATATTAAAATATAAATATAT
Found at i:336931 original size:20 final size:20
Alignment explanation
Indices: 336881--336938 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
336871 TAAAATTTTT
*
336881 ATAAATATATAATA-ATTTAA
1 ATAAA-ATATAATATATTAAA
*
336901 ATATAATTATAATATATTAAA
1 ATA-AAATATAATATATTAAA
336922 ATAAAATATATATATAT
1 ATAAAATATA-ATATAT
336939 ATATATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAAAATATAATATATTAAA
Found at i:336936 original size:21 final size:21
Alignment explanation
Indices: 336883--336938 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
336873 AAATTTTTAT
*
336883 AAATATATA-ATAATTTAAATA
1 AAATATATATAT-ATTAAAATA
*
336904 TAAT-TATAATATATTAAAATA
1 AAATATAT-ATATATTAAAATA
336925 AAATATATATATAT
1 AAATATATATATAT
336939 ATATATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 3 0.10
21 21 0.72
22 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATATATATATTAAAATA
Found at i:336946 original size:21 final size:18
Alignment explanation
Indices: 336833--336969 Score: 83
Period size: 19 Copynumber: 7.7 Consensus size: 18
336823 ATACAAACTC
336833 ATAA-AAAA-ATAT-AAT
1 ATAATAAAATATATAAAT
* *
336848 ATAATATAATTATATGAAT
1 ATAATA-AAATATATAAAT
* *
336867 ATATTAAAATTTTTATAAAT
1 ATAATAAAA--TATATAAAT
336887 AT-ATAATAAT-T-TAAAT
1 ATAATAA-AATATATAAAT
*
336903 ATAATTATAATATATTAAA-
1 ATAA-TAAAATATA-TAAAT
* *
336922 ATAA-AATATATATATAT
1 ATAATAAAATATATAAAT
*
336939 ATATATAAAAGATATAAAT
1 ATA-ATAAAATATATAAAT
336958 ATAATAAAATAT
1 ATAATAAAATAT
336970 TTCATTTAAG
Statistics
Matches: 93, Mismatches: 14, Indels: 27
0.69 0.10 0.20
Matches are distributed among these distances:
15 4 0.04
16 11 0.12
17 16 0.17
18 19 0.20
19 28 0.30
20 15 0.16
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAATAAAATATATAAAT
Found at i:336969 original size:25 final size:26
Alignment explanation
Indices: 336884--336969 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
336874 AATTTTTATA
* *
336884 AATATATAATAATTTAAATATAATTAT
1 AATATATAAAAATATAAATATAA-TAT
*
336911 AATATATTAAAATA-AAATATATATAT
1 AATATATAAAAATATAAATATA-ATAT
*
336937 ATATATATAAAAGATATAAATATAATAA
1 A-ATATATAAAA-ATATAAATATAATAT
336965 AATAT
1 AATAT
336970 TTCATTTAAG
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
26 11 0.22
27 25 0.50
28 7 0.14
29 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (26 bp):
AATATATAAAAATATAAATATAATAT
Found at i:337079 original size:6 final size:6
Alignment explanation
Indices: 337068--337105 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
337058 AAAGCGATTT
*
337068 GGGTCA GGGTCA GGGTCA GGGTCA GGGTCA AGGTCA GG
1 GGGTCA GGGTCA GGGTCA GGGTCA GGGTCA GGGTCA GG
337106 CTGGTGATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.18, C:0.16, G:0.50, T:0.16
Consensus pattern (6 bp):
GGGTCA
Found at i:337229 original size:14 final size:14
Alignment explanation
Indices: 337210--337246 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
337200 TTTTTTAAAA
337210 AAATTAATATATTT
1 AAATTAATATATTT
337224 AAATTAAT-TATTT
1 AAATTAATATATTT
*
337237 -TATTAATATA
1 AAATTAATATA
337247 ATATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 7 0.33
14 8 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTAATATATTT
Found at i:337648 original size:2 final size:2
Alignment explanation
Indices: 337641--337670 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
337631 TTAGAGCAGC
337641 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
337671 TCATTCTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338020 original size:43 final size:39
Alignment explanation
Indices: 337923--338057 Score: 96
Period size: 41 Copynumber: 3.3 Consensus size: 39
337913 AATTTTTATA
* * *
337923 TAAATAATAAATTTTTATTTTTATTTAATTTTTTAATAAAT
1 TAAATAATATA-TATTA-TTTTATTTAATATTTTAATAAAT
* *
337964 TAAATTATTTATATTAATTTTATTTAATAATTTTAATAAAATAT
1 TAAATAATATATATT-ATTTTATTTAAT-ATTTTAAT--AA-AT
*
338008 TAAA-AATATATATTATTATTA-TTAAT-TTTTACATATTAT
1 TAAATAATATATATTATT-TTATTTAATATTTTA-ATA-AAT
338047 TAAAATAATAT
1 T-AAATAATAT
338058 TTAATAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
39 4 0.05
40 22 0.29
41 23 0.30
42 8 0.11
43 13 0.17
44 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (39 bp):
TAAATAATATATATTATTTTATTTAATATTTTAATAAAT
Found at i:341239 original size:30 final size:32
Alignment explanation
Indices: 341191--341251 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
341181 TAAAATAAAA
*
341191 ATATGATAAAAATAATTAAAATATAATATAAT
1 ATATGATAAAAATAATTAAAAAATAATATAAT
* *
341223 ATATGAT-ATAAT-ATTAAAAAATTATATAA
1 ATATGATAAAAATAATTAAAAAATAATATAA
341252 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 4 0.15
32 7 0.27
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (32 bp):
ATATGATAAAAATAATTAAAAAATAATATAAT
Found at i:341283 original size:26 final size:27
Alignment explanation
Indices: 341240--341290 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
341230 ATAATATTAA
341240 AAAATTATATAAAAATAAAAATATTTT
1 AAAATTATATAAAAATAAAAATATTTT
* *
341267 AAAATT-TATATAAATAAAATTATT
1 AAAATTATATAAAAATAAAAATATT
341291 AATATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAAATTATATAAAAATAAAAATATTTT
Found at i:341876 original size:2 final size:2
Alignment explanation
Indices: 341869--341896 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
341859 ATCTATAATT
341869 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
341897 ATGGATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:343334 original size:21 final size:21
Alignment explanation
Indices: 343300--343379 Score: 82
Period size: 20 Copynumber: 4.0 Consensus size: 21
343290 TATTTTTATT
343300 TAAAT-TTAATTATAAAATAAA
1 TAAATATTAA-TATAAAATAAA
343321 TAAATATTAATATAAAATAAA
1 TAAATATTAATATAAAATAAA
*
343342 -AAATTTTAAT-TATAAAT-AA
1 TAAATATTAATATA-AAATAAA
*
343361 TAAATA-TAA-ATAATATAAA
1 TAAATATTAATATAAAATAAA
343380 CGGATAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.06
19 11 0.22
20 17 0.33
21 16 0.31
22 4 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATATTAATATAAAATAAA
Found at i:343358 original size:20 final size:21
Alignment explanation
Indices: 343304--343365 Score: 83
Period size: 20 Copynumber: 3.0 Consensus size: 21
343294 TTTATTTAAA
343304 TTTAATTATAAAATAAATAAAT
1 TTTAATTATAAAATAAA-AAAT
*
343326 ATTAA-TATAAAATAAAAAAT
1 TTTAATTATAAAATAAAAAAT
*
343346 TTTAATTAT-AAATAATAAAT
1 TTTAATTATAAAATAAAAAAT
343366 ATAAATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 18 0.50
21 14 0.39
22 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTAATTATAAAATAAAAAAT
Found at i:343389 original size:46 final size:42
Alignment explanation
Indices: 343304--343379 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 42
343294 TTTATTTAAA
343304 TTTAATTATAAAATAAATAAATATTAATATAAAATAAAAAAT
1 TTTAATTATAAAATAAATAAATATTAATATAAAATAAAAAAT
*
343346 TTTAATTAT-AAAT-AATAAATA-TAA-ATAATATAAA
1 TTTAATTATAAAATAAATAAATATTAATATAAAATAAA
343380 CGGATAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
38 9 0.27
39 3 0.09
40 8 0.24
41 4 0.12
42 9 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (42 bp):
TTTAATTATAAAATAAATAAATATTAATATAAAATAAAAAAT
Found at i:344217 original size:28 final size:30
Alignment explanation
Indices: 344186--344253 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 30
344176 TTTCATACAC
* *
344186 ATATTCAAATAT-ATTATATT-AAACATAA
1 ATATTCAAATATAAATATATTAAAAAATAA
* *
344214 ATA-TCGAATATAAATATTTTAAAAAATAA
1 ATATTCAAATATAAATATATTAAAAAATAA
*
344243 AAATTCAAATA
1 ATATTCAAATA
344254 ACATGCCTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
27 7 0.23
28 9 0.29
29 9 0.29
30 6 0.19
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.35
Consensus pattern (30 bp):
ATATTCAAATATAAATATATTAAAAAATAA
Found at i:346678 original size:18 final size:17
Alignment explanation
Indices: 346637--346680 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
346627 ATTTAAATAA
* *
346637 AAATAAATTTTTTATTT
1 AAATTAATTTTTTAGTT
346654 AAA-TAATTTTTTGAGTT
1 AAATTAATTTTTT-AGTT
346671 AAATTAATTT
1 AAATTAATTT
346681 AAATTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 8 0.35
17 9 0.39
18 6 0.26
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
AAATTAATTTTTTAGTT
Found at i:350351 original size:24 final size:24
Alignment explanation
Indices: 350310--350366 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
350300 ACGTGACTTG
**
350310 TCATAAAAATAACTGTAA-ATTTA
1 TCATAAAAATAAAAGTAATATTTA
* *
350333 TCATAAATAATAAAAGTAATTTTTT
1 TCATAAA-AATAAAAGTAATATTTA
350358 TCATAAAAA
1 TCATAAAAA
350367 ATATGCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 7 0.25
24 11 0.39
25 10 0.36
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.37
Consensus pattern (24 bp):
TCATAAAAATAAAAGTAATATTTA
Found at i:351235 original size:2 final size:2
Alignment explanation
Indices: 351228--351257 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
351218 AGTACATGAT
351228 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
351258 CAAAATAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:355371 original size:17 final size:17
Alignment explanation
Indices: 355325--355372 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
355315 AAAACTGCAT
355325 ATATATATATAATATTA
1 ATATATATATAATATTA
*
355342 ATA-AGTATATAATTTTA
1 ATATA-TATATAATATTA
*
355359 ATATATATCTAATA
1 ATATATATATAATA
355373 AATATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 1 0.04
17 24 0.92
18 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATATATATAATATTA
Found at i:355410 original size:19 final size:20
Alignment explanation
Indices: 355386--355430 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 20
355376 ATTAAAAATA
355386 TAAAAATATAAAATA-T-TTT
1 TAAAAA-ATAAAATAGTATTT
355405 T-AAAAATAAAATAGTATTT
1 TAAAAAATAAAATAGTATTT
355424 TAAAAAA
1 TAAAAAA
355431 AACGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 5 0.22
19 5 0.22
20 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAAAATAAAATAGTATTT
Found at i:355413 original size:17 final size:19
Alignment explanation
Indices: 355388--355429 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
355378 TAAAAATATA
355388 AAAATATAAAATA-T-TTTT
1 AAAA-ATAAAATAGTATTTT
355406 AAAAATAAAATAGTATTTT
1 AAAAATAAAATAGTATTTT
355425 AAAAA
1 AAAAA
355430 AAACGGTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 5 0.23
19 9 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATAAAATAGTATTTT
Found at i:355916 original size:8 final size:9
Alignment explanation
Indices: 355895--355920 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
355885 AATTTAAATA
355895 AAAAATTTT
1 AAAAATTTT
355904 AAAAATTTT
1 AAAAATTTT
355913 AAAAATTT
1 AAAAATTT
355921 CTACACGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AAAAATTTT
Found at i:356624 original size:25 final size:27
Alignment explanation
Indices: 356570--356633 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
356560 TGTATTAAAA
* *
356570 AATATATATT-TTTAATTTTTTATTTAT
1 AATATAT-TTATTTAAATTATTATTTAT
356597 AATATATTTATTTAAATTATT-TTT-T
1 AATATATTTATTTAAATTATTATTTAT
*
356622 AATAAATTTATT
1 AATATATTTATT
356634 AATTAAATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
25 12 0.36
26 5 0.15
27 16 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
AATATATTTATTTAAATTATTATTTAT
Found at i:356993 original size:10 final size:9
Alignment explanation
Indices: 356955--357017 Score: 51
Period size: 8 Copynumber: 6.9 Consensus size: 9
356945 GAATGAAAAT
*
356955 AAATAATTA
1 AAATAATAA
*
356964 ATATAA-AA
1 AAATAATAA
356972 TAAA-AATAA
1 -AAATAATAA
356981 AAATAATTAA
1 AAATAA-TAA
356991 AAATTACATAA
1 AAA-TA-ATAA
357002 AAAT-ATAA
1 AAATAATAA
357010 AAATAATA
1 AAATAATA
357018 TGATATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
8 14 0.32
9 14 0.32
10 7 0.16
11 8 0.18
12 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAATAATAA
Found at i:357314 original size:12 final size:12
Alignment explanation
Indices: 357299--357339 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
357289 ATCTATATTG
357299 ATATTTAATTAT
1 ATATTTAATTAT
357311 ATATTTAATTAT
1 ATATTTAATTAT
357323 -TATTTAATTAT
1 ATATTTAATTAT
357334 ATATTT
1 ATATTT
357340 TTATTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTTAATTAT
Found at i:357326 original size:23 final size:23
Alignment explanation
Indices: 357300--357362 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
357290 TCTATATTGA
357300 TATTTAATTATATATTTAATTAT
1 TATTTAATTATATATTTAATTAT
357323 TATTTAATTATATATTT--TTAT
1 TATTTAATTATATATTTAATTAT
*
357344 T-TGTTAAATATA-ATTTAAT
1 TAT-TTAATTATATATTTAAT
357363 AAATTTTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 5 0.14
21 13 0.36
22 1 0.03
23 17 0.47
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TATTTAATTATATATTTAATTAT
Found at i:357373 original size:18 final size:17
Alignment explanation
Indices: 357356--357422 Score: 55
Period size: 18 Copynumber: 3.8 Consensus size: 17
357346 GTTAAATATA
357356 ATTTAATAAATTTTTAT
1 ATTTAATAAATTTTTAT
* **
357373 ATTTAAACAAATTTAAAT
1 ATTT-AATAAATTTTTAT
*
357391 ATTTAACTAATATTTTTTAA
1 ATTTAA-TAA-A-TTTTTAT
357411 ATTTAA-AAATTT
1 ATTTAATAAATTT
357423 AAATAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
16 3 0.08
17 7 0.18
18 18 0.46
19 1 0.03
20 10 0.26
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAATAAATTTTTAT
Found at i:357439 original size:36 final size:38
Alignment explanation
Indices: 357366--357457 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 38
357356 ATTTAATAAA
* * *
357366 TTTTTATATTTAAACAAATTTAAATATTTAACTAATAT
1 TTTTTAAATTTAAACAAATTTAAATATATAAATAATAT
357404 TTTTTAAATTT-AA-AAATTTAAATA-ATAAATAA-AT
1 TTTTTAAATTTAAACAAATTTAAATATATAAATAATAT
* *
357438 ATTTAAATATTTAAA-AAATT
1 TTTTTAA-ATTTAAACAAATT
357458 GCGGATTTCC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
34 7 0.15
35 10 0.21
36 18 0.38
37 2 0.04
38 10 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (38 bp):
TTTTTAAATTTAAACAAATTTAAATATATAAATAATAT
Found at i:359582 original size:81 final size:81
Alignment explanation
Indices: 359447--359609 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
359437 GTACCGAGAT
359447 TCAACCATCTCTCCTACGTATGCCTTTATCATATATATTGTCCTTTTTGGGTACTTACAGTTCCT
1 TCAACCATCTCTCCTACGTATGCCTTTATCATATATATTGTCCTTTTTGGGTACTTACAGTTCCT
359512 GCAAGGTTTTATCACC
66 GCAAGGTTTTATCACC
359528 TCAACCATCTCTCCTACGTATGCCTTTATCATATATATTGTCCTTTTTGGGTACTTACAGTTCCT
1 TCAACCATCTCTCCTACGTATGCCTTTATCATATATATTGTCCTTTTTGGGTACTTACAGTTCCT
359593 GCAAGGTTTTATCACC
66 GCAAGGTTTTATCACC
359609 T
1 T
359610 GTAGGTGCTC
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (81 bp):
TCAACCATCTCTCCTACGTATGCCTTTATCATATATATTGTCCTTTTTGGGTACTTACAGTTCCT
GCAAGGTTTTATCACC
Found at i:361865 original size:11 final size:11
Alignment explanation
Indices: 361851--361906 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
361841 TTTTAAAATT
361851 TTTTATTTAAA
1 TTTTATTTAAA
*
361862 TTTTAATTAAA
1 TTTTATTTAAA
*
361873 TTTAATTT-AA
1 TTTTATTTAAA
361883 TTTTAAATTTTAAA
1 TTTT--A-TTTAAA
361897 TTATTATTTA
1 TT-TTATTTA
361907 TAAATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
10 5 0.14
11 16 0.44
12 5 0.14
13 4 0.11
14 4 0.11
15 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTATTTAAA
Found at i:363752 original size:22 final size:22
Alignment explanation
Indices: 363727--363782 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
363717 AGATATGTTC
363727 ACCTAAAACACCTAATATATTT
1 ACCTAAAACACCTAATATATTT
* *
363749 ACCTAACACACCTAATATGTTT
1 ACCTAAAACACCTAATATATTT
*
363771 ACCTAATACACC
1 ACCTAAAACACC
363783 ACCTAACACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.41, C:0.29, G:0.02, T:0.29
Consensus pattern (22 bp):
ACCTAAAACACCTAATATATTT
Found at i:363875 original size:23 final size:23
Alignment explanation
Indices: 363822--363882 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
363812 AACATATCAT
* *
363822 CTAACATACCTAAT-ATATTTAT
1 CTAACACACCTAATAATATTTAC
* * *
363844 TTAATACACCTAATAATGTTTAC
1 CTAACACACCTAATAATATTTAC
*
363867 CTAACACACTTAATAA
1 CTAACACACCTAATAA
363883 AGATATTAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.36
Consensus pattern (23 bp):
CTAACACACCTAATAATATTTAC
Found at i:364634 original size:19 final size:19
Alignment explanation
Indices: 364610--364677 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
364600 AATTCAACGA
364610 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
364629 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
364644 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
364661 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
364678 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:364648 original size:32 final size:32
Alignment explanation
Indices: 364612--364674 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
364602 TTCAACGATT
*
364612 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
364644 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
364675 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:364649 original size:13 final size:13
Alignment explanation
Indices: 364631--364655 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364621 ACATAAGTTT
364631 TGTATCGATACAA
1 TGTATCGATACAA
364644 TGTATCGATACA
1 TGTATCGATACA
364656 TAAGTATTGT
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:364735 original size:13 final size:13
Alignment explanation
Indices: 364717--364742 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
364707 CATTTTTCTG
364717 TGTATCGATACAT
1 TGTATCGATACAT
364730 TGTATCGATACAT
1 TGTATCGATACAT
364743 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:364739 original size:33 final size:33
Alignment explanation
Indices: 364697--364763 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
364687 ACCAAGGAAA
***
364697 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
364730 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
364763 T
1 T
364764 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:367293 original size:28 final size:27
Alignment explanation
Indices: 367226--367294 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
367216 CTTCACAATC
*
367226 GGGGATACTCCAACCCCATTAATCATC
1 GGGGATACTCCAACCCCATTAATCATA
* *
367253 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCATTA-ATCAT-A
367281 GGGGATACTCCAAC
1 GGGGATACTCCAAC
367295 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCATTAATCATA
Found at i:367366 original size:52 final size:53
Alignment explanation
Indices: 367281--367450 Score: 190
Period size: 52 Copynumber: 3.3 Consensus size: 53
367271 TTATTTCTGA
* *
367281 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTC-CAAAAACACCAATTTTTCCACAATC
* **
367333 GGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATTTCCAAAAACACCAATTTTTCC-ACAATC
* *
367385 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
* *
367437 GAGGATGCTCCAAC
1 GGGGATACTCCAAC
367451 CTCGTTATTT
Statistics
Matches: 100, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
51 9 0.09
52 72 0.72
53 14 0.14
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACCAATTTTTCCACAATC
Found at i:367497 original size:212 final size:212
Alignment explanation
Indices: 367110--367517 Score: 597
Period size: 212 Copynumber: 1.9 Consensus size: 212
367100 TTATCAATTC
* *
367110 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
367175 TACTCTAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAAC
66 TACTCCAACTCCGATTTTATTTCC--AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * *
367240 CCCATTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACTCCGGTTTTA
129 CCCATTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
367305 TCGCTAAAACACTAATTTT
194 TCGCTAAAACACTAATTTT
* * *
367324 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
367388 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATGCTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * * *
367451 CTCGTTATTTCATCGGGGATACTCCAATCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCATTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
367516 AT
193 AT
367518 TCCCAAAATA
Statistics
Matches: 174, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
211 26 0.15
212 66 0.38
213 3 0.02
214 44 0.25
215 35 0.20
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CATTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:367577 original size:107 final size:107
Alignment explanation
Indices: 367170--367589 Score: 273
Period size: 107 Copynumber: 3.9 Consensus size: 107
367160 TTCTATAATC
* * * * *
367170 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGATACT
1 GGGGATACTCCAACCCCGACTTTATTTCC---AAAAATACCAATTTC-TCACAATCGAGGATACT
* * * * * *
367235 CCAACCCCATTAATCATCGGGGATACTCCAACCCCGTTATTTCTGA
62 CCAACCCCGTTATTTATCGGGGATACTCCAATCCCGTTACTTCCGA
* * * * * * * *
367281 GGGGATACTCCAACTCCG-GTTT-TATCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCCGACTTTATTTC-CAAAAATACCAATTTCT-CACAATCGAGGATACTCC
* * * ***** * * * * *
367344 AATCCTGGT-TTTATTTTCAAAACACCAATTTTCCTTTA-AT-C--
64 AACCCCGTTATTTATCGGGGATACTCCAA--TCCCGTTACTTCCGA
* * * *
367385 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATGCTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
*
367450 CCTCGTTATTTCATCGGGGATACTCCAATCCCGTTACTTCCGA
66 CCCCGTTATTT-ATCGGGGATACTCCAATCCCGTTACTTCCGA
* * *** * * *
367493 GGGGATACTCCAACCCCGGCTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
367557 CCCCGTTATTT-TCGAAGGGATACTCCAATCCCG
66 CCCCGTTATTTATCG--GGGATACTCCAATCCCG
367590 ATTTTTTTTT
Statistics
Matches: 237, Mismatches: 58, Indels: 32
0.72 0.18 0.10
Matches are distributed among these distances:
104 45 0.19
105 24 0.10
106 24 0.10
107 94 0.40
108 26 0.11
109 3 0.01
110 4 0.02
111 17 0.07
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCACAATCGAGGATACTCCAA
CCCCGTTATTTATCGGGGATACTCCAATCCCGTTACTTCCGA
Found at i:367635 original size:80 final size:79
Alignment explanation
Indices: 367464--367667 Score: 214
Period size: 80 Copynumber: 2.6 Consensus size: 79
367454 GTTATTTCAT
* * * *
367464 CGGGGATACTCCAATCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
* * *
367529 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * ** * ** *
367543 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTC-TAATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG-GCTTTATTCCCAAAAT-
367607 ATCGATTTCTCACAAC
64 ATCGATTTCTCACAAC
* *
367623 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
367668 TGTTATTATC
Statistics
Matches: 103, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
79 49 0.48
80 54 0.52
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:379896 original size:13 final size:12
Alignment explanation
Indices: 379878--379934 Score: 71
Period size: 12 Copynumber: 4.7 Consensus size: 12
379868 CATTCTCTTC
*
379878 AAAAAAAAAGCA
1 AAAAAAAAAACA
379890 AAAAAAAAAA-A
1 AAAAAAAAAACA
379901 GAAAAAAAAAACA
1 -AAAAAAAAAACA
379914 AAAAAACAAAACA
1 AAAAAA-AAAACA
*
379927 AAGAAAAA
1 AAAAAAAA
379935 GAGAGAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
11 1 0.03
12 27 0.68
13 12 0.30
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:379897 original size:14 final size:13
Alignment explanation
Indices: 379878--379950 Score: 76
Period size: 14 Copynumber: 5.2 Consensus size: 13
379868 CATTCTCTTC
379878 AAAAAAAAAGCAAA
1 AAAAAAAAAG-AAA
379892 AAAAAAAAAGAAA
1 AAAAAAAAAGAAA
379905 AAAAAAACAA-AAA
1 AAAAAAA-AAGAAA
379918 AACAAAACAAAGAAA
1 AA-AAAA-AAAGAAA
*
379933 AAGAGAGAAAAGAAA
1 AA-A-AAAAAAGAAA
379948 AAA
1 AAA
379951 CCTACTTAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 15 0.29
14 19 0.37
15 16 0.31
16 2 0.04
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:379905 original size:24 final size:24
Alignment explanation
Indices: 379877--379935 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
379867 ACATTCTCTT
379877 CAAAAAAAAAGCAAAAAAAAAAAA
1 CAAAAAAAAAGCAAAAAAAAAAAA
* * *
379901 GAAAAAAAAAACAAAAAAACAAAA
1 CAAAAAAAAAGCAAAAAAAAAAAA
*
379925 CAAAGAAAAAG
1 CAAAAAAAAAG
379936 AGAGAAAAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.85, C:0.08, G:0.07, T:0.00
Consensus pattern (24 bp):
CAAAAAAAAAGCAAAAAAAAAAAA
Found at i:379908 original size:8 final size:8
Alignment explanation
Indices: 379880--379950 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
379870 TTCTCTTCAA
379880 AAAAAAAG
1 AAAAAAAG
379888 CAAAAAAA-
1 -AAAAAAAG
*
379896 AAAAAGAAA
1 AAAAA-AAG
*
379905 AAAAAAAC
1 AAAAAAAG
*
379913 AAAAAAAC
1 AAAAAAAG
379921 AAAACAAAG
1 AAAA-AAAG
*
379930 AAAAAGAG
1 AAAAAAAG
*
379938 -AGAAAAG
1 AAAAAAAG
379945 AAAAAA
1 AAAAAA
379951 CCTACTTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
7 10 0.19
8 23 0.44
9 19 0.37
ACGTcount: A:0.85, C:0.06, G:0.10, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:379950 original size:1 final size:1
Alignment explanation
Indices: 379878--379934 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
379868 CATTCTCTTC
** * * * * *
379878 AAAAAAAAAGCAAAAAAAAAAAAGAAAAAAAAAACAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
379935 GAGAGAAAAG
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:380994 original size:55 final size:55
Alignment explanation
Indices: 380910--381205 Score: 515
Period size: 55 Copynumber: 5.4 Consensus size: 55
380900 TCCGCTTTTT
380910 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
380965 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* ** *
381020 AGTCCCCAAAGAATAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
381075 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
381130 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
381185 AGTCCCCAAAGAGCAGGACAC
1 AGTCCTCAAAGAGCAGGACAC
381206 TTTCCTTTTC
Statistics
Matches: 228, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
54 5 0.02
55 218 0.96
56 5 0.02
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:381152 original size:26 final size:26
Alignment explanation
Indices: 380957--381209 Score: 68
Period size: 28 Copynumber: 9.3 Consensus size: 26
380947 AAGTTGGTGG
*
380957 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
380983 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
* **
381012 CACCTTTCAGTCCCCAAAGAATAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
381038 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
381067 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
381093 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
381122 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
381148 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
381177 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
381203 CA-CTTTC
1 CACCTTTC
381210 CTTTTCTTCT
Statistics
Matches: 155, Mismatches: 51, Indels: 43
0.62 0.20 0.17
Matches are distributed among these distances:
25 16 0.10
26 34 0.22
27 29 0.19
28 35 0.23
29 30 0.19
30 11 0.07
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:381182 original size:165 final size:164
Alignment explanation
Indices: 380910--381209 Score: 573
Period size: 165 Copynumber: 1.8 Consensus size: 164
380900 TCCGCTTTTT
380910 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
380975 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAATAGGACA
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAACAGGACA
381040 CCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
131 -CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
381075 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
*
381140 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACA
66 GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAACAGGACA
381205 CTTTC
131 CTTTC
381210 CTTTTCTTCT
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
164 5 0.04
165 128 0.96
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.20
Consensus pattern (164 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAA
GAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAACAGGACA
CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:381769 original size:19 final size:19
Alignment explanation
Indices: 381745--381812 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
381735 AATTCAACGA
381745 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
381764 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
381779 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
381796 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
381813 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:381783 original size:32 final size:32
Alignment explanation
Indices: 381747--381809 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
381737 TTCAACGATT
*
381747 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
381779 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
381810 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:381784 original size:13 final size:13
Alignment explanation
Indices: 381766--381790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
381756 ACATAAGTTT
381766 TGTATCGATACAA
1 TGTATCGATACAA
381779 TGTATCGATACA
1 TGTATCGATACA
381791 TAAGTATTGT
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:381870 original size:13 final size:13
Alignment explanation
Indices: 381852--381877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
381842 CATTTTTCTA
381852 TGTATCGATACAT
1 TGTATCGATACAT
381865 TGTATCGATACAT
1 TGTATCGATACAT
381878 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:381874 original size:33 final size:33
Alignment explanation
Indices: 381832--381898 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
381822 GCCAAGGAAA
***
381832 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
381865 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
381898 T
1 T
381899 TGGAAATTTT
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:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:384429 original size:28 final size:27
Alignment explanation
Indices: 384362--384430 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
384352 CTTCACAATC
**
384362 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
384389 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
384417 GGGGATACTCCAAC
1 GGGGATACTCCAAC
384431 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:384450 original size:107 final size:105
Alignment explanation
Indices: 384306--384700 Score: 318
Period size: 107 Copynumber: 3.7 Consensus size: 105
384296 TTCTATAATC
* *
384306 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGATACT
1 GGGGATACTCCAACTCCGGTTTTA-TTCC---AAAAACACCAATTT-TTCACAATCGGGGATACT
384371 CCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGA
61 CCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* *
384417 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGGTTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * * ** * *
384481 ATCCTGGTTTTATTTTC---AAAACACCAATTTTCCTTTAAT-C--
64 A-CCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTCCGA
* * * *
384521 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATGCTCCAA
1 GGGGATACTCCAACTCCGGTTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* *
384586 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTA-TTCCGA
* * * * *** * * *
384629 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
384694 CCCGTTA
66 CCCGTTA
384701 TTTTCGAAGG
Statistics
Matches: 221, Mismatches: 47, Indels: 36
0.73 0.15 0.12
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 46 0.21
105 15 0.07
106 20 0.09
107 71 0.32
108 29 0.13
109 8 0.04
110 1 0.00
111 22 0.10
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGGTTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTCCGA
Found at i:384490 original size:52 final size:51
Alignment explanation
Indices: 384417--384586 Score: 175
Period size: 52 Copynumber: 3.3 Consensus size: 51
384407 TTATTTCCGA
*
384417 GGGGATACTCCAACTCCGGTTTTATCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATC-CTAAAACACCAATTTTTCCACAATC
** **
384469 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACACCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATCCT-AAAACACCAATTTTTCC-ACAATC
* * *
384521 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTA--TCCTAAAACACCAATTTTTCCACAATC
* *
384573 GAGGATGCTCCAAC
1 GGGGATACTCCAAC
384587 CTCGTTATTT
Statistics
Matches: 97, Mismatches: 14, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
51 10 0.10
52 69 0.71
53 13 0.13
54 5 0.05
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATCCTAAAACACCAATTTTTCCACAATC
Found at i:384629 original size:212 final size:212
Alignment explanation
Indices: 384246--384653 Score: 624
Period size: 212 Copynumber: 1.9 Consensus size: 212
384236 TTATCAATTC
* *
384246 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
384311 TACTCTAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAAC
66 TACTCCAACTCCGATTTTATTTCC--AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
384376 CCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTA
129 CCCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
384441 TCGCTAAAACACTAATTTT
194 TCGCTAAAACACTAATTTT
* * *
384460 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
384524 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATGCTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* *
384587 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
384652 AT
193 AT
384654 TCCCAAAATA
Statistics
Matches: 177, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
211 27 0.15
212 68 0.38
213 3 0.02
214 44 0.25
215 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.31
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:384779 original size:80 final size:79
Alignment explanation
Indices: 384600--384803 Score: 223
Period size: 80 Copynumber: 2.6 Consensus size: 79
384590 GTTATTTCAT
* * *
384600 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
* * *
384665 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * ** * ** *
384679 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTC-TAATC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCG-GCTTTATTCCCAAAAT-
384743 ATCGATTTCTCACAAC
64 ATCGATTTCTCACAAC
* *
384759 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
384804 TGTTATTATC
Statistics
Matches: 104, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 50 0.48
80 54 0.52
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:384831 original size:80 final size:76
Alignment explanation
Indices: 384600--384834 Score: 209
Period size: 80 Copynumber: 2.9 Consensus size: 76
384590 GTTATTTCAT
* * * * *
384600 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAACCCC-GTTTTATT-CCAAAACAT
* *
384665 TGATTTCTCATAAT
63 TGATTTCTCACAAC
* * * * * *
384679 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTTCTAATCA
1 CGGGGATACTCCAACCCCGTTATTTTC-AAGGGATACTCCAACCCCG---TTTTATTCCAAAACA
*
384744 TCGATTTCTCACAAC
62 TTGATTTCTCACAAC
* * *
384759 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAACCCTGTTATTATCTCCAAAACAT
1 CGGGGATACTCCAACCCCGTTATTTTCAAGGG-ATACTCCAACCCCGTT-TTAT-TCCAAAACAT
*
384824 TAAATTTCTCA
63 T-GATTTCTCA
384835 TCGGGAAATA
Statistics
Matches: 124, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
77 2 0.02
78 4 0.03
79 53 0.43
80 60 0.48
81 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (76 bp):
CGGGGATACTCCAACCCCGTTATTTTCAAGGGATACTCCAACCCCGTTTTATTCCAAAACATTGA
TTTCTCACAAC
Found at i:390637 original size:25 final size:26
Alignment explanation
Indices: 390609--390658 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
390599 GAAATATGAT
*
390609 TTTTTTAAAAAAAATTAA-TTATTTA
1 TTTTTTAAAAAAAATAAATTTATTTA
*
390634 TTTTTTAAAAATAATAAATTTATTT
1 TTTTTTAAAAAAAATAAATTTATTT
390659 TAAAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTTTAAAAAAAATAAATTTATTTA
Found at i:393733 original size:6 final size:6
Alignment explanation
Indices: 393710--393768 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
393700 TATTTTAATA
* *
393710 AAATTT AAA-TT AAA-TT AAATTT AAATTT -AATAAT ATATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT-TT AAATTT AAATTT
393756 -AATTT AAATTT AA
1 AAATTT AAATTT AA
393769 CTCGATTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 18 0.40
6 25 0.56
7 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (6 bp):
AAATTT
Found at i:393764 original size:11 final size:11
Alignment explanation
Indices: 393710--393768 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 11
393700 TATTTTAATA
*
393710 AAATTTAAATT
1 AAATTTAATTT
*
393721 AAATTAAATTT
1 AAATTTAATTT
393732 AAATTTAA--T
1 AAATTTAATTT
*
393741 -AATAT-ATTT
1 AAATTTAATTT
393750 AAATTTAATTT
1 AAATTTAATTT
393761 AAATTTAA
1 AAATTTAA
393769 CTCGATTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 1 0.03
8 4 0.10
9 2 0.05
10 4 0.10
11 28 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:394369 original size:2 final size:2
Alignment explanation
Indices: 394362--394391 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
394352 CTAAGTAACC
394362 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
394392 TCGAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:395122 original size:17 final size:17
Alignment explanation
Indices: 395100--395134 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
395090 AAAATTAAGT
395100 TATAAATACAAATA-AAA
1 TATAAATA-AAATATAAA
395117 TATAAATAAAATATAAA
1 TATAAATAAAATATAAA
395134 T
1 T
395135 TTTATTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
TATAAATAAAATATAAA
Found at i:395123 original size:11 final size:11
Alignment explanation
Indices: 395103--395134 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
395093 ATTAAGTTAT
*
395103 AAATACAAATA
1 AAATATAAATA
395114 AAATATAAATA
1 AAATATAAATA
395125 AAATATAAAT
1 AAATATAAAT
395135 TTTATTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATATAAATA
Found at i:395356 original size:51 final size:52
Alignment explanation
Indices: 395294--395408 Score: 180
Period size: 52 Copynumber: 2.2 Consensus size: 52
395284 TAAATTTTTT
* * *
395294 AAAATAAATTTTTATATTTATAT-TAAATATATA-TATATAAAATATCAAATA
1 AAAATATATTTTTATATCTATATCTAAATATATATTA-AAAAAATATCAAATA
395345 AAAATATATTTTTATATCTATATCTAAATATATATTAAAAAAATATCAAATA
1 AAAATATATTTTTATATCTATATCTAAATATATATTAAAAAAATATCAAATA
395397 AAAATATATTTT
1 AAAATATATTTT
395409 AAAAAATAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
51 21 0.36
52 36 0.61
53 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (52 bp):
AAAATATATTTTTATATCTATATCTAAATATATATTAAAAAAATATCAAATA
Found at i:395413 original size:26 final size:26
Alignment explanation
Indices: 395318--395413 Score: 77
Period size: 26 Copynumber: 3.6 Consensus size: 26
395308 TATTTATATT
395318 AAATATATATATATAAAATATCAAATAA
1 AAATATAT-TATA-AAAATATCAAATAA
* * ** **
395346 AAATATATTTTTATATCTAT-ATCTAA
1 AAATATA-TTATAAAAATATCAAATAA
* *
395372 ATATATATTAAAAAAATATCAAATAA
1 AAATATATTATAAAAATATCAAATAA
*
395398 AAATATATTTTAAAAA
1 AAATATATTATAAAAA
395414 ATAAAAAATT
Statistics
Matches: 49, Mismatches: 17, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
25 7 0.14
26 27 0.55
27 4 0.08
28 10 0.20
29 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
AAATATATTATAAAAATATCAAATAA
Found at i:395877 original size:11 final size:11
Alignment explanation
Indices: 395851--395939 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 11
395841 AAAAAATTCG
*
395851 TTATTTATATAT
1 TTATTT-TATAA
395863 TTATTTTATAA
1 TTATTTTATAA
395874 TTATTTT-TAAA
1 TTATTTTAT-AA
**
395885 TTA-TTTATTT
1 TTATTTTATAA
395895 TTA-TTTATTATA
1 TTATTTTA-TA-A
395907 TTATATTT-TAA
1 TTAT-TTTATAA
*
395918 TTATTTTTTATA
1 TTATTTTATA-A
395930 TTATATTTAT
1 TTAT-TTTAT
395940 TGAATCGTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
10 14 0.23
11 25 0.40
12 16 0.26
13 4 0.06
14 3 0.05
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTTTATAA
Found at i:395928 original size:18 final size:19
Alignment explanation
Indices: 395884--395931 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
395874 TTATTTTTAA
*
395884 ATTA-TTTAT-TTTTATTT
1 ATTATTTTATATTTTAATT
*
395901 ATTATATTATATTTTAATT
1 ATTATTTTATATTTTAATT
395920 ATT-TTTTATATT
1 ATTATTTTATATT
395932 ATATTTATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 12 0.46
19 10 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTATTTTATATTTTAATT
Found at i:395928 original size:23 final size:23
Alignment explanation
Indices: 395858--395937 Score: 78
Period size: 23 Copynumber: 3.5 Consensus size: 23
395848 TCGTTATTTA
395858 TATATT-TATTTTATAATTA-TTTT
1 TATATTATA-TTT-TAATTATTTTT
* * *
395881 TAAATTAT-TTATT-TTTATTTAT
1 TATATTATATT-TTAATTATTTTT
395903 TATATTATATTTTAATTATTTTT
1 TATATTATATTTTAATTATTTTT
395926 TATATTATATTT
1 TATATTATATTT
395938 ATTGAATCGT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
21 3 0.07
22 15 0.33
23 27 0.59
24 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TATATTATATTTTAATTATTTTT
Found at i:396424 original size:31 final size:32
Alignment explanation
Indices: 396389--396451 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
396379 TTTAATTTTT
*
396389 TATTTAATATTTTTATAT-A-TTTAAAATATAA
1 TATTTAATATTTATATATAATTTTAAAA-ATAA
**
396420 TATTTTTTATTTATATATAATTTTAAAAATAA
1 TATTTAATATTTATATATAATTTTAAAAATAA
396452 AAAATTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 15 0.56
32 5 0.19
33 7 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTTAATATTTATATATAATTTTAAAAATAA
Found at i:397819 original size:25 final size:22
Alignment explanation
Indices: 397780--397835 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
397770 AAATTTTTTA
*
397780 ATTTTATATACATTAAGCTAAATAT
1 ATTTT-TATAAATT-AG-TAAATAT
*
397805 CATTTTTATAAATTAGTAACTAT
1 -ATTTTTATAAATTAGTAAATAT
397828 ATTTTTAT
1 ATTTTTAT
397836 TTTTATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 8 0.29
23 6 0.21
24 2 0.07
25 7 0.25
26 5 0.18
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTTTATAAATTAGTAAATAT
Found at i:399108 original size:17 final size:18
Alignment explanation
Indices: 399071--399109 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
399061 TAATAAATTT
* *
399071 TTAAATTTTTAACTGTTA
1 TTAAATTTTTAACTATCA
399089 TTAAA-TTTTAACTATCA
1 TTAAATTTTTAACTATCA
399106 TTAA
1 TTAA
399110 TGATCATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (18 bp):
TTAAATTTTTAACTATCA
Found at i:399202 original size:21 final size:22
Alignment explanation
Indices: 399169--399247 Score: 83
Period size: 21 Copynumber: 3.6 Consensus size: 22
399159 TACATATTTG
399169 ATTATTAAT-TTTAATTTCATT
1 ATTATTAATATTTAATTTCATT
399190 ATTA-TAATATTTAATATT-ATT
1 ATTATTAATATTTAAT-TTCATT
* *
399211 ATTATTGTAGTATTTAATTTCAGT
1 ATTA-T-TAATATTTAATTTCATT
*
399235 ATTATTATTATTT
1 ATTATTAATATTT
399248 TTAATTTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
20 4 0.08
21 17 0.35
22 9 0.18
23 3 0.06
24 16 0.33
ACGTcount: A:0.34, C:0.03, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTATTAATATTTAATTTCATT
Found at i:399237 original size:24 final size:24
Alignment explanation
Indices: 399187--399252 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
399177 TTTTAATTTC
*
399187 ATTATTATAATATTTAATATTATT
1 ATTATTATAATATTTAATATTAGT
* *
399211 ATTATTGTAGTATTTAAT-TTCAGT
1 ATTATTATAATATTTAATATT-AGT
* *
399235 ATTATTATTATTTTTAAT
1 ATTATTATAATATTTAAT
399253 TTTATCAAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.59
Consensus pattern (24 bp):
ATTATTATAATATTTAATATTAGT
Found at i:399253 original size:24 final size:23
Alignment explanation
Indices: 399169--399254 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 23
399159 TACATATTTG
399169 ATTATTA-ATTTTAATTTC--ATT
1 ATTATTATA-TTTAATTTCATATT
*
399190 ATTATAATATTTAATATT-ATTATT
1 ATTATTATATTTAAT-TTCA-TATT
*
399214 ATT-GTAGTATTTAATTTCAGTATT
1 ATTATTA-TATTTAATTTCA-TATT
*
399238 ATTATTATTTTTAATTT
1 ATTATTATATTTAATTT
399255 TATCAAAGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
21 12 0.24
22 3 0.06
23 3 0.06
24 31 0.61
25 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (23 bp):
ATTATTATATTTAATTTCATATT
Found at i:399688 original size:16 final size:16
Alignment explanation
Indices: 399669--399710 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
399659 ATTTAATAAT
399669 TAAATTATATAAAATA
1 TAAATTATATAAAATA
*
399685 TAAA-TATAAAAAAATA
1 TAAATTAT-ATAAAATA
*
399701 AAAATTATAT
1 TAAATTATAT
399711 GTCACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 3 0.14
16 15 0.71
17 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAATTATATAAAATA
Found at i:400290 original size:28 final size:27
Alignment explanation
Indices: 400257--400316 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 27
400247 ATTAAAAAAT
*
400257 AAAATATTTATTTTCTTAAATTTTTATAA
1 AAAATATTTATTTT-TTAAATATTTA-AA
*
400286 AAATATATTTATTTTTTTAATATTTAAA
1 AAA-ATATTTATTTTTTAAATATTTAAA
400314 AAA
1 AAA
400317 TATCAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.18
29 12 0.43
30 11 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
AAAATATTTATTTTTTAAATATTTAAA
Found at i:400296 original size:30 final size:30
Alignment explanation
Indices: 400260--400360 Score: 93
Period size: 30 Copynumber: 3.3 Consensus size: 30
400250 AAAAAATAAA
*
400260 ATATTTATTTTCTTAAATTTTTATAAAAAT
1 ATATTTATTTTCTTAAATATTTATAAAAAT
*
400290 ATATTTATTTT-TTTAATATTTA-AAAAAT
1 ATATTTATTTTCTTAAATATTTATAAAAAT
* *
400318 ATCAATTTACCTTTC-TAAA-GTTTAGGTAAAAAT
1 AT--ATTTA-TTTTCTTAAATATTTA--TAAAAAT
400351 ATATTTATTT
1 ATATTTATTT
400361 CTCGAAGCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
28 8 0.14
29 9 0.16
30 22 0.38
31 11 0.19
33 8 0.14
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATTTATTTTCTTAAATATTTATAAAAAT
Found at i:400333 original size:61 final size:61
Alignment explanation
Indices: 400242--400360 Score: 145
Period size: 61 Copynumber: 1.9 Consensus size: 61
400232 TTGTTATGTA
* *
400242 AATATATTAAAAAATAAAATATTTATTTTCTTAAATTTTTA-TAAAAATATATTTATTTTTTT
1 AATATATTAAAAAATAAAATATTTACTTTC-TAAA-GTTTAGTAAAAATATATTTATTTTTTT
**
400304 AATAT-TTAAAAAATATCA-ATTTACCTTTCTAAAGTTTAGGTAAAAATATATTTATTT
1 AATATATTAAAAAATAAAATATTTA-CTTTCTAAAGTTTA-GTAAAAATATATTTATTT
400361 CTCGAAGCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
59 4 0.08
60 9 0.18
61 32 0.64
62 5 0.10
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (61 bp):
AATATATTAAAAAATAAAATATTTACTTTCTAAAGTTTAGTAAAAATATATTTATTTTTTT
Found at i:405085 original size:10 final size:10
Alignment explanation
Indices: 405072--405104 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
405062 AATAAATTTT
405072 TTAATTTAAA
1 TTAATTTAAA
*
405082 TTAATTTAAT
1 TTAATTTAAA
405092 TTAATTTAAA
1 TTAATTTAAA
405102 TTA
1 TTA
405105 TCATTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTAATTTAAA
Found at i:405087 original size:4 final size:5
Alignment explanation
Indices: 405041--405100 Score: 52
Period size: 5 Copynumber: 12.2 Consensus size: 5
405031 AATAGAATAG
* * * * *
405041 ATTTAA ATTTT ATTAA ATTTA AATAA ATTT- -TTTA ATTTA AATTA ATTTA
1 ATTT-A ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
405090 ATTTA ATTTA A
1 ATTTA ATTTA A
405101 ATTATCATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
3 3 0.07
5 35 0.83
6 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:410848 original size:2 final size:2
Alignment explanation
Indices: 410841--410866 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
410831 TTTGTGAAGA
410841 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
410867 GAAATGTTTG
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:414977 original size:50 final size:50
Alignment explanation
Indices: 414918--415176 Score: 412
Period size: 50 Copynumber: 5.2 Consensus size: 50
414908 TATACTTAGA
* * *
414918 GTCAACAATTATGGTCACCTCCCTCTATTGTCAAAAGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
414968 GTCAACAATTATGACCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
*
415018 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
415068 GTCAACAATTATAGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
415118 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATC
415168 GTCAACAAT
1 GTCAACAAT
415177 GACAACAACT
Statistics
Matches: 193, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 192 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:419632 original size:50 final size:50
Alignment explanation
Indices: 419573--419831 Score: 394
Period size: 50 Copynumber: 5.2 Consensus size: 50
419563 TATACTTAGA
* *
419573 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
*
419623 GTCAACAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* *
419673 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* *
419723 GTCAACAATTATAGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* * * * *
419773 ATCAACAATTATGGCCACCTCTTTCTATTGTCAAAAGTCGGTGAATG-ATA
1 GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAA-GAATC
419823 GTCAACAAT
1 GTCAACAAT
419832 GACAACAACT
Statistics
Matches: 190, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 189 0.99
51 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:419746 original size:100 final size:100
Alignment explanation
Indices: 419573--419831 Score: 439
Period size: 100 Copynumber: 2.6 Consensus size: 100
419563 TATACTTAGA
*
419573 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATGGT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATAGT
419638 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
419673 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATAGT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATAGT
419738 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
66 CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
* ** * * *
419773 ATCAACAATTATGGCCACCTCTTTCTATTGTCAAAAGTCGGTGAATG-ATAGTCAACAAT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAA-GAATTGTCAACAAT
419832 GACAACAACT
Statistics
Matches: 151, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
100 150 0.99
101 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATTGTCAACAATTATAGT
CACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:420003 original size:15 final size:15
Alignment explanation
Indices: 419985--420017 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
419975 ATATTTTTAA
419985 TATATTTA-TTATATT
1 TATATTTAGTTAT-TT
420000 TATATTTAGTTATTT
1 TATATTTAGTTATTT
420015 TAT
1 TAT
420018 TATGTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TATATTTAGTTATTT
Found at i:420007 original size:24 final size:24
Alignment explanation
Indices: 419980--420027 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
419970 ATTAAATATT
419980 TTTAA-TATATTTATTATATTTATA
1 TTTAATTAT-TTTATTATATTTATA
* *
420004 TTTAGTTATTTTATTATGTTTATA
1 TTTAATTATTTTATTATATTTATA
420028 ATTACACCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (24 bp):
TTTAATTATTTTATTATATTTATA
Found at i:420682 original size:2 final size:2
Alignment explanation
Indices: 420675--420716 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
420665 TCTTTTTCTT
420675 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
420717 ATAAATTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:421179 original size:31 final size:29
Alignment explanation
Indices: 421144--421202 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
421134 TAATTACATA
* * *
421144 ATATATTTAATATTTATATAATATTAAATTT
1 ATATAGTTAATAATTAAAT-AT-TTAAATTT
421175 ATATAGTTAATAATTAAATATTTAAATT
1 ATATAGTTAATAATTAAATATTTAAATT
421203 GAATTGGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
30 2 0.08
31 16 0.64
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
ATATAGTTAATAATTAAATATTTAAATTT
Found at i:421871 original size:22 final size:20
Alignment explanation
Indices: 421846--421887 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
421836 ATTTAAATAA
*
421846 ATTTAATTTAACTTAAAATATT
1 ATTTAA-TTAA-TAAAAATATT
421868 ATTTAATTAATAAAAATATT
1 ATTTAATTAATAAAAATATT
421888 TTATTAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAATTAATAAAAATATT
Found at i:423300 original size:21 final size:20
Alignment explanation
Indices: 423276--423314 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
423266 AATTAATAGA
423276 TATGTATACATTGAAAAATAT
1 TATGTATAC-TTGAAAAATAT
*
423297 TATGTATACTTGTAAAAT
1 TATGTATACTTGAAAAAT
423315 TAACACTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TATGTATACTTGAAAAATAT
Found at i:423502 original size:16 final size:16
Alignment explanation
Indices: 423483--423513 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
423473 AAATATATAT
423483 TTTAAATTAAATTTAA
1 TTTAAATTAAATTTAA
423499 TTTAAATTAAATTTA
1 TTTAAATTAAATTTA
423514 TGAAATCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTAAATTAAATTTAA
Found at i:423956 original size:21 final size:20
Alignment explanation
Indices: 423932--423974 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
423922 TTTTTAGAAA
423932 ATATTTAAAAAATTAATTATT
1 ATATTTAAAAAATT-ATTATT
*
423953 ATATTTAATAAATTATTATT
1 ATATTTAAAAAATTATTATT
423973 AT
1 AT
423975 TATAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTTAAAAAATTATTATT
Found at i:423982 original size:20 final size:18
Alignment explanation
Indices: 423941--423982 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
423931 AATATTTAAA
*
423941 AAATTAATTATTATATTT
1 AAATAAATTATTATATTT
423959 -AATAAATTATTATTATTAT
1 AAATAAATTATTA-TATT-T
423978 AAATA
1 AAATA
423983 TTATGTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 11 0.55
18 4 0.20
19 1 0.05
20 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATAAATTATTATATTT
Found at i:424228 original size:5 final size:5
Alignment explanation
Indices: 424218--424256 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
424208 AATATTTTTG
* *
424218 ATTTA ATTTA ATTTA GTTTA ATTTA GTTTA ATTTGA ATT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTT-A ATT
424257 ATCGTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (5 bp):
ATTTA
Found at i:424237 original size:10 final size:10
Alignment explanation
Indices: 424218--424251 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
424208 AATATTTTTG
*
424218 ATTTAATTTA
1 ATTTAGTTTA
424228 ATTTAGTTTA
1 ATTTAGTTTA
424238 ATTTAGTTTA
1 ATTTAGTTTA
424248 ATTT
1 ATTT
424252 GAATTATCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (10 bp):
ATTTAGTTTA
Found at i:424635 original size:14 final size:14
Alignment explanation
Indices: 424605--424637 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
424595 TGACATGTTT
424605 TATAA-ATAAAAAA
1 TATAATATAAAAAA
424618 -ATAATATAAAAAA
1 TATAATATAAAAAA
424631 TATAATA
1 TATAATA
424638 AGATAGTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.22
13 8 0.44
14 6 0.33
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TATAATATAAAAAA
Found at i:425272 original size:18 final size:19
Alignment explanation
Indices: 425227--425273 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
425217 AGAAAAAATT
425227 TTATATTAAAAAAA-TAAA
1 TTATATTAAAAAAATTAAA
*
425245 TT-TGAGTAAAAAAATTAAA
1 TTAT-ATTAAAAAAATTAAA
425264 TTAT-TTAAAA
1 TTATATTAAAA
425274 TAACAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 16 0.67
19 6 0.25
20 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TTATATTAAAAAAATTAAA
Done.