Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold105
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: 2918491
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 41655 characters in sequence are not A, C, G, or T
File 14 of 16
Found at i:2274917 original size:17 final size:17
Alignment explanation
Indices: 2274886--2274935 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
2274876 GCATGCGGTC
*
2274886 ATTTAT-ATTTATAATA
1 ATTTATAATATATAATA
2274902 ATTT-TAATATATTAATA
1 ATTTATAATATA-TAATA
*
2274919 ATTTATATTATATAATA
1 ATTTATAATATATAATA
2274936 TCTATTCACG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 1 0.03
16 8 0.28
17 14 0.48
18 6 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATAATATATAATA
Found at i:2276772 original size:51 final size:52
Alignment explanation
Indices: 2276670--2276826 Score: 158
Period size: 52 Copynumber: 3.0 Consensus size: 52
2276660 TCATTTTCAC
* * * * *
2276670 GTGATTTGGTTTCCAAAAAGGACATGAGCTT-ATGTATTATACACTCATGGTT
1 GTGATTTGGTCTCCAAAAAGGACATG-GATTCATGTATTAAATACTCTTGGTT
* * * * *
2276722 GTGGTTT-GTGTCCAAACAGGACATGGATTCATGTATTACATACCCTTGGTT
1 GTGATTTGGTCTCCAAAAAGGACATGGATTCATGTATTAAATACTCTTGGTT
** *
2276773 GTGATTTGGTCTCCAAAAAGGTTATGGGTTCATAG-ATTAAATACTCTTGGTT
1 GTGATTTGGTCTCCAAAAAGGACATGGATTCAT-GTATTAAATACTCTTGGTT
2276825 GT
1 GT
2276827 CTTTTTTTAT
Statistics
Matches: 86, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
50 3 0.03
51 39 0.45
52 43 0.50
53 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (52 bp):
GTGATTTGGTCTCCAAAAAGGACATGGATTCATGTATTAAATACTCTTGGTT
Found at i:2276909 original size:17 final size:18
Alignment explanation
Indices: 2276887--2276921 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2276877 AAGGTAAAAG
2276887 AATTTA-TAATATTTTTT
1 AATTTATTAATATTTTTT
*
2276904 AATTTATTCATATTTTTT
1 AATTTATTAATATTTTTT
2276922 TAATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTATTAATATTTTTT
Found at i:2277197 original size:7 final size:7
Alignment explanation
Indices: 2277181--2277228 Score: 51
Period size: 7 Copynumber: 6.3 Consensus size: 7
2277171 AAAAAATTAT
*
2277181 TAAAATA
1 TAAAAAA
2277188 TAAAAAA
1 TAAAAAA
2277195 TAAAGTAAA
1 TAAA--AAA
2277204 TAATAAAAA
1 T-A-AAAAA
2277213 TAAAAAA
1 TAAAAAA
2277220 TAAAAAA
1 TAAAAAA
2277227 TA
1 TA
2277229 TGTATATCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
7 24 0.67
8 1 0.03
9 8 0.22
10 1 0.03
11 2 0.06
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAAAAA
Found at i:2277418 original size:2 final size:2
Alignment explanation
Indices: 2277413--2277444 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2277403 ACAAAAAAAT
2277413 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
2277445 AAACTCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2277752 original size:2 final size:2
Alignment explanation
Indices: 2277745--2277771 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2277735 TTTGAATTTA
2277745 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 A
2277772 AAATAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2288063 original size:6 final size:6
Alignment explanation
Indices: 2288038--2288171 Score: 62
Period size: 6 Copynumber: 21.8 Consensus size: 6
2288028 TAGATTTAAT
* * *
2288038 AATATTA AATATA ATTATATA AATAT- AATATA CAGA-A AATAATA AAAATA
1 AATA-TA AATATA A--ATATA AATATA AATATA AATATA AAT-ATA AATATA
* * * * *
2288088 TAATAT- AATATA AATATA TATTTA AATTTT GATAT- AATATA AATATTA
1 -AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATA-TA
* * *
2288136 AA-ATT TATATA AATATAA AATATA AAAATA TAATAT
1 AATATA AATATA AATAT-A AATATA AATATA -AATAT
2288172 TAATCCACCA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
5 18 0.19
6 47 0.49
7 25 0.26
8 6 0.06
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (6 bp):
AATATA
Found at i:2288102 original size:25 final size:25
Alignment explanation
Indices: 2288036--2288171 Score: 84
Period size: 25 Copynumber: 5.3 Consensus size: 25
2288026 GTTAGATTTA
* *
2288036 ATAATATTAA-ATATAATTATATAAAT
1 ATAATA-TAATATA-AATAATAAAAAT
*
2288062 ATAATATACAGA-AAATAATAAAAAT
1 ATAATATA-ATATAAATAATAAAAAT
*
2288087 ATAATATAATATAAATATATATTTAAATT
1 ATAATATAATATAAATA-ATA---AAAAT
* * *
2288116 TTGATATAATATAAAT-ATTAAAAT
1 ATAATATAATATAAATAATAAAAAT
*
2288140 -TTATATAAATATAAA-ATATAAAAAT
1 ATAATAT-AATATAAATA-ATAAAAAT
2288165 ATAATAT
1 ATAATAT
2288172 TAATCCACCA
Statistics
Matches: 88, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
23 5 0.06
24 14 0.16
25 32 0.36
26 16 0.18
27 3 0.03
29 18 0.20
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (25 bp):
ATAATATAATATAAATAATAAAAAT
Found at i:2288123 original size:24 final size:24
Alignment explanation
Indices: 2288095--2288164 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
2288085 ATATAATATA
* *
2288095 ATATAAATATATAT-TTAAATTTT
1 ATATAAATATAAATATTAAAATTT
2288118 GATAT-AATATAAATATTAAAATTT
1 -ATATAAATATAAATATTAAAATTT
*
2288142 ATATAAATATAAAATATAAAAAT
1 ATATAAATAT-AAATATTAAAAT
2288165 ATAATATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
23 12 0.30
24 17 0.43
25 11 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (24 bp):
ATATAAATATAAATATTAAAATTT
Found at i:2288820 original size:17 final size:16
Alignment explanation
Indices: 2288787--2288824 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
2288777 AAGGAAAATG
2288787 AAGAAGATGATTAGAA
1 AAGAAGATGATTAGAA
2288803 AGAGAAGATGATCT-GAA
1 A-AGAAGATGAT-TAGAA
2288820 AAGAA
1 AAGAA
2288825 TTTGTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 14 0.70
18 1 0.05
ACGTcount: A:0.55, C:0.03, G:0.26, T:0.16
Consensus pattern (16 bp):
AAGAAGATGATTAGAA
Found at i:2289327 original size:15 final size:14
Alignment explanation
Indices: 2289301--2289332 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
2289291 TACTTGTATA
2289301 ATTTTATTTATATT
1 ATTTTATTTATATT
2289315 ATTTTATTTTATATT
1 ATTTTA-TTTATATT
2289330 ATT
1 ATT
2289333 AAATTCAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTATTTATATT
Found at i:2295037 original size:16 final size:16
Alignment explanation
Indices: 2294995--2295037 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
2294985 TAATTAATTA
2294995 TTATAAT-TATTAATAT
1 TTATAATAT-TTAATAT
2295011 TTAATAA-ATTTAATAT
1 TT-ATAATATTTAATAT
2295027 TTATAATATTT
1 TTATAATATTT
2295038 TTAATCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATAATATTTAATAT
Found at i:2297739 original size:15 final size:15
Alignment explanation
Indices: 2297719--2297751 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2297709 AATTATTTTA
*
2297719 TATTTTTAAAAAAAT
1 TATTTTAAAAAAAAT
2297734 TATTTTAAAAAAAAT
1 TATTTTAAAAAAAAT
2297749 TAT
1 TAT
2297752 AAAAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTTAAAAAAAAT
Found at i:2298622 original size:72 final size:72
Alignment explanation
Indices: 2298546--2298687 Score: 173
Period size: 73 Copynumber: 2.0 Consensus size: 72
2298536 AATTTTTATT
* * * *
2298546 TATTATCAAATAAATTTTATTTATTTAAAGTCTTCCAATA-ATATTAAAA-TT-ATTTATAAATA
1 TATTATCAAATAAA-TTCATTTAATTAAA-TCTT-CAATATAAATAAAAATTTAATTTATAAATA
*
2298608 TGATAAATAC
63 TAATAAATAC
*
2298618 TATTATCTAATAAATTCATTTAATTAAATCTTCAATATAAATAAAAATTTTAATTTATAAATATA
1 TATTATCAAATAAATTCATTTAATTAAATCTTCAATATAAATAAAAA-TTTAATTTATAAATATA
2298683 ATAAA
65 ATAAA
2298688 ACTTATTGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
69 5 0.08
70 11 0.18
71 12 0.20
72 15 0.25
73 17 0.28
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (72 bp):
TATTATCAAATAAATTCATTTAATTAAATCTTCAATATAAATAAAAATTTAATTTATAAATATAA
TAAATAC
Found at i:2312659 original size:2 final size:2
Alignment explanation
Indices: 2312652--2312683 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2312642 CTGGCAAATT
2312652 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
2312684 AATGATTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2313061 original size:15 final size:14
Alignment explanation
Indices: 2313041--2313121 Score: 62
Period size: 14 Copynumber: 5.8 Consensus size: 14
2313031 TTTTTTATTA
2313041 AATAAAATTATAATT
1 AATAAAATT-TAATT
*
2313056 AATAAAATTTATTT
1 AATAAAATTTAATT
*
2313070 AA-AAATATTTAATA
1 AATAAA-ATTTAATT
2313084 AAT-AAATTTAA--
1 AATAAAATTTAATT
* *
2313095 AGTTAAATTTAATT
1 AATAAAATTTAATT
2313109 ATATAAAAATTTA
1 A-AT-AAAATTTA
2313122 TATAAAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
11 2 0.04
12 8 0.15
13 9 0.17
14 17 0.32
15 10 0.19
16 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (14 bp):
AATAAAATTTAATT
Found at i:2314362 original size:57 final size:57
Alignment explanation
Indices: 2314257--2314368 Score: 136
Period size: 57 Copynumber: 2.0 Consensus size: 57
2314247 GACATAATTT
* * *
2314257 TTAATTAAATCATTATAACAAATTATGAAAAAATATCACGAATTGAGATATGATACA
1 TTAATTAAATCATTAGAACAAATTATGAAAAAATATCACGAATAGAGATACGATACA
* * * * *
2314314 TTAATTAAATTATTAGAA-AAATTATGTAAAATATGTTATGAATAGAGATACGATA
1 TTAATTAAATCATTAGAACAAATTATG-AAAAAATATCACGAATAGAGATACGATA
2314369 TGAATATGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
56 8 0.17
57 38 0.83
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (57 bp):
TTAATTAAATCATTAGAACAAATTATGAAAAAATATCACGAATAGAGATACGATACA
Found at i:2315133 original size:14 final size:14
Alignment explanation
Indices: 2315113--2315175 Score: 78
Period size: 14 Copynumber: 4.5 Consensus size: 14
2315103 TACAAATTTT
2315113 TTTCTTTTTTCTT-
1 TTTCTTTTTTCTTC
2315126 TGTTCTTTTTTCCTTC
1 T-TTCTTTTTT-CTTC
2315142 TTTCTTTTTT-TTC
1 TTTCTTTTTTCTTC
2315155 TTT-TTTTTTCTTTC
1 TTTCTTTTTTC-TTC
2315169 TTTCTTT
1 TTTCTTT
2315176 CTCTCCTGCC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.14
13 7 0.16
14 15 0.34
15 15 0.34
16 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTCTTC
Found at i:2315148 original size:4 final size:4
Alignment explanation
Indices: 2315113--2315177 Score: 59
Period size: 4 Copynumber: 17.2 Consensus size: 4
2315103 TACAAATTTT
* * *
2315113 TTTC TTT- TTTC TTT- GTTC TTT- TTTC CTTC TTTC TTTTT TTTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC
2315158 TTT- TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC T
2315178 CTCCTGCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
3 14 0.28
4 33 0.66
5 3 0.06
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (4 bp):
TTTC
Found at i:2315155 original size:31 final size:31
Alignment explanation
Indices: 2315117--2315177 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2315107 AATTTTTTTC
2315117 TTTTTTCTTTGTTCTTT-TTTCCTTCTTTCTT
1 TTTTTTCTTT-TTCTTTCTTTCCTTCTTTCTT
* *
2315148 TTTTTTCTTTTTTTTTCTTTCTTTCTTTCT
1 TTTTTTCTTTTTCTTTCTTTCCTTCTTTCT
2315178 CTCCTGCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (31 bp):
TTTTTTCTTTTTCTTTCTTTCCTTCTTTCTT
Found at i:2315161 original size:27 final size:29
Alignment explanation
Indices: 2315113--2315175 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 29
2315103 TACAAATTTT
2315113 TTTCTTTTTTCTTTGTTCTTTTTTCCTTC
1 TTTCTTTTTTCTTTGTTCTTTTTTCCTTC
*
2315142 TTTCTTTTTT-TTCT-TT-TTTTTTCTTTC
1 TTTCTTTTTTCTT-TGTTCTTTTTTCCTTC
2315169 TTTCTTT
1 TTTCTTT
2315176 CTCTCCTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 17 0.53
28 4 0.12
29 11 0.34
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (29 bp):
TTTCTTTTTTCTTTGTTCTTTTTTCCTTC
Found at i:2315804 original size:22 final size:22
Alignment explanation
Indices: 2315790--2315839 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
2315780 TTTATTTTTT
*
2315790 TAATTAATTATTTTTAAATATA
1 TAATTAATTATTTTTATATATA
*
2315812 TAATTAATTATTATTTATAAATA
1 TAATTAATTATT-TTTATATATA
2315835 TAATT
1 TAATT
2315840 TTTTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATTAATTATTTTTATATATA
Found at i:2318800 original size:2 final size:2
Alignment explanation
Indices: 2318789--2318819 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2318779 AGATTACAGC
2318789 TA TA -A 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
2318820 AACACATATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2324154 original size:15 final size:15
Alignment explanation
Indices: 2324134--2324167 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
2324124 TCCTATTACC
2324134 TATTATTTAATTTAA
1 TATTATTTAATTTAA
2324149 TATTATTTAATTTAA
1 TATTATTTAATTTAA
2324164 TATT
1 TATT
2324168 GATATTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTTAATTTAA
Found at i:2327311 original size:15 final size:15
Alignment explanation
Indices: 2327291--2327321 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2327281 TGATGGGTAT
2327291 ATTAAAAAAATAATA
1 ATTAAAAAAATAATA
2327306 ATTAAAAAAATAATA
1 ATTAAAAAAATAATA
2327321 A
1 A
2327322 ACTAAATCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATTAAAAAAATAATA
Found at i:2327480 original size:3 final size:3
Alignment explanation
Indices: 2327474--2327500 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2327464 GGTAGCTTGC
2327474 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2327501 AAGAAGGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2331684 original size:21 final size:19
Alignment explanation
Indices: 2331624--2331723 Score: 67
Period size: 21 Copynumber: 4.9 Consensus size: 19
2331614 AATTGATTTC
2331624 AAAATTATTATAAATATTATA
1 AAAATTA-TA-AAATATTATA
* *
2331645 AGAAATATATAAAAAATTATT
1 A-AAAT-TATAAAATATTATA
*
2331666 AAAATTATCACAAATATTATC
1 AAAATTAT-A-AAATATTATA
* **
2331687 AAAATTATAATATAAGATA
1 AAAATTATAAAATATTATA
*
2331706 TAAAATTTTAAAAT-TTAT
1 -AAAATTATAAAATATTAT
2331724 CAAATAATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
19 11 0.18
20 17 0.27
21 26 0.42
22 6 0.10
23 2 0.03
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATTATAAAATATTATA
Found at i:2333863 original size:2 final size:2
Alignment explanation
Indices: 2333852--2333884 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2333842 CAGCGGCCAT
2333852 TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2333885 CAGGTCTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:2339245 original size:2 final size:2
Alignment explanation
Indices: 2339238--2339263 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2339228 TCATGATAAG
2339238 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
2339264 TTTAAAAAAA
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:2340073 original size:23 final size:23
Alignment explanation
Indices: 2340022--2340073 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
2340012 AACTAATCAA
* *
2340022 ATTTAAATTAAATTTAATTAATT
1 ATTTAAATCAAACTTAATTAATT
*
2340045 AATTAAATCAAACTTAATTAATT
1 ATTTAAATCAAACTTAATTAATT
*
2340068 GTTTAA
1 ATTTAA
2340074 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (23 bp):
ATTTAAATCAAACTTAATTAATT
Found at i:2340088 original size:23 final size:23
Alignment explanation
Indices: 2339990--2340094 Score: 66
Period size: 27 Copynumber: 4.2 Consensus size: 23
2339980 AATAATAAAA
*
2339990 AATTAATTAAATTAATTAATTAAACT
1 AATTAATTAAATTAATT--TT-AATT
* *
2340016 AATCAAATTTAAATTAAATTTAATT
1 AAT-TAA-TTAAATTAATTTTAATT
*
2340041 AATTAATTAAATCAAACTTAATTAATT
1 AATTAATTAAAT-TAA-TT--TTAATT
** *
2340068 GTTTAATTAAATTAATTTTAATC
1 AATTAATTAAATTAATTTTAATT
2340091 AATT
1 AATT
2340095 CCTATTTTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 15
0.69 0.14 0.17
Matches are distributed among these distances:
23 13 0.21
24 4 0.07
25 9 0.15
26 7 0.11
27 18 0.30
28 10 0.16
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (23 bp):
AATTAATTAAATTAATTTTAATT
Found at i:2340088 original size:27 final size:25
Alignment explanation
Indices: 2340024--2340094 Score: 74
Period size: 27 Copynumber: 2.8 Consensus size: 25
2340014 CTAATCAAAT
2340024 TTAAATTAAATTTAATTAA--TTAA
1 TTAAATTAAATTTAATTAATTTTAA
* *
2340047 TTAAATCAAACTTAATTAATTGTTTAA
1 TTAAATTAAATTTAATTAA-T-TTTAA
* *
2340074 TTAAATTAATTTTAATCAATT
1 TTAAATTAAATTTAATTAATT
2340095 CCTATTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 17 0.45
25 1 0.03
26 1 0.03
27 19 0.50
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (25 bp):
TTAAATTAAATTTAATTAATTTTAA
Found at i:2340563 original size:10 final size:10
Alignment explanation
Indices: 2340548--2340577 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2340538 AATTAATCAT
2340548 ATATTAAAAA
1 ATATTAAAAA
2340558 ATATTAAAAA
1 ATATTAAAAA
*
2340568 ATAATAAAAA
1 ATATTAAAAA
2340578 GAAATTGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
ATATTAAAAA
Found at i:2341595 original size:3 final size:3
Alignment explanation
Indices: 2341587--2341638 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
2341577 ATAACAATCG
* * * * * *
2341587 CAA CAA CAA CAG CAA CAG CAG CAA TAG CAA CAA CAA CAA CAG CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
2341635 CAA C
1 CAA C
2341639 CATAATAGAA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.56, C:0.33, G:0.10, T:0.02
Consensus pattern (3 bp):
CAA
Found at i:2351094 original size:32 final size:34
Alignment explanation
Indices: 2351054--2351126 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 34
2351044 TTGCAGAAAT
*
2351054 TAATT-TTTAAAAAATAAATA-TTAATATTTTAA
1 TAATTATTTTAAAAATAAATATTTAATATTTTAA
** *
2351086 -AA-TATTTTAATTATATATATTTAATATTTTAA
1 TAATTATTTTAAAAATAAATATTTAATATTTTAA
2351118 TAATTATTT
1 TAATTATTT
2351127 GAATATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.03
31 13 0.39
32 12 0.36
33 2 0.06
34 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
TAATTATTTTAAAAATAAATATTTAATATTTTAA
Found at i:2351098 original size:22 final size:20
Alignment explanation
Indices: 2351073--2351133 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
2351063 AAAAATAAAT
2351073 ATTAATATTTTAAAATATTTTA
1 ATTAATATTTT--AATATTTTA
2351095 ATTATATATATTTAATATTTTA
1 ATTA-ATAT-TTTAATATTTTA
*
2351117 A-TAATTATTTGAATATT
1 ATTAA-TATTTTAATATT
2351134 ATTATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
20 9 0.26
21 5 0.14
22 14 0.40
23 4 0.11
24 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTAATATTTTAATATTTTA
Found at i:2351143 original size:34 final size:32
Alignment explanation
Indices: 2351074--2351153 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 32
2351064 AAAATAAATA
*
2351074 TTAATATTTTAAAATATTTTAATTATATATAT
1 TTAATATTTTAAAATATTTAAATTATATATAT
2351106 TTAATATTTTAATAATTATTTGAATATTAT-TAT-T
1 TTAATATTTTAA-AA-TATTT-AA-ATTATATATAT
*
2351140 TTAATTTTTTAAAA
1 TTAATATTTTAAAA
2351154 GCAATCAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 12 0.29
33 4 0.10
34 17 0.40
35 4 0.10
36 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
TTAATATTTTAAAATATTTAAATTATATATAT
Found at i:2359097 original size:2 final size:2
Alignment explanation
Indices: 2359090--2359121 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2359080 ATGTTGCACC
2359090 CT 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 CT
2359122 TACCAAAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2367299 original size:18 final size:18
Alignment explanation
Indices: 2367264--2367301 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2367254 TTGCATTGAA
2367264 AAATAATATACCATGGGG
1 AAATAATATACCATGGGG
*
2367282 AAATAGATATATCA-GGGG
1 AAATA-ATATACCATGGGG
2367300 AA
1 AA
2367302 GAACTGCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (18 bp):
AAATAATATACCATGGGG
Found at i:2369186 original size:15 final size:17
Alignment explanation
Indices: 2369166--2369198 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2369156 TTATTAATAA
2369166 TTTAAA-AT-TTTTTAT
1 TTTAAATATATTTTTAT
2369181 TTTAAATATATTTTTAT
1 TTTAAATATATTTTTAT
2369198 T
1 T
2369199 GAATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATATATTTTTAT
Found at i:2369591 original size:24 final size:24
Alignment explanation
Indices: 2369564--2369615 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2369554 ACTGTAATTA
*
2369564 ATTTTTTTAAT-ATTAATTAAAAAT
1 ATTTATTTAATAATT-ATTAAAAAT
* *
2369588 ATTTATTTATTAATTTTTAAAAAT
1 ATTTATTTAATAATTATTAAAAAT
2369612 ATTT
1 ATTT
2369616 GTATTATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTTATTTAATAATTATTAAAAAT
Found at i:2369631 original size:24 final size:24
Alignment explanation
Indices: 2369579--2369632 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2369569 TTTAATATTA
2369579 ATTAAAAATATTTATTTATTAATT
1 ATTAAAAATATTTATTTATTAATT
* * *
2369603 TTTAAAAATATTTGTATTATTTA-T
1 ATTAAAAATATTTAT-TTATTAATT
2369627 ATTAAA
1 ATTAAA
2369633 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTAAAAATATTTATTTATTAATT
Found at i:2369672 original size:24 final size:23
Alignment explanation
Indices: 2369624--2369682 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 23
2369614 TTGTATTATT
2369624 TATATTAAATTTAAATAAAAATAA
1 TATATT-AATTTAAATAAAAATAA
*
2369648 TATATTAATTT-AATAAATACTTAA
1 TATATTAATTTAAATAAA-A-ATAA
2369672 TAATATTAATT
1 T-ATATTAATT
2369683 AATTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 6 0.19
23 6 0.19
24 10 0.32
25 9 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TATATTAATTTAAATAAAAATAA
Found at i:2369754 original size:3 final size:3
Alignment explanation
Indices: 2369741--2369803 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
2369731 AATACTTTTA
* * *
2369741 AAT ATAT AAT AAT AAT AAT AAT AAT GAT GAT AAT AAT ATT AAT -AT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2369786 TAT ATAT AAT AATT AAT A
1 AAT A-AT AAT AA-T AAT A
2369804 TTTTTAATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.04
3 40 0.78
4 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (3 bp):
AAT
Found at i:2369794 original size:21 final size:21
Alignment explanation
Indices: 2369742--2369841 Score: 87
Period size: 21 Copynumber: 4.6 Consensus size: 21
2369732 ATACTTTTAA
*
2369742 ATATATAATAATAATAATAATA
1 ATATATAATAATAATAAT-ATT
*
2369764 ATGATGATAATAATATTAATATT
1 AT-AT-ATAATAATAATAATATT
* *
2369787 ATATATAATAATTAATATTTTT
1 ATATATAATAA-TAATAATATT
* *
2369809 A-ATATATTAAATAAAAATATT
1 ATATATAAT-AATAATAATATT
2369830 AT-TATAATAATA
1 ATATATAATAATA
2369842 GTTTTAAAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
20 4 0.06
21 26 0.41
22 14 0.22
23 6 0.10
24 13 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
ATATATAATAATAATAATATT
Found at i:2369912 original size:16 final size:16
Alignment explanation
Indices: 2369875--2369926 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2369865 TTTATTAATA
* *
2369875 AAATTTATAAAAAATT
1 AAATTTTTATAAAATT
*
2369891 -AATTTTTTTAAGAA-T
1 AAATTTTTATAA-AATT
2369906 AAATTTTTATAAAATT
1 AAATTTTTATAAAATT
2369922 AAATT
1 AAATT
2369927 AAACAAACGT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (16 bp):
AAATTTTTATAAAATT
Found at i:2371349 original size:2 final size:2
Alignment explanation
Indices: 2371342--2371385 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
2371332 GAACAACTAC
2371342 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2371383 AT A
1 AT A
2371386 AATGTCCATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2375859 original size:23 final size:22
Alignment explanation
Indices: 2375833--2375895 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
2375823 ATTTATAAAA
2375833 TTATATAAATATTAAAATTATTT
1 TTATATAAATATT-AAATTATTT
* * *
2375856 TTATATTAATATTTATTTATTT
1 TTATATAAATATTAAATTATTT
2375878 TTATAATTAAAT-TTAAAT
1 TTAT-A-TAAATATTAAAT
2375896 AAAAATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 11 0.34
23 17 0.53
24 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATATAAATATTAAATTATTT
Found at i:2375861 original size:17 final size:17
Alignment explanation
Indices: 2375815--2375916 Score: 52
Period size: 17 Copynumber: 6.1 Consensus size: 17
2375805 TTATAGACTC
*
2375815 AAATTATTATT-TA-TA
1 AAATTATTTTTATATTA
* **
2375830 AAATTATATAAATATTA
1 AAATTATTTTTATATTA
2375847 AAATTATTTTTATATTA
1 AAATTATTTTTATATTA
*
2375864 ATATTTATTTATT-T-TTA
1 A-AATTATTT-TTATATTA
* ** *
2375881 TAATTAAATTTA-AATA
1 AAATTATTTTTATATTA
*
2375897 AAAATATTTTTATTATTA
1 AAATTATTTTTA-TATTA
2375915 AA
1 AA
2375917 TAATAACTTA
Statistics
Matches: 61, Mismatches: 18, Indels: 13
0.66 0.20 0.14
Matches are distributed among these distances:
15 9 0.15
16 17 0.28
17 20 0.33
18 13 0.21
19 2 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAATTATTTTTATATTA
Found at i:2375878 original size:22 final size:22
Alignment explanation
Indices: 2375850--2375892 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2375840 AATATTAAAA
2375850 TTATTTTTAT-ATTAATATTTAT
1 TTATTTTTATAATTAA-ATTTAT
2375872 TTATTTTTATAATTAAATTTA
1 TTATTTTTATAATTAAATTTA
2375893 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTTTTATAATTAAATTTAT
Found at i:2386799 original size:2 final size:2
Alignment explanation
Indices: 2386792--2386834 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2386782 TTTTCTATTT
2386792 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
2386834 T
1 T
2386835 TGTTTTTGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2389934 original size:19 final size:19
Alignment explanation
Indices: 2389912--2389949 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2389902 ATTTTAAATT
*
2389912 TAAATTATTATTTA-ATAAA
1 TAAAATATT-TTTATATAAA
2389931 TAAAATATTTTTATATAAA
1 TAAAATATTTTTATATAAA
2389950 AGATATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAAATATTTTTATATAAA
Found at i:2390193 original size:17 final size:17
Alignment explanation
Indices: 2390173--2390208 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2390163 TAATTTAATA
*
2390173 AATTTAAAAATTAAAAT
1 AATTAAAAAATTAAAAT
2390190 AATTAAAAAATTAAAAT
1 AATTAAAAAATTAAAAT
2390207 AA
1 AA
2390209 ATAATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATTAAAAAATTAAAAT
Found at i:2390201 original size:8 final size:8
Alignment explanation
Indices: 2390167--2390205 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
2390157 ATATCGTAAT
*
2390167 TTAATAAA
1 TTAAAAAA
*
2390175 TTTAAAAA
1 TTAAAAAA
2390183 TTAAAATAA
1 TTAAAA-AA
2390192 TTAAAAAA
1 TTAAAAAA
2390200 TTAAAA
1 TTAAAA
2390206 TAAATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 19 0.70
9 8 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TTAAAAAA
Found at i:2392525 original size:2 final size:2
Alignment explanation
Indices: 2392520--2392545 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2392510 AGCGTCACAC
2392520 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
2392546 GAGAGTCAAG
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:2392760 original size:3 final size:3
Alignment explanation
Indices: 2392752--2392777 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2392742 AAATTCTCTT
2392752 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2392778 TGGTTCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2407630 original size:27 final size:26
Alignment explanation
Indices: 2407595--2407675 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 26
2407585 AATTTTTATG
2407595 TTTTT-TAAATATTAAAAAAAGGA-ATT
1 TTTTTGTAAATATTAAAAAAA--ATATT
2407621 TTTTTGTAAATATTTTAAATAAAAATATT
1 TTTTTGTAAATA--TTAAA-AAAAATATT
*
2407650 TGTTTTGAAAATATT-AAAAAAATATT
1 T-TTTTGTAAATATTAAAAAAAATATT
2407676 AATATTTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 12
0.79 0.02 0.20
Matches are distributed among these distances:
26 14 0.29
27 8 0.17
28 3 0.06
29 9 0.19
30 14 0.29
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
TTTTTGTAAATATTAAAAAAAATATT
Found at i:2408383 original size:19 final size:19
Alignment explanation
Indices: 2408372--2408407 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2408362 TAAATGATAT
2408372 TAAAT-TAATTAAAAATAA
1 TAAATATAATTAAAAATAA
2408390 TAAATATAATTAAAAATA
1 TAAATATAATTAAAAATA
2408408 TTACAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAATATAATTAAAAATAA
Found at i:2408655 original size:11 final size:11
Alignment explanation
Indices: 2408605--2408653 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
2408595 TTAATTTAAT
2408605 TAAAAATTATA
1 TAAAAATTATA
2408616 TAAAAATTA-A
1 TAAAAATTATA
*
2408626 -AATAATTATA
1 TAAAAATTATA
2408636 TAAAAA-TATAA
1 TAAAAATTAT-A
2408647 TAAAAAT
1 TAAAAAT
2408654 ATTTAAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 7 0.22
10 5 0.16
11 20 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:2408655 original size:19 final size:20
Alignment explanation
Indices: 2408613--2408655 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2408603 ATTAAAAATT
**
2408613 ATATAAAAATTAAAATAATT
1 ATATAAAAATTAAAATAAAA
*
2408633 ATATAAAAA-TATAATAAAA
1 ATATAAAAATTAAAATAAAA
2408652 ATAT
1 ATAT
2408656 TTAAATCTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAAAATTAAAATAAAA
Found at i:2408977 original size:19 final size:20
Alignment explanation
Indices: 2408949--2408990 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
2408939 TTTACATGAT
2408949 TTTTTAAATATTTTTTAATA
1 TTTTTAAATATTTTTTAATA
*
2408969 TTTTT-AATATTTTTTTATA
1 TTTTTAAATATTTTTTAATA
2408988 TTT
1 TTT
2408991 GAAATAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTAAATATTTTTTAATA
Found at i:2408981 original size:8 final size:9
Alignment explanation
Indices: 2408949--2408982 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
2408939 TTTACATGAT
2408949 TTTTTAAATA
1 TTTTT-AATA
2408959 TTTTTTAATA
1 -TTTTTAATA
2408969 TTTTTAATA
1 TTTTTAATA
2408978 TTTTT
1 TTTTT
2408983 TTATATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 4 0.17
11 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (9 bp):
TTTTTAATA
Found at i:2408983 original size:10 final size:10
Alignment explanation
Indices: 2408947--2408990 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
2408937 ACTTTACATG
2408947 ATTTTTTAAAT
1 ATTTTTT-AAT
2408958 ATTTTTTAAT
1 ATTTTTTAAT
2408968 A-TTTTTAAT
1 ATTTTTTAAT
*
2408977 ATTTTTTTAT
1 ATTTTTTAAT
2408987 ATTT
1 ATTT
2408991 GAAATAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
9 9 0.29
10 15 0.48
11 7 0.23
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATTTTTTAAT
Found at i:2408996 original size:19 final size:19
Alignment explanation
Indices: 2408954--2408996 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2408944 ATGATTTTTT
*
2408954 AAATATTTTTTAATATTTT
1 AAATATTTTTTAATATTTG
* *
2408973 TAATATTTTTTTATATTTG
1 AAATATTTTTTAATATTTG
2408992 AAATA
1 AAATA
2408997 AATCTAAATG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
AAATATTTTTTAATATTTG
Found at i:2423384 original size:2 final size:2
Alignment explanation
Indices: 2423379--2423417 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2423369 TGTACATACG
*
2423379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2423418 GCTGGTCAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2428986 original size:48 final size:48
Alignment explanation
Indices: 2428930--2429027 Score: 178
Period size: 48 Copynumber: 2.0 Consensus size: 48
2428920 GGAAAAAGGC
*
2428930 ATGGCTTCATGGTTCAGACTGTAAAAGATGTTATTTTTATTGAGAATG
1 ATGGCTTCATGGTTCAGACTGTAAAAGATGTTACTTTTATTGAGAATG
*
2428978 ATGGCTTCATGGTTCAGACTGTAAAAGATGTTGCTTTTATTGAGAATG
1 ATGGCTTCATGGTTCAGACTGTAAAAGATGTTACTTTTATTGAGAATG
2429026 AT
1 AT
2429028 TGGGATAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (48 bp):
ATGGCTTCATGGTTCAGACTGTAAAAGATGTTACTTTTATTGAGAATG
Found at i:2429886 original size:2 final size:2
Alignment explanation
Indices: 2429881--2429917 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2429871 TTAGGTTTTT
*
2429881 TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2429918 CTGTCGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2437091 original size:27 final size:27
Alignment explanation
Indices: 2437053--2437107 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2437043 ACCATTCTTA
*
2437053 GTGAAGTATCTTTCTTCCCTATATTGT
1 GTGAAATATCTTTCTTCCCTATATTGT
2437080 GTGAAATATCTTTCTTCCCTATATTGT
1 GTGAAATATCTTTCTTCCCTATATTGT
2437107 G
1 G
2437108 CAAATTTGCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (27 bp):
GTGAAATATCTTTCTTCCCTATATTGT
Found at i:2444019 original size:29 final size:29
Alignment explanation
Indices: 2443987--2444054 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
2443977 AATTTTATTT
2443987 AAATAAATTTTTATATTTTTA-TTATAATC
1 AAATAAATTTTTATA-TTTTACTTATAATC
* * *
2444016 AAATAAA-TTATATATTTTACTTGTAATT
1 AAATAAATTTTTATATTTTACTTATAATC
2444044 AAATAAATTTT
1 AAATAAATTTT
2444055 AATCTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 5 0.15
28 19 0.58
29 9 0.27
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (29 bp):
AAATAAATTTTTATATTTTACTTATAATC
Found at i:2444074 original size:17 final size:16
Alignment explanation
Indices: 2444039--2444086 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
2444029 ATTTTACTTG
*
2444039 TAAT-TAAATAAATTT
1 TAATCTAAATTAATTT
2444054 TAATCTAAATTAATATT
1 TAATCTAAATTAAT-TT
*
2444071 TAATCTAAATTTATTT
1 TAATCTAAATTAATTT
2444087 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 4 0.14
16 10 0.34
17 15 0.52
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATCTAAATTAATTT
Found at i:2448583 original size:20 final size:20
Alignment explanation
Indices: 2448545--2448583 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2448535 TATTATTTTT
*
2448545 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
2448565 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
2448584 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:2448603 original size:25 final size:26
Alignment explanation
Indices: 2448545--2448653 Score: 109
Period size: 25 Copynumber: 4.2 Consensus size: 26
2448535 TATTATTTTT
2448545 TATTATAATT-ATATTTAA-AATATTATA
1 TATTAT-ATTAAT-TTTAATAAT-TTATA
*
2448572 TATTTATATAAATTTTAATAATTTA-A
1 TA-TTATATTAATTTTAATAATTTATA
* *
2448598 TATTATATTAATTTTAAT-ATATATC
1 TATTATATTAATTTTAATAATTTATA
*
2448623 TATTATATTAATTTTAATATATTTGTA
1 TATTATATTAATTTTAATA-ATTTATA
2448650 TATT
1 TATT
2448654 TTTATTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
24 4 0.06
25 33 0.48
26 3 0.04
27 20 0.29
28 9 0.13
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (26 bp):
TATTATATTAATTTTAATAATTTATA
Found at i:2448645 original size:14 final size:14
Alignment explanation
Indices: 2448601--2448645 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2448591 AATTTAATAT
2448601 TATATTAATTTTAA
1 TATATTAATTTTAA
* *
2448615 TATA-T-A-TCTAT
1 TATATTAATTTTAA
2448626 TATATTAATTTTAA
1 TATATTAATTTTAA
2448640 TATATT
1 TATATT
2448646 TGTATATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
11 7 0.29
12 2 0.08
13 2 0.08
14 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTAATTTTAA
Found at i:2449638 original size:2 final size:2
Alignment explanation
Indices: 2449631--2449656 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2449621 GGGTCCTTAG
2449631 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
2449657 ACTTTTTTCT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2453014 original size:79 final size:79
Alignment explanation
Indices: 2452879--2453027 Score: 235
Period size: 79 Copynumber: 1.9 Consensus size: 79
2452869 AATTATTGAC
* ** * * *
2452879 ATATATCCCCAAGAACTTGAAGTCTTGCTATGAGTTTATAGTTAGATTCACTTTTGCATTGTGGT
1 ATATATACCCAAGAACTTGAAGTCTTGCTACAAGTTTATAGTCAGAATCACCTTTGCATTGTGGT
2452944 CAATCCATATTTAA
66 CAATCCATATTTAA
*
2452958 ATATATACCCAGGAACTTGAAGTCTTGCTACAAGTTTATAGTCAGAATCACCTTTGCATTGTGGT
1 ATATATACCCAAGAACTTGAAGTCTTGCTACAAGTTTATAGTCAGAATCACCTTTGCATTGTGGT
2453023 CAATC
66 CAATC
2453028 AGCTAGTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 63 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (79 bp):
ATATATACCCAAGAACTTGAAGTCTTGCTACAAGTTTATAGTCAGAATCACCTTTGCATTGTGGT
CAATCCATATTTAA
Found at i:2461944 original size:26 final size:27
Alignment explanation
Indices: 2461863--2462013 Score: 133
Period size: 29 Copynumber: 5.3 Consensus size: 27
2461853 TAATATTTTT
*
2461863 ATTTTAATTATTATTTAAAATAAAATATA
1 ATTTTAATTATT-TTTAATAT-AAATATA
** *
2461892 ACGTTAATTTATATTTTATTATAAATATA
1 ATTTTAA-TTAT-TTTTAATATAAATATA
*
2461921 ATTTTAA-TATTTTTAATATGAATATA
1 ATTTTAATTATTTTTAATATAAATATA
*
2461947 ATTTTTAATTATTATTTGATATAAATATA
1 A-TTTTAATTATT-TTTAATATAAATATA
* * *
2461976 ATTTTATTTATATTTTATTATTTAATATA
1 ATTTTAATTAT-TTTTAATA-TAAATATA
*
2462005 ATTATAATT
1 ATTTTAATT
2462014 TTAATAATTT
Statistics
Matches: 99, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
26 15 0.15
27 9 0.09
28 18 0.18
29 46 0.46
30 10 0.10
31 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (27 bp):
ATTTTAATTATTTTTAATATAAATATA
Found at i:2461974 original size:35 final size:35
Alignment explanation
Indices: 2461935--2462012 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
2461925 TAATATTTTT
* *
2461935 AATATGAATATAATTTTTA-ATTATTATTTGATATA
1 AATAT-AATATAATTTATATATTATTATTTAATATA
* * *
2461970 AATATAATTTTATTTATATTTTATTATTTAATATA
1 AATATAATATAATTTATATATTATTATTTAATATA
*
2462005 ATTATAAT
1 AATATAAT
2462013 TTTAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (35 bp):
AATATAATATAATTTATATATTATTATTTAATATA
Found at i:2462025 original size:29 final size:28
Alignment explanation
Indices: 2461863--2462038 Score: 110
Period size: 29 Copynumber: 6.0 Consensus size: 28
2461853 TAATATTTTT
* *
2461863 ATTTTAATTATTATTTAAAATAAAATATA
1 ATTTTAATAATTATTTAATAT-AAATATA
** * *
2461892 ACGTTAAT-TTATATTTTATTATAAATATA
1 ATTTTAATAAT-TA-TTTAATATAAATATA
*
2461921 ATTTTAAT-ATT-TTTAATATGAATATA
1 ATTTTAATAATTATTTAATATAAATATA
* *
2461947 ATTTTTAATTATTATTTGATATAAATATA
1 A-TTTTAATAATTATTTAATATAAATATA
*
2461976 ATTTTATTTATATTTTATTATTTAATATAATTATA
1 ATTTTA---ATA----ATTATTTAATATAAATATA
*
2462011 ATTTTAATAATT-TATT-ATATACATATA
1 ATTTTAATAATTAT-TTAATATAAATATA
2462038 A
1 A
2462039 ATATTTTAAT
Statistics
Matches: 117, Mismatches: 17, Indels: 28
0.72 0.10 0.17
Matches are distributed among these distances:
26 14 0.12
27 18 0.15
28 15 0.13
29 36 0.31
30 6 0.05
31 2 0.02
32 3 0.03
35 23 0.20
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTTAATAATTATTTAATATAAATATA
Found at i:2462029 original size:25 final size:23
Alignment explanation
Indices: 2461983--2462029 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
2461973 ATAATTTTAT
*
2461983 TTATATTTTATTATTTAATATAA
1 TTATATTTTATAATTTAATATAA
*
2462006 TTATAATTTTAATAATTTATTATA
1 TTAT-ATTTT-ATAATTTAATATA
2462030 TACATATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTATATTTTATAATTTAATATAA
Found at i:2462419 original size:20 final size:20
Alignment explanation
Indices: 2462396--2462435 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2462386 TAATATATTA
2462396 TAAAAATAAAATAAATATAT
1 TAAAAATAAAATAAATATAT
* * *
2462416 TAAAATTTATATAAATATAT
1 TAAAAATAAAATAAATATAT
2462436 AATATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATAAAATAAATATAT
Found at i:2462444 original size:20 final size:20
Alignment explanation
Indices: 2462406--2462471 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
2462396 TAAAAATAAA
2462406 ATAAATATATTAAAATTTAT
1 ATAAATATATTAAAATTTAT
*
2462426 ATAAATATA-TAATA-TT-T
1 ATAAATATATTAAAATTTAT
*
2462443 -TAAATATAATTAATAATATAT
1 ATAAATAT-ATTAA-AATTTAT
2462464 A-AAATATA
1 ATAAATATA
2462472 CAAACACAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
16 7 0.19
17 2 0.05
18 5 0.14
19 5 0.14
20 11 0.30
21 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAATATATTAAAATTTAT
Found at i:2462460 original size:21 final size:22
Alignment explanation
Indices: 2462424--2462471 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
2462414 ATTAAAATTT
* *
2462424 ATATAAATATATAATATTTTAA
1 ATATAAATATATAATATATAAA
*
2462446 ATATAATTA-ATAATATATAAA
1 ATATAAATATATAATATATAAA
2462467 ATATA
1 ATATA
2462472 CAAACACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATATAAATATATAATATATAAA
Found at i:2470954 original size:23 final size:23
Alignment explanation
Indices: 2470926--2470971 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
2470916 AATATAAGTA
2470926 TAAAATAAATTATTAAACATGTT
1 TAAAATAAATTATTAAACATGTT
2470949 TAAAATAAATTATTAAACATGTT
1 TAAAATAAATTATTAAACATGTT
2470972 GCTTTCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
TAAAATAAATTATTAAACATGTT
Found at i:2477067 original size:17 final size:17
Alignment explanation
Indices: 2477047--2477083 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2477037 CTGTCAGTAA
*
2477047 AAATATAAGATTTTTTT
1 AAATATAAAATTTTTTT
*
2477064 AAATTTAAAATTTTTTT
1 AAATATAAAATTTTTTT
2477081 AAA
1 AAA
2477084 AAATGCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATATAAAATTTTTTT
Found at i:2477110 original size:23 final size:22
Alignment explanation
Indices: 2477090--2477156 Score: 89
Period size: 24 Copynumber: 2.9 Consensus size: 22
2477080 TAAAAAATGC
2477090 AAAAATTCAAAAAATAAAAATTTA
1 AAAAATTCAAAAAATAAAAA--TA
*
2477114 TAAAATTCAAAAAATAAAAATA
1 AAAAATTCAAAAAATAAAAATA
*
2477136 AAAATATTCAAAAATTAAAAA
1 AAAA-ATTCAAAAAATAAAAA
2477157 ATAATTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 5 0.13
23 15 0.38
24 19 0.49
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
AAAAATTCAAAAAATAAAAATA
Found at i:2477133 original size:30 final size:30
Alignment explanation
Indices: 2477099--2477160 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2477089 CAAAAATTCA
2477099 AAAAATAAAAAT-TT-ATAAAATTCAAAAAAT
1 AAAAATAAAAATATTCA-AAAATT-AAAAAAT
2477129 AAAAATAAAAATATTCAAAAATTAAAAAAT
1 AAAAATAAAAATATTCAAAAATTAAAAAAT
2477159 AA
1 AA
2477161 TTTTAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 21 0.70
31 8 0.27
32 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (30 bp):
AAAAATAAAAATATTCAAAAATTAAAAAAT
Found at i:2477194 original size:55 final size:55
Alignment explanation
Indices: 2477129--2477232 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 55
2477119 TTCAAAAAAT
2477129 AAAAATAAAAATATTCAAAAATT-AAAA-A-ATAATTTTAAAATTT-TAAAATACATA
1 AAAAATAAAAATA-TCAAAAATTGAAAAGAGATAA--TTAAAATTTATAAAATACATA
*
2477183 AAAAATAAAAAATATCAAAACTTGAAAAGAGATAATTAAAATTTATAAAA
1 AAAAAT-AAAAATATCAAAAATTGAAAAGAGATAATTAAAATTTATAAAA
2477233 GATTGAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
54 14 0.32
55 20 0.45
56 6 0.14
57 4 0.09
ACGTcount: A:0.65, C:0.04, G:0.03, T:0.28
Consensus pattern (55 bp):
AAAAATAAAAATATCAAAAATTGAAAAGAGATAATTAAAATTTATAAAATACATA
Found at i:2477940 original size:18 final size:19
Alignment explanation
Indices: 2477913--2477948 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2477903 TTAATTAAAG
*
2477913 TAATTTATAT-TTATATAA
1 TAATTGATATATTATATAA
2477931 TAATTGATATATTATATA
1 TAATTGATATATTATATA
2477949 TTTATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TAATTGATATATTATATAA
Found at i:2477968 original size:10 final size:10
Alignment explanation
Indices: 2477945--2477975 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
2477935 TGATATATTA
2477945 TATATTTATAT
1 TATATTT-TAT
2477956 TATATTTTAT
1 TATATTTTAT
2477966 TATATTTTAT
1 TATATTTTAT
2477976 AATTATGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.65
11 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TATATTTTAT
Found at i:2477968 original size:15 final size:13
Alignment explanation
Indices: 2477918--2477981 Score: 57
Period size: 11 Copynumber: 5.1 Consensus size: 13
2477908 TAAAGTAATT
*
2477918 TATATTTATATAA
1 TATATTTATATTA
2477931 TA-ATTGATATATTA
1 TATATT--TATATTA
2477945 TATATTTATA-T-
1 TATATTTATATTA
2477956 TATATTT-TATTA
1 TATATTTATATTA
2477968 TAT-TTTATAATTA
1 TATATTTAT-ATTA
2477981 T
1 T
2477982 GGTAAAGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 14
0.74 0.02 0.24
Matches are distributed among these distances:
10 2 0.05
11 11 0.26
12 8 0.19
13 11 0.26
14 8 0.19
15 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TATATTTATATTA
Found at i:2482594 original size:2 final size:2
Alignment explanation
Indices: 2482587--2482615 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2482577 GCTTTTTGCC
2482587 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 A
2482616 AGCAAACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2482883 original size:20 final size:21
Alignment explanation
Indices: 2482860--2482921 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 21
2482850 TAATCAGATT
2482860 TAAAATATTATATAT-TTATA
1 TAAAATATTATATATATTATA
*
2482880 T-AAATTTTA-ATATATTA-A
1 TAAAATATTATATATATTATA
*
2482898 TAATTTATATTATATATATTATA
1 TAA--AATATTATATATATTATA
2482921 T
1 T
2482922 TATATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 6 0.18
19 11 0.33
20 1 0.03
21 5 0.15
22 8 0.24
23 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TAAAATATTATATATATTATA
Found at i:2482921 original size:14 final size:14
Alignment explanation
Indices: 2482864--2482926 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
2482854 CAGATTTAAA
2482864 ATATTATATAT-TT
1 ATATTATATATATT
* * *
2482877 ATA-TAAATTTTAAT
1 ATATTATA-TATATT
2482891 ATATTA-ATA-ATTT
1 ATATTATATATA-TT
2482904 ATATTATATATATT
1 ATATTATATATATT
2482918 ATATTATAT
1 ATATTATAT
2482927 TTTATAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
12 4 0.10
13 13 0.33
14 19 0.49
15 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTATATATATT
Found at i:2485212 original size:212 final size:210
Alignment explanation
Indices: 2484548--2485594 Score: 1805
Period size: 212 Copynumber: 5.0 Consensus size: 210
2484538 CTGTTACAAA
* * * * * *
2484548 TTATAAGAATGGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAGCTAAGTTCAAACCTTAA
1 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
2484613 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
66 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGT----
2484678 GGGGGGGGGGTTTAAAACTCAAACCCACCCA-TGAACACTTCTATTTCCATTCATAGCTTCAAAT
127 GGGGGGGGGGTTTAAAACTCAAACCCACCCACT-AACACTTCTATTTCCATTCATAGCTTCAAAT
2484742 CTTCCAAGTTCAATGATGGG
191 CTTCCAAGTTCAATGATGGG
2484762 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
1 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
2484827 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
66 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
*
2484892 GGGGGTTTTAAAACTCAAACCCACCCACTAACACTTCTATTTCCATTCATAGCTTC-AATCTTCC
131 GGGGGGTTTAAAACTCAAACCCACCCACTAACACTTCTATTTCCATTCATAGCTTCAAATCTTCC
2484956 AAGTTCAATGATGGG
196 AAGTTCAATGATGGG
*
2484971 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAATCAAATTGAACAGAACCAAGTTTAAATCTTGA
1 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
2485036 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
66 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGT-GGG
2485101 GGAGGGGGTTTTAAAACTCAAACCCACCCACTAACACTTCTATTTCCATTCATAGCTTC-AATCT
130 GG-GGGGG-TTTAAAACTCAAACCCACCCACTAACACTTCTATTTCCATTCATAGCTTCAAATCT
2485165 TCCAAGTTCAATGATGGG
193 TCCAAGTTCAATGATGGG
2485183 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
1 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
*
2485248 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTCTATTTGGGA--GTGTGGGG
66 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
*
2485311 GGGGTGTTTAAAACTCAAACCCACCCA-TGAACACTTCTATTTCCATTCATAGCTTCAAATCTTC
131 GGGGGGTTTAAAACTCAAACCCACCCACT-AACACTTCTATTTCCATTCATAGCTTCAAATCTTC
2485375 CAAGTTCAATGATGGG
195 CAAGTTCAATGATGGG
2485391 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
1 TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
*
2485456 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGA-------AGG
66 ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
* *
2485514 GGGGGGTGTAAAACTCAAACCCACCCACGAACACTTCTATTTCCATTCATAGCTTCAAATCTTCC
131 GGGGGGTTTAAAACTCAAACCCACCCACTAACACTTCTATTTCCATTCATAGCTTCAAATCTTCC
2485579 AAGTTCAATGATGGG
196 AAGTTCAATGATGGG
2485594 T
1 T
2485595 CTCCAATTAA
Statistics
Matches: 809, Mismatches: 17, Indels: 25
0.95 0.02 0.03
Matches are distributed among these distances:
203 79 0.10
206 1 0.00
207 48 0.06
208 146 0.18
209 153 0.19
210 66 0.08
211 5 0.01
212 191 0.24
214 120 0.15
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (210 bp):
TTATAAGAATTGTTGGAACCAAAGCCTTGAAAAACAAATTGAACAGAACCAAGTTTAAATCTTGA
ATATTAAAGCCGAAAGCTTTATTCTGATTTTTCAATAAACCCTTTTTATTTGGGAGTGTGTGGGG
GGGGGGTTTAAAACTCAAACCCACCCACTAACACTTCTATTTCCATTCATAGCTTCAAATCTTCC
AAGTTCAATGATGGG
Found at i:2492660 original size:3 final size:3
Alignment explanation
Indices: 2492654--2492786 Score: 176
Period size: 3 Copynumber: 44.3 Consensus size: 3
2492644 GGCTGCTGGG
* * * * * * * *
2492654 GCT GCT GCT GTT GCT GCT GCT GCT GTT GCT GTT GTT GTT GTT GTT GTT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
2492702 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
* *
2492750 GTT GCT GCT GCT GCT GCT GCT GCT GCT GTT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
2492787 AGCATGCCTC
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 120 1.00
ACGTcount: A:0.00, C:0.26, G:0.34, T:0.41
Consensus pattern (3 bp):
GCT
Found at i:2492848 original size:15 final size:15
Alignment explanation
Indices: 2492830--2492896 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 15
2492820 CAATTGTGGA
2492830 TGCTGCTGCTGCTGT
1 TGCTGCTGCTGCTGT
2492845 TGCTG-T--TGCTGT
1 TGCTGCTGCTGCTGT
* * **
2492857 TGATGTTGAGGCTGT
1 TGCTGCTGCTGCTGT
** *
2492872 TGAGGTTGCTGCTGT
1 TGCTGCTGCTGCTGT
2492887 TGCTGCTGCT
1 TGCTGCTGCT
2492897 CCCGAGCTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
12 10 0.24
13 1 0.02
14 1 0.02
15 29 0.71
ACGTcount: A:0.04, C:0.18, G:0.36, T:0.42
Consensus pattern (15 bp):
TGCTGCTGCTGCTGT
Found at i:2496024 original size:18 final size:18
Alignment explanation
Indices: 2496001--2496036 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2495991 ATATTTTTTT
2496001 TATTTTA-GCTTTTAAAAA
1 TATTTTATGC-TTTAAAAA
2496019 TATTTTATGCTTTAAAAA
1 TATTTTATGCTTTAAAAA
2496037 AAGCACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.88
19 2 0.12
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
TATTTTATGCTTTAAAAA
Found at i:2496036 original size:19 final size:18
Alignment explanation
Indices: 2496001--2496037 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2495991 ATATTTTTTT
*
2496001 TATTTTAGCTTTTAAAAA
1 TATTTTAGCTTTAAAAAA
2496019 TATTTTATGCTTTAAAAAA
1 TATTTTA-GCTTTAAAAAA
2496038 AGCACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
TATTTTAGCTTTAAAAAA
Found at i:2497747 original size:18 final size:18
Alignment explanation
Indices: 2497726--2497797 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 18
2497716 TTTAAAACAT
2497726 TTTTTATTAATTTATTTA
1 TTTTTATTAATTTATTTA
*
2497744 TTTTT-TAAATTTTATTTTA
1 TTTTTATTAA-TTTA-TTTA
2497763 TTTTTAATT-ATTTAATTTA
1 TTTTT-ATTAATTT-ATTTA
*
2497782 -ATTTATTAATTTATTT
1 TTTTTATTAATTTATTT
2497798 TGACATCGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
17 10 0.22
18 16 0.36
19 16 0.36
20 2 0.04
21 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTATTAATTTATTTA
Found at i:2497766 original size:38 final size:37
Alignment explanation
Indices: 2497724--2497798 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
2497714 TTTTTAAAAC
* *
2497724 ATTTTTTATTAATTT-ATTT-ATTTTTTAAATTTTATTTT
1 ATTTTTAATT-ATTTAATTTAATTTATT-AA-TTTATTTT
2497762 ATTTTTAATTATTTAATTTAATTTATTAATTTATTTT
1 ATTTTTAATTATTTAATTTAATTTATTAATTTATTTT
2497799 GACATCGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
37 12 0.36
38 15 0.45
39 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (37 bp):
ATTTTTAATTATTTAATTTAATTTATTAATTTATTTT
Found at i:2498262 original size:8 final size:7
Alignment explanation
Indices: 2498240--2498275 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
2498230 TAATTACTGC
2498240 TTCTTCTT
1 TTCTT-TT
2498248 TTCTTTT
1 TTCTTTT
2498255 TTCTTTT
1 TTCTTTT
2498262 TTC-TTT
1 TTCTTTT
2498268 TTCTTTT
1 TTCTTTT
2498275 T
1 T
2498276 AATTCCATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.22
7 16 0.59
8 5 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTCTTTT
Found at i:2498268 original size:13 final size:14
Alignment explanation
Indices: 2498240--2498275 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2498230 TAATTACTGC
2498240 TTCTTCTTTTCTTTT
1 TTCTT-TTTTCTTTT
2498255 TTCTTTTTTC-TTT
1 TTCTTTTTTCTTTT
2498268 TTCTTTTT
1 TTCTTTTT
2498276 AATTCCATGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.52
14 5 0.24
15 5 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTCTTTTTTCTTTT
Found at i:2500651 original size:25 final size:22
Alignment explanation
Indices: 2500613--2500671 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 22
2500603 ATTTTTAAAA
2500613 ATTTA-TAATAATAAGATGATATTT
1 ATTTATTAAT-ATAA-AT-ATATTT
2500637 CATTTATTAATATAAATATATTT
1 -ATTTATTAATATAAATATATTT
*
2500660 ATATATTAATAT
1 ATTTATTAATAT
2500672 TTATTAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 11 0.34
23 6 0.19
24 2 0.06
25 9 0.28
26 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (22 bp):
ATTTATTAATATAAATATATTT
Found at i:2501881 original size:17 final size:19
Alignment explanation
Indices: 2501861--2501909 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2501851 TCGTATTATT
2501861 TTTATATATTATT-A-TAC
1 TTTATATATTATTAATTAC
2501878 TTTATATTATATATTAATTAC
1 TTTATA-TAT-TATTAATTAC
2501899 TTT-TATATTAT
1 TTTATATATTAT
2501910 ATCAAAGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 6 0.21
19 7 0.25
20 3 0.11
21 6 0.21
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTATATATTATTAATTAC
Found at i:2501887 original size:22 final size:22
Alignment explanation
Indices: 2501862--2501911 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2501852 CGTATTATTT
*
2501862 TTATATATTATTATAC-TTTATA
1 TTATATATTAAT-TACTTTTATA
2501884 TTATATATTAATTACTTTTATA
1 TTATATATTAATTACTTTTATA
2501906 TTATAT
1 TTATAT
2501912 CAAAGTCGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATATTAATTACTTTTATA
Found at i:2501903 original size:39 final size:35
Alignment explanation
Indices: 2501828--2501911 Score: 91
Period size: 39 Copynumber: 2.3 Consensus size: 35
2501818 AAATTTTGAC
*
2501828 ATATTTATATATTTATATTATATTCGTATTATTTTT
1 ATATTTATATATTTATATTATATTC-TATTACTTTT
2501864 ATATATTATTATACTTTATATTATATAT-TAATTACTTTT
1 ATAT-TTA-TATA-TTTATATTATAT-TCT-ATTACTTTT
2501903 ATA-TTATAT
1 ATATTTATAT
2501912 CAAAGTCGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
36 7 0.17
37 6 0.14
38 5 0.12
39 23 0.55
40 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.61
Consensus pattern (35 bp):
ATATTTATATATTTATATTATATTCTATTACTTTT
Found at i:2503486 original size:21 final size:22
Alignment explanation
Indices: 2503440--2503487 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2503430 TTTATAATTA
*
2503440 AAATTTAATAAAAATATTATTT
1 AAATTAAATAAAAATATTATTT
*
2503462 -AATTAAATAAATA-ATTATTT
1 AAATTAAATAAAAATATTATTT
2503482 AAATTA
1 AAATTA
2503488 GATTTAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTAAATAAAAATATTATTT
Found at i:2509676 original size:17 final size:17
Alignment explanation
Indices: 2509656--2509703 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
2509646 ACAAAAAAAT
2509656 AATAATT-ATTATAATTA
1 AATAATTAATTA-AATTA
2509673 AAT-ATTAAATTAAATTA
1 AATAATT-AATTAAATTA
*
2509690 AATAATAAATTAAA
1 AATAATTAATTAAA
2509704 ATACTATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 3 0.11
17 18 0.67
18 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATAATTAATTAAATTA
Found at i:2510625 original size:2 final size:2
Alignment explanation
Indices: 2510620--2510648 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2510610 TCTCTCTCTC
2510620 TA TA 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 TA TA T
2510649 GTAATTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2512864 original size:15 final size:15
Alignment explanation
Indices: 2512837--2512868 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2512827 TAAAATATAA
2512837 TATTTTAAATTAAAT
1 TATTTTAAATTAAAT
*
2512852 TATTTTAATTTAAAT
1 TATTTTAAATTAAAT
2512867 TA
1 TA
2512869 CTATTTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTAAATTAAAT
Found at i:2514247 original size:2 final size:2
Alignment explanation
Indices: 2514240--2514278 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2514230 GGGACCATGC
2514240 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
2514279 TTCTTACCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2514771 original size:15 final size:16
Alignment explanation
Indices: 2514747--2514781 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2514737 TAAATATGAA
2514747 TTTAAAATAT-AATTT
1 TTTAAAATATAAATTT
*
2514762 TTTAATATATAAATTT
1 TTTAAAATATAAATTT
2514778 TTTA
1 TTTA
2514782 TAAAATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAAATATAAATTT
Found at i:2515289 original size:32 final size:30
Alignment explanation
Indices: 2515204--2515311 Score: 98
Period size: 32 Copynumber: 3.6 Consensus size: 30
2515194 ACAAAATATA
* * *
2515204 TATAGTAAATATGATATAAAATA-TAATAA-
1 TATA-TAAATATAATATAATATATTAAAAAT
*
2515233 TA-A-AAATATAATATAATATTTTAAAAAT
1 TATATAAATATAATATAATATATTAAAAAT
* *
2515261 TATATAATTATAATTATTAATATATTAAAATT
1 TATATAAATATAA-TA-TAATATATTAAAAAT
*
2515293 TATATAAATATAAAATAAT
1 TATATAAATATAATATAAT
2515312 TTAAATATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
26 14 0.22
27 5 0.08
28 3 0.05
29 3 0.05
30 11 0.17
31 3 0.05
32 25 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
TATATAAATATAATATAATATATTAAAAAT
Found at i:2515326 original size:22 final size:21
Alignment explanation
Indices: 2515294--2515341 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2515284 ATTAAAATTT
*
2515294 ATATAAATATAAAATAATTTAA
1 ATATAAATATAAAATAA-TAAA
* *
2515316 ATATAATTATAATATAATAAA
1 ATATAAATATAAAATAATAAA
2515337 ATATA
1 ATATA
2515342 TAAATACAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAATATAAAATAATAAA
Found at i:2515336 original size:20 final size:18
Alignment explanation
Indices: 2515262--2515332 Score: 60
Period size: 17 Copynumber: 4.0 Consensus size: 18
2515252 TTTAAAAATT
*
2515262 ATATAATTATAATTATTA
1 ATATAATTATAATTATAA
*
2515280 ATAT-ATTAAAATTTATATAA
1 ATATAATTATAA--T-TATAA
*
2515300 ATATAA-AATAATT-TAA
1 ATATAATTATAATTATAA
2515316 ATATAATTATAA-TATAA
1 ATATAATTATAATTATAA
2515333 TAAAATATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
16 10 0.24
17 14 0.33
18 5 0.12
19 1 0.02
20 11 0.26
21 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTATAATTATAA
Found at i:2516825 original size:19 final size:19
Alignment explanation
Indices: 2516801--2516860 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 19
2516791 TCAATTTATG
2516801 TATTTTATTATATTTATAT
1 TATTTTATTATATTTATAT
2516820 TA-TTT-TTATATGTTATAAT
1 TATTTTATTATAT-TTAT-AT
*
2516839 TATATTTAATATATTATATAT
1 TAT-TTTATTATATT-TATAT
2516860 T
1 T
2516861 TATATAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 6 0.18
21 7 0.21
22 8 0.24
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TATTTTATTATATTTATAT
Found at i:2516876 original size:27 final size:26
Alignment explanation
Indices: 2516842--2516892 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 26
2516832 TTATAATTAT
2516842 ATTTAATATATT-ATATATTTATATAA
1 ATTTAATATATTAATA-ATTTATATAA
2516868 ATTTAAATATATTAATAATTTATAT
1 ATTT-AATATATTAATAATTTATAT
2516893 TGTATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 4 0.17
27 16 0.70
28 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATTTAATATATTAATAATTTATATAA
Found at i:2516910 original size:32 final size:34
Alignment explanation
Indices: 2516839--2516920 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 34
2516829 ATGTTATAAT
2516839 TATATTTAATATATTATATATTTATATAAATTTAAA
1 TATATTTAATA-ATT-TATATTTATATAAATTTAAA
* **
2516875 TATA-TTAATAATTTATA-TTGTATAAATTTTGA
1 TATATTTAATAATTTATATTTATATAAATTTAAA
2516907 TATATTTAA-AATTT
1 TATATTTAATAATTT
2516921 TTGTATCGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 21 0.50
33 8 0.19
34 3 0.07
35 6 0.14
36 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (34 bp):
TATATTTAATAATTTATATTTATATAAATTTAAA
Found at i:2519003 original size:2 final size:2
Alignment explanation
Indices: 2518998--2519036 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2518988 CCAAAAATCT
*
2518998 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2519037 CATGAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2523874 original size:2 final size:2
Alignment explanation
Indices: 2523831--2523864 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2523821 CAACACTACC
2523831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2523865 GTTGATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.