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 9 of 10
Found at i:959294 original size:21 final size:21
Alignment explanation
Indices: 959270--959313 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
959260 AAAAAAGTTT
*
959270 TATTTAAAT-TTAATTATAAAA
1 TATTTAAATATCAA-TATAAAA
959291 TATTTAAATATCAATATAAAA
1 TATTTAAATATCAATATAAAA
959312 TA
1 TA
959314 ATTTTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATTTAAATATCAATATAAAA
Found at i:961845 original size:20 final size:20
Alignment explanation
Indices: 961804--961844 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
961794 TATTATTTAT
*
961804 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
*
961824 ATATTATATATTTTATATAAA
1 ATATTATA-ATTATATATAAA
961845 TTTAAATACG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:961928 original size:17 final size:20
Alignment explanation
Indices: 961894--961958 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 20
961884 TATATTCATA
961894 TATTTTTGTTATGTTTATAT
1 TATTTTTGTTATGTTTATAT
961914 TATTTTT-TT-TG-TTATAT
1 TATTTTTGTTATGTTTATAT
* *
961931 TATATTTTAATTATTTTTATAT
1 TAT-TTTT-GTTATGTTTATAT
*
961953 TGTTTT
1 TATTTT
961959 CGTATATACC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
17 9 0.24
18 6 0.16
19 2 0.05
20 9 0.24
21 4 0.11
22 8 0.21
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (20 bp):
TATTTTTGTTATGTTTATAT
Found at i:962302 original size:23 final size:23
Alignment explanation
Indices: 962262--962307 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
962252 CCATTTTAGA
* *
962262 TTTAAATCATTTTTAATTAAAAT
1 TTTAAATCAATTTAAATTAAAAT
* *
962285 TTTAAATTAATTTAAATTTAAAT
1 TTTAAATCAATTTAAATTAAAAT
962308 CATTTCGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAATCAATTTAAATTAAAAT
Found at i:962306 original size:16 final size:16
Alignment explanation
Indices: 962274--962361 Score: 63
Period size: 17 Copynumber: 5.4 Consensus size: 16
962264 TAAATCATTT
*
962274 TTAATTAAAATTTTAAA
1 TTAATTTAAA-TTTAAA
962291 TTAATTTAAATTTAAA
1 TTAATTTAAATTTAAA
* * *
962307 -TCATTTCGAATCTAAA
1 TTAATTT-AAATTTAAA
*
962323 -TAATTTTAAATTCAAA
1 TTAA-TTTAAATTTAAA
* *
962339 TTACTTTTGAATTTAAA
1 TTA-ATTTAAATTTAAA
962356 TTAATT
1 TTAATT
962362 AATTTGAAGT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
15 5 0.09
16 23 0.42
17 27 0.49
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:972846 original size:26 final size:26
Alignment explanation
Indices: 972811--972864 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
972801 AATTAGATAA
*
972811 TAAATGAATTTAAAT-TTTAAATAAAT
1 TAAATAAATTTAAATATTTAAA-AAAT
972837 TAAATAAATTTAAATATTTAAAAAAT
1 TAAATAAATTTAAATATTTAAAAAAT
972863 TA
1 TA
972865 TAGATCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
TAAATAAATTTAAATATTTAAAAAAT
Found at i:973786 original size:7 final size:7
Alignment explanation
Indices: 973774--973803 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
973764 ATTTGAACCC
973774 ATAAAAA
1 ATAAAAA
973781 ATAAAAAA
1 AT-AAAAA
973789 ATAAAAA
1 ATAAAAA
973796 ATAAAAA
1 ATAAAAA
973803 A
1 A
973804 CCGAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
ATAAAAA
Found at i:973794 original size:15 final size:15
Alignment explanation
Indices: 973774--973803 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
973764 ATTTGAACCC
973774 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
973789 ATAAAAAATAAAAAA
1 ATAAAAAATAAAAAA
973804 CCGAATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (15 bp):
ATAAAAAATAAAAAA
Found at i:975202 original size:86 final size:86
Alignment explanation
Indices: 975101--975271 Score: 270
Period size: 86 Copynumber: 2.0 Consensus size: 86
975091 AGCTCAATGA
* * * *
975101 ATGTCTACATCTAAAATATACATCACCAATTATTTTATTTATCAAATTAAAAGAATTTGTATAAT
1 ATGTCAACATCTAAAAGATACATCACCAATTATTTTATATATCAAATTAAAAGAATTTATATAAT
* *
975166 AGTATCTATCAAAAGCACATG
66 AGTACCTATCAAAAACACATG
* *
975187 ATGTCAACATTTAAAAGATACATCACCAATTATTTTATATATTAAATTAAAAGAATTTATATAAT
1 ATGTCAACATCTAAAAGATACATCACCAATTATTTTATATATCAAATTAAAAGAATTTATATAAT
975252 AGTACCTATCAAAAACACAT
66 AGTACCTATCAAAAACACAT
975272 TTATTTTCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 77 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (86 bp):
ATGTCAACATCTAAAAGATACATCACCAATTATTTTATATATCAAATTAAAAGAATTTATATAAT
AGTACCTATCAAAAACACATG
Found at i:977165 original size:64 final size:64
Alignment explanation
Indices: 977076--977197 Score: 181
Period size: 64 Copynumber: 1.9 Consensus size: 64
977066 AATCAGAGAT
** *
977076 TTAATTCATTTAATTTGGATAATTATTCATAAAAAACTATATTTAATAAATTTAAATTTGAATA
1 TTAATTCATTTAATTCAGATAATTATTCATAAAAAACTATATTTAAAAAATTTAAATTTGAATA
* * * *
977140 TTAATTCATTTAGTTCATATAATTATTTATAAAAAATTATATTTAAAAAATTTAAATT
1 TTAATTCATTTAATTCAGATAATTATTCATAAAAAACTATATTTAAAAAATTTAAATT
977198 CAAATCCTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (64 bp):
TTAATTCATTTAATTCAGATAATTATTCATAAAAAACTATATTTAAAAAATTTAAATTTGAATA
Found at i:977682 original size:2 final size:2
Alignment explanation
Indices: 977675--977703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
977665 TCTTTTATCA
977675 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
977704 AGCGTTGCCA
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:978433 original size:11 final size:11
Alignment explanation
Indices: 978408--978444 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
978398 TTTTTATTAA
978408 TAATTTAATA-
1 TAATTTAATAT
*
978418 T-ATTTGATAT
1 TAATTTAATAT
978428 TAATTTAATAT
1 TAATTTAATAT
978439 TAATTT
1 TAATTT
978445 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 7 0.30
10 2 0.09
11 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (11 bp):
TAATTTAATAT
Found at i:978464 original size:19 final size:21
Alignment explanation
Indices: 978440--978481 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
978430 ATTTAATATT
*
978440 AATTTTTTTTAAA-AAAT-AA
1 AATTTTATTTAAATAAATCAA
978459 AATTTTATTTAAATAAATCAA
1 AATTTTATTTAAATAAATCAA
978480 AA
1 AA
978482 ATCATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTTATTTAAATAAATCAA
Found at i:978866 original size:21 final size:21
Alignment explanation
Indices: 978841--978881 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
978831 TTTTTTATAT
978841 TTATAAATATAATAAATATTA
1 TTATAAATATAATAAATATTA
* * *
978862 TTATAATTATTATAATTATT
1 TTATAAATATAATAAATATT
978882 TTAATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTATAAATATAATAAATATTA
Found at i:978870 original size:9 final size:9
Alignment explanation
Indices: 978858--978931 Score: 73
Period size: 9 Copynumber: 8.2 Consensus size: 9
978848 TATAATAAAT
978858 ATTATTATA
1 ATTATTATA
978867 ATTATTATA
1 ATTATTATA
*
978876 ATTATTTTA
1 ATTATTATA
*
978885 ATTTTATATA
1 ATTAT-TATA
978895 ATTTATTATAA
1 A-TTATTAT-A
*
978906 AATATTAT-
1 ATTATTATA
978914 A--ATTATA
1 ATTATTATA
978921 ATTATTATA
1 ATTATTATA
978930 AT
1 AT
978932 AAAAATTAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 5 0.09
7 1 0.02
8 1 0.02
9 29 0.54
10 13 0.24
11 5 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATTATTATA
Found at i:978879 original size:15 final size:15
Alignment explanation
Indices: 978835--978931 Score: 63
Period size: 15 Copynumber: 6.5 Consensus size: 15
978825 ATCGTATTTT
* *
978835 TTATATTTATAAATA
1 TTATAATTATAATTA
* * *
978850 TAATAAATATTATTA
1 TTATAATTATAATTA
* *
978865 TAATTATTATAATTA
1 TTATAATTATAATTA
* * *
978880 TTTTAATTTTATATAA
1 TTATAATTATA-ATTA
*
978896 TT-T-ATTATAAAATA
1 TTATAATTAT-AATTA
978910 TTATAATTATAATTA
1 TTATAATTATAATTA
978925 TTATAAT
1 TTATAAT
978932 AAAAATTAAT
Statistics
Matches: 61, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
14 8 0.13
15 43 0.70
16 10 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATAATTATAATTA
Found at i:978941 original size:25 final size:25
Alignment explanation
Indices: 978891--978947 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
978881 TTTAATTTTA
* *
978891 TATAATTTATTATAAAATATTATAAT
1 TATAA-TTATTATAAAAAAATATAAT
978917 TATAATTATTATAATAAAAAT-TAAT
1 TATAATTATTATAA-AAAAATATAAT
*
978942 TTTAAT
1 TATAAT
978948 AATTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATAATTATTATAAAAAAATATAAT
Found at i:978970 original size:51 final size:54
Alignment explanation
Indices: 978857--978972 Score: 143
Period size: 54 Copynumber: 2.2 Consensus size: 54
978847 ATATAATAAA
* **
978857 TATTATTATAATTATTATAATTATTTTAATTTTATATAATTTATTATAAAATAT
1 TATTATTATAATTATTATAATAAAATTAATTTTATATAATTTATTATAAAATAT
*
978911 TATAATTATAATTATTATAATAAAAATTAATTTTA-ATAATTT-TT-T-AAATAT
1 TATTATTATAATTATTATAAT-AAAATTAATTTTATATAATTTATTATAAAATAT
978962 T-TGTATTATAA
1 TAT-TATTATAA
978973 ATTTATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
50 1 0.02
51 14 0.25
52 1 0.02
53 2 0.04
54 27 0.49
55 10 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (54 bp):
TATTATTATAATTATTATAATAAAATTAATTTTATATAATTTATTATAAAATAT
Found at i:980117 original size:20 final size:19
Alignment explanation
Indices: 980094--980140 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
980084 AATTTATATA
980094 ATTATATTAATATTTAAAAT
1 ATTAT-TTAATATTTAAAAT
980114 ATTATTTAAATATTTAAAAT
1 ATTATTT-AATATTTAAAAT
980134 ATTATTT
1 ATTATTT
980141 TAAATTGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATTTAATATTTAAAAT
Found at i:981049 original size:12 final size:12
Alignment explanation
Indices: 981027--981064 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
981017 TTTTTAATAT
981027 ATTTAAATATTAA
1 ATTT-AATATTAA
981040 ATTTAATATTAA
1 ATTTAATATTAA
*
981052 A-ATAATATTAA
1 ATTTAATATTAA
981063 AT
1 AT
981065 ATATCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 9 0.39
13 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:981059 original size:11 final size:12
Alignment explanation
Indices: 981032--981067 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
981022 AATATATTTA
*
981032 AATATTAAATTT
1 AATATTAAATAT
981044 AATATTAAA-AT
1 AATATTAAATAT
981055 AATATTAAATAT
1 AATATTAAATAT
981067 A
1 A
981068 TCATAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
AATATTAAATAT
Found at i:981064 original size:30 final size:27
Alignment explanation
Indices: 981029--981098 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 27
981019 TTTAATATAT
981029 TTAAATATTAAATTTAATATTAAAATAATA
1 TTAAATATTAAA-TTAATA--AAAATAATA
981059 TTAAATATATCATAATTAATAAAAATAATA
1 TTAAATAT-T-A-AATTAATAAAAATAATA
*
981089 TTTAAT-TTAA
1 TTAAATATTAA
981099 TGATATAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 1 0.03
29 1 0.03
30 22 0.61
31 1 0.03
32 7 0.19
33 2 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
TTAAATATTAAATTAATAAAAATAATA
Found at i:981526 original size:13 final size:10
Alignment explanation
Indices: 981488--981519 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
981478 ATATAAAAAT
981488 AATTTTTTAA
1 AATTTTTTAA
981498 AATTTTTTAA
1 AATTTTTTAA
981508 AATTATTTTAA
1 AATT-TTTTAA
981519 A
1 A
981520 TAATTATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:981683 original size:18 final size:17
Alignment explanation
Indices: 981652--981696 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
981642 ATTTATGTAT
* *
981652 TTATATTGTTTTTACATA
1 TTATATTATATTTA-ATA
981670 TTATATTATATTTAATA
1 TTATATTATATTTAATA
981687 -TATATTATAT
1 TTATATTATAT
981697 GCTTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 3 0.12
18 12 0.48
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATATTATATTTAATA
Found at i:981754 original size:17 final size:17
Alignment explanation
Indices: 981693--981755 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 17
981683 AATATATATT
981693 ATATGCTTATATAAGTTTTA
1 ATATG-TTA-ATAA-TTTTA
*
981713 ATATGATAATAA-TTT-
1 ATATGTTAATAATTTTA
* *
981728 GTAT-TAAATAATTTTA
1 ATATGTTAATAATTTTA
981744 ATATGTTAATAA
1 ATATGTTAATAA
981756 ATTATATTGT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
16 6 0.18
17 6 0.18
18 4 0.12
19 2 0.06
20 5 0.15
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (17 bp):
ATATGTTAATAATTTTA
Found at i:982127 original size:24 final size:24
Alignment explanation
Indices: 982073--982131 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
982063 AAATAATTTT
* *
982073 TATTTAAAT-TTAATTTATAAAAA
1 TATTTAAATATTAATTAAAAAAAA
*
982096 TATATAAATATTAATATAAAAAAAA
1 TATTTAAATATTAAT-TAAAAAAAA
982121 T-TTTAAATATT
1 TATTTAAATATT
982132 TTAATATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 8 0.27
24 14 0.47
25 8 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATTTAAATATTAATTAAAAAAAA
Found at i:983546 original size:2 final size:2
Alignment explanation
Indices: 983539--983563 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
983529 TTATTATAAC
983539 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
983564 GAAGAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:984211 original size:2 final size:2
Alignment explanation
Indices: 984204--984232 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
984194 AAATTACATT
984204 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
984233 TCTTGGGTTG
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:986236 original size:24 final size:24
Alignment explanation
Indices: 986148--986237 Score: 76
Period size: 24 Copynumber: 3.7 Consensus size: 24
986138 GTTAGTCATA
* *
986148 ATTACTTTTTAATAAAAAAATATT
1 ATTATTTTTTAATATAAAAATATT
*
986172 TTTATTTAATTTAATTATAAAAATATT
1 ATTATTT--TTTAA-TATAAAAATATT
* ** *
986199 ATAAAATATTAATATAAAAATA-T
1 ATTATTTTTTAATATAAAAATATT
986222 ATTATTTTTTAA-ATAA
1 ATTATTTTTTAATATAA
986238 TAATTTAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
22 4 0.08
23 9 0.18
24 15 0.29
25 4 0.08
26 5 0.10
27 14 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTATTTTTTAATATAAAAATATT
Found at i:988555 original size:13 final size:13
Alignment explanation
Indices: 988523--988564 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
988513 AATATTAATA
*
988523 TAATATTATTTTT
1 TAATATTAATTTT
988536 TAA-ATTAATTTT
1 TAATATTAATTTT
988548 TAATATT-ATTTT
1 TAATATTAATTTT
*
988560 AAATA
1 TAATA
988565 ATAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 20 0.77
13 6 0.23
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATTAATTTT
Found at i:988762 original size:2 final size:2
Alignment explanation
Indices: 988751--988782 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
988741 AACCATATTT
988751 TA TA TA -A TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
988783 AAGTTTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:989921 original size:15 final size:15
Alignment explanation
Indices: 989901--989930 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
989891 TTCGTTATAT
989901 TTACAAATATGATAA
1 TTACAAATATGATAA
989916 TTACAAATATGATAA
1 TTACAAATATGATAA
989931 GATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
TTACAAATATGATAA
Found at i:990202 original size:26 final size:25
Alignment explanation
Indices: 990115--990221 Score: 77
Period size: 21 Copynumber: 4.5 Consensus size: 25
990105 ATCCGATTCG
*
990115 AAATAATAA-TTTTTAATTA-AAAT
1 AAATAATAATTTTTTAAATATAAAT
990138 -AAT-AT-ATTTTTTAAA-A-AAAT
1 AAATAATAATTTTTTAAATATAAAT
* * * * *
990158 TAATTATAAAATATATAAATATTAATAT
1 AAATAAT-AATTTTTTAAATA-TAA-AT
990186 AAA-AATAATTTTTTAAATATAAAT
1 AAATAATAATTTTTTAAATATAAAT
990210 AAATAATAATTT
1 AAATAATAATTT
990222 AAACTTACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 18
0.71 0.10 0.20
Matches are distributed among these distances:
20 6 0.09
21 12 0.18
22 5 0.08
24 12 0.18
25 12 0.18
26 10 0.15
27 4 0.06
28 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATAATAATTTTTTAAATATAAAT
Found at i:990222 original size:22 final size:20
Alignment explanation
Indices: 990181--990224 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
990171 TATAAATATT
**
990181 AATATAAAAATAATTTTTTA
1 AATATAAAAATAATAATTTA
990201 AATATAAATAAATAATAATTTA
1 AATAT-AA-AAATAATAATTTA
990223 AA
1 AA
990225 CTTACAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 2 0.10
22 13 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAAAAATAATAATTTA
Found at i:990789 original size:2 final size:2
Alignment explanation
Indices: 990782--990818 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
990772 TGTATACGTG
990782 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 T
990819 GATCTTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:992500 original size:14 final size:14
Alignment explanation
Indices: 992483--992510 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
992473 CATAGACTGG
992483 CTGTCATAGTTGTT
1 CTGTCATAGTTGTT
992497 CTGTCATAGTTGTT
1 CTGTCATAGTTGTT
992511 AACGATGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
CTGTCATAGTTGTT
Found at i:994344 original size:26 final size:26
Alignment explanation
Indices: 994306--994363 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
994296 AATATTAATA
*
994306 TTATATTAATTTA-ATTTTTTTATTAT
1 TTATATTAATTTATATTATTTT-TTAT
**
994332 TTATATTCGTTTATATTATTTTTTAT
1 TTATATTAATTTATATTATTTTTTAT
994358 TTATAT
1 TTATAT
994364 ATATAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATATTAATTTATATTATTTTTTAT
Found at i:994452 original size:20 final size:20
Alignment explanation
Indices: 994415--994452 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
994405 AAAAATTTTA
*
994415 AATTTTTTATTTTCTTAAAT
1 AATTTTTTATTTTATTAAAT
994435 AATTTTTTCA-TTTATTAA
1 AATTTTTT-ATTTTATTAA
994453 TTATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
AATTTTTTATTTTATTAAAT
Found at i:995035 original size:18 final size:18
Alignment explanation
Indices: 995008--995072 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
994998 AATTTTTATA
995008 TAATA-TTTTTAAAAAAT
1 TAATATTTTTTAAAAAAT
*
995025 TAATCATTTTTTAAAAAAC
1 TAAT-ATTTTTTAAAAAAT
** *
995044 TAGCATTTTCTT-AAAAAG
1 TAATATTTT-TTAAAAAAT
995062 TAAT-TTTTTTA
1 TAATATTTTTTA
995073 TTTTTCTCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 13 0.34
19 15 0.39
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (18 bp):
TAATATTTTTTAAAAAAT
Found at i:995035 original size:19 final size:18
Alignment explanation
Indices: 995013--995060 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
995003 TTATATAATA
* *
995013 TTTTTAAAAAATTAATCAT
1 TTTTTAAAAAACT-AGCAT
995032 TTTTTAAAAAACTAGCAT
1 TTTTTAAAAAACTAGCAT
995050 TTTCTTAAAAA
1 TTT-TTAAAAA
995061 GTAATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTTTAAAAAACTAGCAT
Found at i:1001285 original size:2 final size:2
Alignment explanation
Indices: 1001278--1001318 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1001268 CGTTTCTCAC
1001278 TA 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 TA T
1001319 TTTCTTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1001410 original size:29 final size:27
Alignment explanation
Indices: 1001378--1001441 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 27
1001368 TGTAACGATT
1001378 ATATAATATTAAAAGATAATTAAAATATA
1 ATATAATATTAAAAGAT-ATTAAAA-ATA
* *
1001407 ATATAAAATATTATAATATATTAAAAATA
1 ATAT--AATATTAAAAGATATTAAAAATA
1001436 ATATAA
1 ATATAA
1001442 ATATAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
29 11 0.35
30 7 0.23
31 11 0.35
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATAATATTAAAAGATATTAAAAATA
Found at i:1001411 original size:5 final size:5
Alignment explanation
Indices: 1001401--1001457 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
1001391 AGATAATTAA
* * * *
1001401 AATAT AATAT AAAAT ATTAT AATAT ATTA- AAAAT AATAT AAATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT
1001451 AAATAT A
1 -AATAT A
1001458 TTAAATTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
4 2 0.05
5 29 0.71
6 10 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:1001427 original size:10 final size:10
Alignment explanation
Indices: 1001396--1001513 Score: 61
Period size: 10 Copynumber: 12.2 Consensus size: 10
1001386 TTAAAAGATA
*
1001396 ATTAAAATAT
1 ATTATAATAT
* *
1001406 AATATAAAAT
1 ATTATAATAT
1001416 ATTATAATAT
1 ATTATAATAT
*
1001426 ATTA-AAAAT
1 ATTATAATAT
*
1001435 AATATAAATAT
1 ATTAT-AATAT
*
1001446 AATATAAATAT
1 ATTAT-AATAT
1001457 ATTA-AAT-T
1 ATTATAATAT
1001465 -TTAT-ATAAT
1 ATTATAAT-AT
* *
1001474 TTTTTAATAT
1 ATTATAATAT
*
1001484 TTTA-AATA-
1 ATTATAATAT
1001492 ATTATAATAT
1 ATTATAATAT
* *
1001502 ATAAAAATAT
1 ATTATAATAT
1001512 AT
1 AT
1001514 GATCATAATA
Statistics
Matches: 85, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
7 5 0.06
8 4 0.05
9 19 0.22
10 37 0.44
11 20 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATAATAT
Found at i:1001434 original size:31 final size:29
Alignment explanation
Indices: 1001377--1001462 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 29
1001367 ATGTAACGAT
* * *
1001377 TATATAATATTAAAAGATAATTAAAATATAA
1 TATAAAATATTATAATAT-ATTAAAA-ATAA
1001408 TATAAAATATTATAATATATTAAAAATAA
1 TATAAAATATTATAATATATTAAAAATAA
*
1001437 TATAAATATAATATAAATATATTAAA
1 TATAAA-ATATTAT-AATATATTAAA
1001463 TTTTATATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.20
30 13 0.27
31 26 0.53
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
TATAAAATATTATAATATATTAAAAATAA
Found at i:1001438 original size:22 final size:21
Alignment explanation
Indices: 1001387--1001463 Score: 65
Period size: 20 Copynumber: 3.8 Consensus size: 21
1001377 TATATAATAT
*
1001387 TAAAAGATAAT-TAAAATATAA
1 TAAAA-ATAATATTAAATATAA
* *
1001408 T-ATAA-AATATTATAATATAT
1 TAAAAATAATATTA-AATATAA
1001428 TAAAAATAATA-TAAATATAA
1 TAAAAATAATATTAAATATAA
*
1001448 TATAAAT-ATATTAAAT
1 TAAAAATAATATTAAAT
1001464 TTTATATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
18 3 0.07
19 6 0.13
20 26 0.58
21 6 0.13
22 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (21 bp):
TAAAAATAATATTAAATATAA
Found at i:1001454 original size:11 final size:11
Alignment explanation
Indices: 1001378--1001457 Score: 71
Period size: 11 Copynumber: 7.5 Consensus size: 11
1001368 TGTAACGATT
1001378 ATATAATATTAAA
1 ATATAATA-T-AA
*
1001391 AGATAAT-TAAA
1 ATATAATAT-AA
1001402 ATATAATATAA
1 ATATAATATAA
*
1001413 A-ATATTAT-A
1 ATATAATATAA
1001422 ATAT-AT-TAA
1 ATATAATATAA
*
1001431 AAATAATATAA
1 ATATAATATAA
1001442 ATATAATATAA
1 ATATAATATAA
1001453 ATATA
1 ATATA
1001458 TTAAATTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.02
9 7 0.12
10 10 0.18
11 31 0.55
12 1 0.02
13 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1001462 original size:20 final size:20
Alignment explanation
Indices: 1001400--1001463 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
1001390 AAGATAATTA
1001400 AAATATAATATAAA-ATATT
1 AAATATAATATAAATATATT
* *
1001419 ATAATATATTAAAAATA-ATAT
1 A-AATATAATATAAATATAT-T
1001440 AAATATAATATAAATATATT
1 AAATATAATATAAATATATT
1001460 AAAT
1 AAAT
1001464 TTTATATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 31 0.84
21 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATAATATAAATATATT
Found at i:1001472 original size:31 final size:29
Alignment explanation
Indices: 1001396--1001462 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 29
1001386 TTAAAAGATA
*
1001396 ATTAAAATATAATATAAAATATTATAATAT
1 ATTAAAA-ATAATATAAAATAATATAATAT
1001426 ATTAAAAATAATATAAATATAATATAAATAT
1 ATTAAAAATAATATAAA-ATAATAT-AATAT
1001457 ATTAAA
1 ATTAAA
1001463 TTTTATATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 10 0.29
30 13 0.38
31 11 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
ATTAAAAATAATATAAAATAATATAATAT
Found at i:1001692 original size:2 final size:2
Alignment explanation
Indices: 1001652--1001681 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1001642 GAGGGACTTT
1001652 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
1001682 AAATTATATA
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:1002426 original size:3 final size:3
Alignment explanation
Indices: 1002412--1002454 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1002402 AGCTTAACAT
*
1002412 ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1002455 AGTCCAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1002918 original size:3 final size:3
Alignment explanation
Indices: 1002910--1002940 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1002900 AAGCCTTGAT
1002910 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1002941 AGTGAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1003713 original size:32 final size:29
Alignment explanation
Indices: 1003675--1003742 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 29
1003665 TATTTTATAT
* * *
1003675 TTATATAAATTTTAATATATTAATAATTCGTA
1 TTATATAAAGTTTAAAATA-T-AT-ATCCGTA
1003707 TTATATAAAGTTTAAAATATATATCCGTA
1 TTATATAAAGTTTAAAATATATATCCGTA
1003736 TTATATA
1 TTATATA
1003743 TTAAATAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 13 0.39
30 2 0.06
31 1 0.03
32 17 0.52
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (29 bp):
TTATATAAAGTTTAAAATATATATCCGTA
Found at i:1004329 original size:14 final size:13
Alignment explanation
Indices: 1004306--1004335 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1004296 ATAATTTTTA
1004306 TTAAATTTAATAT
1 TTAAATTTAATAT
1004319 TTAAATATTAATAT
1 TTAAAT-TTAATAT
1004333 TTA
1 TTA
1004336 TAATCTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAATTTAATAT
Found at i:1006692 original size:47 final size:46
Alignment explanation
Indices: 1006623--1006718 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 46
1006613 CAAGCAATGG
1006623 AAACTGTTGATATTTTTATAAAATTAGTTCAAAAAAAAAAGAAAAAA
1 AAACTGTTGATATTTTTATAAAATTAGTTCAAAAAAAAAA-AAAAAA
* *
1006670 AAACTGTTGATATTTTTATAAAATTAGTTCCAAAAAAAGAAAAAAA
1 AAACTGTTGATATTTTTATAAAATTAGTTCAAAAAAAAAAAAAAAA
1006716 AAA
1 AAA
1006719 GAGTAGCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 9 0.19
47 38 0.81
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.29
Consensus pattern (46 bp):
AAACTGTTGATATTTTTATAAAATTAGTTCAAAAAAAAAAAAAAAA
Found at i:1008833 original size:51 final size:50
Alignment explanation
Indices: 1008771--1008868 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 50
1008761 ATTAGCCTTG
* * * *
1008771 ATTTTCTACGTCAAATATACGAATTTGAACGAAAACTGTTAAAAGAAAGGA
1 ATTTTCAACGTCAAAGAAACGAATTTG-ACGAAAACTATTAAAAGAAAGGA
* * *
1008822 ATTTTCAACGTCAAAGAAAGGAGTTTGATGAAAACTATTAAAAGAAA
1 ATTTTCAACGTCAAAGAAACGAATTTGACGAAAACTATTAAAAGAAA
1008869 AAGAAAATGA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
50 18 0.45
51 22 0.55
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (50 bp):
ATTTTCAACGTCAAAGAAACGAATTTGACGAAAACTATTAAAAGAAAGGA
Found at i:1009055 original size:19 final size:20
Alignment explanation
Indices: 1009031--1009078 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
1009021 TTTTTAAAAA
1009031 ATATTAAAAATTTAT-TTTT
1 ATATTAAAAATTTATATTTT
*
1009050 ATATTAAAATTTTATATTTT
1 ATATTAAAAATTTATATTTT
1009070 ATAATTAAA
1 AT-ATTAAA
1009079 TTTAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 14 0.54
20 6 0.23
21 6 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTAAAAATTTATATTTT
Found at i:1009278 original size:26 final size:26
Alignment explanation
Indices: 1009248--1009319 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
1009238 AAAATTTATT
* *
1009248 TTATTTTTTATAATAATATTAAAATA
1 TTATTTTTTAAAATAATATAAAAATA
*
1009274 TTATTTATTAAAAATAA-ATAAAAATA
1 TTATTT-TTTAAAATAATATAAAAATA
*
1009300 TTTTTATTATTAAAATAATA
1 TTATT-TT-TTAAAATAATA
1009320 ATTTAAGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
26 19 0.51
27 17 0.46
28 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TTATTTTTTAAAATAATATAAAAATA
Found at i:1009652 original size:19 final size:19
Alignment explanation
Indices: 1009620--1009667 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1009610 ACTCACGTAA
*
1009620 ATTAATAATAAAATTATAAA-
1 ATTAAAAAT-AAATTA-AAAT
*
1009640 ATTATAAATAAATTAAAAT
1 ATTAAAAATAAATTAAAAT
1009659 ATTAAAAAT
1 ATTAAAAAT
1009668 TATATTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 3 0.12
19 14 0.58
20 7 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAATAAATTAAAAT
Found at i:1009836 original size:2 final size:2
Alignment explanation
Indices: 1009829--1009873 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1009819 TGGCCGTAAG
1009829 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
1009871 TA T
1 TA T
1009874 TCCATTGCTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1010123 original size:8 final size:8
Alignment explanation
Indices: 1010089--1010243 Score: 72
Period size: 8 Copynumber: 19.1 Consensus size: 8
1010079 ATGATACGAT
1010089 TATATAATA
1 TATATAA-A
* *
1010098 TAAAAAAA
1 TATATAAA
*
1010106 TAATAAAAA
1 T-ATATAAA
1010115 TATATAAA
1 TATATAAA
1010123 TATATAAA
1 TATATAAA
1010131 TATATCAAA
1 TATAT-AAA
* *
1010140 AAT-TAAG
1 TATATAAA
*
1010147 TAAAATAAA
1 T-ATATAAA
*
1010156 T-TATTAA
1 TATATAAA
1010163 TATAATAAA
1 TAT-ATAAA
* *
1010172 -ATTTATA
1 TATATAAA
1010179 TATAT-AA
1 TATATAAA
* *
1010186 TATTTTAA
1 TATATAAA
1010194 T-TAT-AA
1 TATATAAA
1010200 T-TATAATA
1 TATATAA-A
*
1010208 TATAAAAA
1 TATATAAA
1010216 TATATAAA
1 TATATAAA
1010224 TATAACATAAA
1 TAT---ATAAA
1010235 TATATAAA
1 TATATAAA
1010243 T
1 T
1010244 TACGAGGACT
Statistics
Matches: 112, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
6 6 0.05
7 18 0.16
8 51 0.46
9 29 0.26
11 8 0.07
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (8 bp):
TATATAAA
Found at i:1010245 original size:43 final size:44
Alignment explanation
Indices: 1010151--1010245 Score: 99
Period size: 43 Copynumber: 2.2 Consensus size: 44
1010141 ATTAAGTAAA
* * * *
1010151 ATAAATTATTAATATAATAAAATTTATATATATAATATTTTAATT
1 ATAAATTATTAATATAATAAAATATATAAATATAACA-TTAAATT
1010196 AT-AATTA-TAATAT-ATAAAAATATATAAATATAACA-TAAATAT
1 ATAAATTATTAATATAAT-AAAATATATAAATATAACATTAAAT-T
1010238 ATAAATTA
1 ATAAATTA
1010246 CGAGGACTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
41 4 0.09
42 5 0.12
43 27 0.63
44 5 0.12
45 2 0.05
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (44 bp):
ATAAATTATTAATATAATAAAATATATAAATATAACATTAAATT
Found at i:1010983 original size:22 final size:21
Alignment explanation
Indices: 1010948--1010997 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1010938 GATTTATTTT
1010948 ATTAAATTT-TAT-TTTTAT-
1 ATTAAATTTATATATTTTATA
1010966 ATTAATATTTATATATTTTATA
1 ATTAA-ATTTATATATTTTATA
1010988 ATTAAATTTA
1 ATTAAATTTA
1010998 AATAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.18
19 4 0.14
20 3 0.11
21 11 0.39
22 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTAAATTTATATATTTTATA
Found at i:1012157 original size:13 final size:14
Alignment explanation
Indices: 1012135--1012173 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1012125 TATTTACGAA
*
1012135 CAAACCCAAATTT-
1 CAAACGCAAATTTC
1012148 CAAACGCAAATTTC
1 CAAACGCAAATTTC
1012162 CGAAACGCAAAT
1 C-AAACGCAAAT
1012174 CCCCCAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 1 0.04
15 10 0.43
ACGTcount: A:0.46, C:0.28, G:0.08, T:0.18
Consensus pattern (14 bp):
CAAACGCAAATTTC
Found at i:1013008 original size:16 final size:15
Alignment explanation
Indices: 1012989--1013085 Score: 56
Period size: 15 Copynumber: 6.3 Consensus size: 15
1012979 AAATATATTT
1012989 TAAAAAATTTATAATA
1 TAAAAAATTTA-AATA
**
1013005 TAAATTA-TTAACATA
1 TAAAAAATTTAA-ATA
*
1013020 TAAAAATTTTATAAATA
1 TAAAAA-ATT-TAAATA
*
1013037 TAAAATATATTAAATA
1 TAAAAAAT-TTAAATA
* *
1013053 T-AAATATAT-AATA
1 TAAAAAATTTAAATA
*
1013066 TAATAAAATATAAATA
1 TAA-AAAATTTAAATA
1013082 TAAA
1 TAAA
1013086 TAGAACAAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
13 5 0.08
14 3 0.05
15 23 0.36
16 20 0.31
17 10 0.16
18 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAAAATTTAAATA
Found at i:1013015 original size:24 final size:25
Alignment explanation
Indices: 1012966--1013015 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1012956 ATAAAATAAT
*
1012966 AAAAATTTGATATAAATATATTTTA
1 AAAAATTTGATATAAATAAATTTTA
*
1012991 AAAAATTT-ATA-ATATAAATTATTA
1 AAAAATTTGATATAAATAAATT-TTA
1013015 A
1 A
1013016 CATATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (25 bp):
AAAAATTTGATATAAATAAATTTTA
Found at i:1013022 original size:15 final size:14
Alignment explanation
Indices: 1013001--1013086 Score: 59
Period size: 16 Copynumber: 5.6 Consensus size: 14
1012991 AAAAATTTAT
1013001 AATATAAATTATTA
1 AATATAAATTATTA
*
1013015 ACATATAAAAATTTTATA
1 A-ATAT--AAATTAT-TA
1013033 AATATAAAATATATTA
1 AATAT-AAAT-TATTA
1013049 AATATAAA-TATATA
1 AATATAAATTAT-TA
*
1013063 ATATAATAAAATA-TA
1 A-AT-ATAAATTATTA
1013078 AATATAAAT
1 AATATAAAT
1013087 AGAACAAGGT
Statistics
Matches: 60, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
13 8 0.13
14 6 0.10
15 12 0.20
16 17 0.28
17 14 0.23
18 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATAAATTATTA
Found at i:1013031 original size:31 final size:33
Alignment explanation
Indices: 1012989--1013056 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 33
1012979 AAATATATTT
1012989 TAAAAAATTTAT-AATAT-AAAT-TATTAACATA
1 TAAAAAATTTATAAATATAAAATATATTAA-ATA
*
1013020 TAAAAATTTTATAAATATAAAATATATTAAATA
1 TAAAAAATTTATAAATATAAAATATATTAAATA
1013053 TAAA
1 TAAA
1013057 TATATAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
31 11 0.33
32 5 0.15
33 11 0.33
34 6 0.18
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (33 bp):
TAAAAAATTTATAAATATAAAATATATTAAATA
Found at i:1013037 original size:17 final size:17
Alignment explanation
Indices: 1012989--1013041 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1012979 AAATATATTT
*
1012989 TAAAAAATTTAT-AATA
1 TAAAAATTTTATAAATA
*
1013005 T--AAATTATTA-ACATA
1 TAAAAATT-TTATAAATA
1013020 TAAAAATTTTATAAATA
1 TAAAAATTTTATAAATA
1013037 TAAAA
1 TAAAA
1013042 TATATTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.14
15 7 0.24
16 4 0.14
17 14 0.48
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATTTTATAAATA
Found at i:1013055 original size:22 final size:23
Alignment explanation
Indices: 1013029--1013085 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
1013019 ATAAAAATTT
*
1013029 TATAAATATAAAATAT-ATTAAA
1 TATAAATATAAAATATAATAAAA
*
1013051 TATAAATATATAATATAATAAAA
1 TATAAATATAAAATATAATAAAA
1013074 TATAAATATAAA
1 TATAAATATAAA
1013086 TAGAACAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (23 bp):
TATAAATATAAAATATAATAAAA
Found at i:1013074 original size:32 final size:33
Alignment explanation
Indices: 1012998--1013077 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
1012988 TTAAAAAATT
* *
1012998 TATAATATAAAT-TATTAACATATAAAAATTTTA
1 TATAATA-AAATATATTAACATATAAAAATATAA
* *
1013031 TAAATATAAAATATATTAA-ATATAAATATATAA
1 TATA-ATAAAATATATTAACATATAAAAATATAA
1013064 TATAATAAAATATA
1 TATAATAAAATATA
1013078 AATATAAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 10 0.25
33 21 0.52
34 9 0.22
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TATAATAAAATATATTAACATATAAAAATATAA
Found at i:1013079 original size:29 final size:28
Alignment explanation
Indices: 1013029--1013087 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
1013019 ATAAAAATTT
*
1013029 TATAAATATAAAATATATTAAATATAAA
1 TATAAATATAAAAAATATTAAATATAAA
1013057 TATATAATATAATAAAATA-TAAATATAAA
1 TATA-AATATAA-AAAATATTAAATATAAA
1013086 TA
1 TA
1013088 GAACAAGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 4 0.14
29 19 0.68
30 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TATAAATATAAAAAATATTAAATATAAA
Found at i:1013428 original size:15 final size:15
Alignment explanation
Indices: 1013374--1013425 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
1013364 ATATTATAAA
1013374 AAATTAAAATAATAT
1 AAATTAAAATAATAT
*
1013389 AATTTAAAATAATAT
1 AAATTAAAATAATAT
*
1013404 AAATTTAAAT-ATAT
1 AAATTAAAATAATAT
1013418 -AATTAAAA
1 AAATTAAAA
1013426 AATTATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 22 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAAATAATAT
Found at i:1013639 original size:17 final size:17
Alignment explanation
Indices: 1013617--1013683 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1013607 TATCATATTT
1013617 AATATAAAAATTATATA
1 AATATAAAAATTATATA
*
1013634 AATATAAAAATAAT-TA
1 AATATAAAAATTATATA
* *
1013650 CAATAATTAAAATTTTA-A
1 -AAT-ATAAAAATTATATA
*
1013668 AATTTTAAAAATTATA
1 AA-TATAAAAATTATA
1013684 AATACGTAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 2 0.05
17 27 0.69
18 10 0.26
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAAAAATTATATA
Found at i:1013870 original size:19 final size:19
Alignment explanation
Indices: 1013848--1013904 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 19
1013838 TAAAAAAATA
1013848 TTATATTT-TTAAATTTTAT
1 TTATATTTATTAAATTTT-T
*
1013867 TTATAATTTATATTATATTTTT
1 TTAT-A-TT-TATTAAATTTTT
1013889 TTATATTTATTAAATT
1 TTATATTTATTAAATT
1013905 AAAATTTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
19 12 0.38
20 3 0.09
21 3 0.09
22 6 0.19
23 8 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATATTTATTAAATTTTT
Found at i:1017335 original size:3 final size:3
Alignment explanation
Indices: 1017323--1017360 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1017313 GGGTATGTAC
1017323 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1017361 GAGGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1017857 original size:41 final size:42
Alignment explanation
Indices: 1017780--1017863 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 42
1017770 TATTGTTTGA
1017780 TTATAATATAATTAATAATATTATATTATTTGTA-TTTTATT
1 TTATAATATAATTAATAATATTATATTATTTGTATTTTTATT
* *
1017821 TTATAATATAGTTAATAATATT-TATGT-TTTATTATTTTTATT
1 TTATAATATAATTAATAATATTATAT-TATTT-GTATTTTTATT
1017863 T
1 T
1017864 AAAATTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
40 6 0.16
41 24 0.63
42 8 0.21
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (42 bp):
TTATAATATAATTAATAATATTATATTATTTGTATTTTTATT
Found at i:1017900 original size:10 final size:10
Alignment explanation
Indices: 1017885--1017911 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1017875 ATGTATTTGT
1017885 TTTGTTTAAA
1 TTTGTTTAAA
1017895 TTTGTTTAAA
1 TTTGTTTAAA
1017905 TTTGTTT
1 TTTGTTT
1017912 GTTTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (10 bp):
TTTGTTTAAA
Found at i:1018945 original size:7 final size:8
Alignment explanation
Indices: 1018926--1018950 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1018916 TAATATAATT
1018926 TTTTTTAA
1 TTTTTTAA
1018934 TTTTTTAA
1 TTTTTTAA
1018942 TTTTTTAA
1 TTTTTTAA
1018950 T
1 T
1018951 AATAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTAA
Found at i:1019471 original size:12 final size:13
Alignment explanation
Indices: 1019448--1019476 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1019438 TACAATTTTT
1019448 TTTAATATTTATA
1 TTTAATATTTATA
1019461 TTTAATA-TTATA
1 TTTAATATTTATA
1019473 TTTA
1 TTTA
1019477 TATGAGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:1019473 original size:18 final size:18
Alignment explanation
Indices: 1019452--1019549 Score: 67
Period size: 17 Copynumber: 5.3 Consensus size: 18
1019442 ATTTTTTTTA
*
1019452 ATATTTATATTTAATATT
1 ATATTTATATTAAATATT
* * *
1019470 ATATTTATATGAGATATA
1 ATATTTATATTAAATATT
*
1019488 ATATTTTAAATATATAAAAAATT
1 ATA-TTT--ATAT-T-AAATATT
1019511 A-ATTTATATTAAATA-T
1 ATATTTATATTAAATATT
* *
1019527 ATATTCATATTTAATA-T
1 ATATTTATATTAAATATT
1019544 ATATTT
1 ATATTT
1019550 TCGAGTATAA
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
16 2 0.03
17 22 0.35
18 18 0.29
19 7 0.11
21 7 0.11
22 1 0.02
23 5 0.08
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATTTATATTAAATATT
Found at i:1020951 original size:16 final size:16
Alignment explanation
Indices: 1020930--1020982 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
1020920 TAAATATCTT
1020930 TAAATTTATATAATTA
1 TAAATTTATATAATTA
1020946 TAAA-TTAT-TAATATA
1 TAAATTTATATAAT-TA
1020961 TTAAAATTTATATAATTA
1 -T-AAATTTATATAATTA
1020979 TAAA
1 TAAA
1020983 ATATTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.12
15 6 0.19
16 8 0.25
17 4 0.12
18 6 0.19
19 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTTATATAATTA
Found at i:1020959 original size:33 final size:33
Alignment explanation
Indices: 1020922--1020987 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1020912 TTATTAGATA
* * *
1020922 AATATCTTTAAATTTATATAATTATAAATTATT
1 AATATATTAAAATTTATATAATTATAAAATATT
1020955 AATATATTAAAATTTATATAATTATAAAATATT
1 AATATATTAAAATTTATATAATTATAAAATATT
1020988 TTAAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (33 bp):
AATATATTAAAATTTATATAATTATAAAATATT
Found at i:1020982 original size:17 final size:17
Alignment explanation
Indices: 1020931--1020984 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
1020921 AAATATCTTT
1020931 AAATTTATATAATTAT-
1 AAATTTATATAATTATA
1020947 AAA-TTAT-TAATATATTA
1 AAATTTATATAAT-TA-TA
1020964 AAATTTATATAATTATA
1 AAATTTATATAATTATA
1020981 AAAT
1 AAAT
1020985 ATTTTAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.12
15 6 0.18
16 4 0.12
17 9 0.27
18 6 0.18
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AAATTTATATAATTATA
Found at i:1021817 original size:19 final size:18
Alignment explanation
Indices: 1021778--1021850 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 18
1021768 ATAACAATTT
*
1021778 ATATTATATAAATTTTATC
1 ATATT-TATATATTTTATC
*
1021797 ATTTTTATATATTTATATC
1 ATATTTATATATTT-TATC
*
1021816 ATATTTATATTATTTT-TT
1 ATATTTATA-TATTTTATC
1021834 ATATTATATTATATTTT
1 ATATT-TA-TATATTTT
1021851 TTTTATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 14 0.30
19 25 0.54
20 7 0.15
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
ATATTTATATATTTTATC
Found at i:1021835 original size:23 final size:21
Alignment explanation
Indices: 1021808--1021856 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 21
1021798 TTTTTATATA
1021808 TTTATATCATATTTATATTATTT
1 TTTATATCATA-TTATATT-TTT
*
1021831 TTTATATTATATTATATTTTT
1 TTTATATCATATTATATTTTT
1021852 TTTAT
1 TTTAT
1021857 TTTTTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 8 0.32
22 7 0.28
23 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATATCATATTATATTTTT
Found at i:1021836 original size:31 final size:29
Alignment explanation
Indices: 1021777--1021870 Score: 106
Period size: 28 Copynumber: 3.3 Consensus size: 29
1021767 GATAACAATT
* *
1021777 TATATTATAT-AAATTT-TATCATTTTTA
1 TATATTATATCATATTTATATTATTTTTA
1021804 TATATTTATATCATATTTATATTATTTTT-
1 TATA-TTATATCATATTTATATTATTTTTA
* * *
1021833 TATATTATATTATATTTTTTTTATTTTT-
1 TATATTATATCATATTTATATTATTTTTA
1021861 TATATTATAT
1 TATATTATAT
1021871 AATTATACGT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.07
28 37 0.63
29 9 0.15
30 9 0.15
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (29 bp):
TATATTATATCATATTTATATTATTTTTA
Found at i:1024203 original size:17 final size:17
Alignment explanation
Indices: 1024178--1024232 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
1024168 TTAATAAAAA
*
1024178 AAATTAAAAATAATATT
1 AAATAAAAAATAATATT
1024195 AAATAAAAAATAATA-T
1 AAATAAAAAATAATATT
* *
1024211 AAAT--ATAATATTATT
1 AAATAAAAAATAATATT
1024226 AAATAAA
1 AAATAAA
1024233 TATTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.22
15 5 0.16
16 5 0.16
17 15 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAAATAATATT
Found at i:1024220 original size:14 final size:14
Alignment explanation
Indices: 1024185--1024234 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1024175 AAAAAATTAA
1024185 AAATAATATTAAAT
1 AAATAATATTAAAT
*
1024199 AAAAAATAATATAAAT
1 AAATAAT-AT-TAAAT
*
1024215 ATAATATTATTAAAT
1 A-AATAATATTAAAT
1024230 AAATA
1 AAATA
1024235 TTTTTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.33
15 8 0.27
16 8 0.27
17 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:1024226 original size:31 final size:30
Alignment explanation
Indices: 1024146--1024232 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
1024136 TAATAATATT
*
1024146 ATATATAATATGAATATTAATGTTAATAAAAAAA
1 ATATA-AATAT-AATATT-AT-TAAATAAAAAAA
*
1024180 AT-T-AA-A-AATAATATTAAATAAAAAATA
1 ATATAAATATAATATTATTAAATAAAAAA-A
1024207 ATATAAATATAATATTATTAAATAAA
1 ATATAAATATAATATTATTAAATAAA
1024233 TATTTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
26 10 0.22
27 5 0.11
28 6 0.13
29 2 0.04
30 2 0.04
31 17 0.38
33 1 0.02
34 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
ATATAAATATAATATTATTAAATAAAAAAA
Found at i:1024233 original size:28 final size:27
Alignment explanation
Indices: 1024150--1024234 Score: 93
Period size: 28 Copynumber: 3.1 Consensus size: 27
1024140 AATATTATAT
* *
1024150 ATAATATGAATATTAATGTTAATAAAAA
1 ATAATATAAATA-TAATATTAATAAAAA
*
1024178 A-AAT-TAAAAATAATATTAAATAAAAA
1 ATAATATAAATATAATATT-AATAAAAA
*
1024204 ATAATATAAATATAATATTATTAAATAA
1 ATAATATAAATATAATATTAATAAA-AA
1024232 ATA
1 ATA
1024235 TTTTTAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 6 0.12
26 13 0.27
27 11 0.23
28 18 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
ATAATATAAATATAATATTAATAAAAA
Found at i:1024235 original size:14 final size:14
Alignment explanation
Indices: 1024185--1024243 Score: 55
Period size: 15 Copynumber: 4.0 Consensus size: 14
1024175 AAAAAATTAA
*
1024185 AAATAATATTAAAT
1 AAATATTATTAAAT
* *
1024199 AAAAAATAATATAAAT
1 -AAATATTAT-TAAAT
1024215 ATAATATTATTAAAT
1 A-AATATTATTAAAT
*
1024230 AAATATTTTTAAAT
1 AAATATTATTAAAT
1024244 TTATAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
14 12 0.33
15 13 0.36
16 11 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AAATATTATTAAAT
Found at i:1024260 original size:16 final size:16
Alignment explanation
Indices: 1024239--1024291 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
1024229 TAAATATTTT
1024239 TAAATTTATAAAATTA
1 TAAATTTATAAAATTA
1024255 TAAA-TTATTAATATATTA
1 TAAATTTA-TAA-A-ATTA
*
1024273 -AAATTTATATAATTA
1 TAAATTTATAAAATTA
1024288 TAAA
1 TAAA
1024292 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
15 7 0.23
16 11 0.35
17 6 0.19
18 7 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTATAAAATTA
Found at i:1024277 original size:33 final size:33
Alignment explanation
Indices: 1024214--1024296 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
1024204 ATAATATAAA
* * * *
1024214 TATAATATTATTAAATA--AATATTTTTAAATT
1 TATAAAATTATAAAATATTAATATATTAAAATT
*
1024245 TATAAAATTATAAATTATTAATATATTAAAATT
1 TATAAAATTATAAAATATTAATATATTAAAATT
*
1024278 TATATAATTATAAAATATT
1 TATAAAATTATAAAATATT
1024297 TTAAATATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 14 0.33
33 29 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
TATAAAATTATAAAATATTAATATATTAAAATT
Found at i:1024295 original size:25 final size:24
Alignment explanation
Indices: 1024247--1024296 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1024237 TTTAAATTTA
*
1024247 TAAAATTATAAATTATTAATATAT
1 TAAAATTATAAATTATTAAAATAT
1024271 TAAAATTTATATAATTA-TAAAATAT
1 TAAAA-TTATA-AATTATTAAAATAT
1024296 T
1 T
1024297 TTAAATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 5 0.22
25 13 0.57
26 5 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAATTATAAATTATTAAAATAT
Found at i:1024300 original size:27 final size:24
Alignment explanation
Indices: 1024242--1024312 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 24
1024232 ATATTTTTAA
*
1024242 ATTTATAAAATTATAAATTATTAAT
1 ATTT-TAAAATTATAAATTATAAAT
*
1024267 ATATTAAAATTTATATAATTATAAAAT
1 ATTTTAAAA-TTATA-AATTAT-AAAT
1024294 ATTTT-AAA-TAT-AATTATAA
1 ATTTTAAAATTATAAATTATAA
1024313 TATAAAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
21 2 0.05
22 6 0.15
24 8 0.20
25 8 0.20
26 9 0.22
27 7 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTTTAAAATTATAAATTATAAAT
Found at i:1025021 original size:8 final size:8
Alignment explanation
Indices: 1025010--1025130 Score: 54
Period size: 8 Copynumber: 15.0 Consensus size: 8
1025000 AAATTCAATA
*
1025010 ATTTATTT
1 ATTTATAT
1025018 ATTTATAT
1 ATTTATAT
1025026 ATTT-T-T
1 ATTTATAT
*
1025032 ATGTATTAT
1 ATTTA-TAT
*
1025041 AATTATAT
1 ATTTATAT
* *
1025049 -TTAAAAT
1 ATTTATAT
1025056 ATTTTATAT
1 A-TTTATAT
* *
1025065 TTTTATAA
1 ATTTATAT
*
1025073 ATTTTTAT
1 ATTTATAT
*
1025081 A-TGATAAT
1 ATTTAT-AT
1025089 AATTTATAT
1 -ATTTATAT
* *
1025098 -TATATAA
1 ATTTATAT
1025105 ATTTTATTAT
1 A-TTTA-TAT
1025115 ATTTATAT
1 ATTTATAT
1025123 ATTTATAT
1 ATTTATAT
1025131 CATATTTATA
Statistics
Matches: 81, Mismatches: 21, Indels: 22
0.65 0.17 0.18
Matches are distributed among these distances:
6 4 0.05
7 12 0.15
8 40 0.49
9 19 0.23
10 6 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (8 bp):
ATTTATAT
Found at i:1025038 original size:10 final size:10
Alignment explanation
Indices: 1025019--1025154 Score: 52
Period size: 9 Copynumber: 14.0 Consensus size: 10
1025009 AATTTATTTA
1025019 TTTATATATT
1 TTTATATATT
*
1025029 TTTATGTATT
1 TTTATATATT
* * *
1025039 ATAAT-TATA
1 TTTATATATT
* *
1025048 TTTA-AAATA
1 TTTATATATT
1025057 TTT-TATATT
1 TTTATATATT
*
1025066 TTTATAAATT
1 TTTATATATT
*
1025076 TTTATATGATA
1 TTTATAT-ATT
* * *
1025087 ATAATTTA-T
1 TTTATATATT
* *
1025096 ATTATATAAAT
1 TTTATAT-ATT
*
1025107 TTTAT-TATA
1 TTTATATATT
1025116 TTTATATATT
1 TTTATATATT
*
1025126 TATATCATATT
1 TTTAT-ATATT
*
1025137 TATAT-TATT
1 TTTATATATT
1025146 TTT-TATATT
1 TTTATATATT
1025155 ATATAATTAT
Statistics
Matches: 93, Mismatches: 24, Indels: 19
0.68 0.18 0.14
Matches are distributed among these distances:
8 1 0.01
9 38 0.41
10 33 0.35
11 21 0.23
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
TTTATATATT
Found at i:1025109 original size:49 final size:47
Alignment explanation
Indices: 1025006--1025135 Score: 129
Period size: 47 Copynumber: 2.7 Consensus size: 47
1024996 ATCCAAATTC
* * *
1025006 AATAATTTAT-TTATTTATATATTTTTATGTATTATAATTATATTTAA
1 AATATTTTATATT-TTTATATATTTTTATATATAATAATTATATTTAA
* *
1025053 AATATTTTATATTTTTATAAATTTTTATATGATAATAATTTATATTATAT
1 AATATTTTATATTTTTATATATTTTTATAT-ATAATAA-TTATATT-TAA
* *
1025103 AA-ATTTTATTATATTTATATATTTATATCATAT
1 AATATTTTA-TATTTTTATATATTTTTAT-ATAT
1025136 TTATATTATT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
47 24 0.35
48 8 0.12
49 13 0.19
50 22 0.32
51 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (47 bp):
AATATTTTATATTTTTATATATTTTTATATATAATAATTATATTTAA
Found at i:1025112 original size:14 final size:15
Alignment explanation
Indices: 1025058--1025160 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 15
1025048 TTTAAAATAT
*
1025058 TTTATATTTTTATAAA
1 TTTATA-TTATATAAA
*
1025074 TTTTTA-TATGATAATAA
1 TTTATATTAT-AT-A-AA
1025091 TTTATATTATATAAA
1 TTTATATTATATAAA
**
1025106 TTT-TATTATATTTA
1 TTTATATTATATAAA
* *
1025120 TATAT-TTATATCATA
1 TTTATATTATAT-AAA
*
1025135 TTTATATTAT-T--T
1 TTTATATTATATAAA
1025147 TTTATATTATATAA
1 TTTATATTATATAA
1025161 TTATGTATGA
Statistics
Matches: 68, Mismatches: 9, Indels: 21
0.69 0.09 0.21
Matches are distributed among these distances:
12 10 0.15
13 1 0.01
14 19 0.28
15 15 0.22
16 11 0.16
17 9 0.13
18 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (15 bp):
TTTATATTATATAAA
Found at i:1025116 original size:19 final size:18
Alignment explanation
Indices: 1025042--1025160 Score: 72
Period size: 18 Copynumber: 6.7 Consensus size: 18
1025032 ATGTATTATA
*
1025042 ATTATATTTAAAATATTTT
1 ATTATATTTATAA-ATTTT
*
1025061 A-TATTTTTATAAA-TTT
1 ATTATATTTATAAATTTT
* *
1025077 -TTATA-TGATAATAATTT
1 ATTATATTTATAA-ATTTT
*
1025094 A-TAT-TATATAAATTTT
1 ATTATATTTATAAATTTT
*
1025110 ATTATATTTATATATTTAT
1 ATTATATTTATAAATTT-T
* *
1025129 ATCATATTTATATTATTTT
1 ATTATATTTATA-AATTTT
1025148 -TTATATTATATAA
1 ATTATATT-TATAA
1025161 TTATGTATGA
Statistics
Matches: 78, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
15 5 0.06
16 12 0.15
17 14 0.18
18 24 0.31
19 18 0.23
20 5 0.06
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (18 bp):
ATTATATTTATAAATTTT
Found at i:1025127 original size:33 final size:32
Alignment explanation
Indices: 1025009--1025135 Score: 88
Period size: 33 Copynumber: 4.0 Consensus size: 32
1024999 CAAATTCAAT
*
1025009 AATTTATT-TATTTATATATTTTTATGTAT-TA
1 AATTTATTATATTTATATATTTATAT-TATATA
* * *
1025040 TAA-TTA-TAT-TTAAAATATTTTATATTTTTATA
1 -AATTTATTATATTTATATA-TTTATA-TTATATA
*
1025072 AATTT-TTATA-TGATAATAATTTATATTATATA
1 AATTTATTATATTTAT-AT-ATTTATATTATATA
*
1025104 AATTTTATTATATTTATATATTTATATCATAT
1 AA-TTTATTATATTTATATATTTATATTATAT
1025136 TTATATTATT
Statistics
Matches: 74, Mismatches: 9, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
30 7 0.09
31 13 0.18
32 20 0.27
33 23 0.31
34 8 0.11
35 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.59
Consensus pattern (32 bp):
AATTTATTATATTTATATATTTATATTATATA
Found at i:1025145 original size:33 final size:32
Alignment explanation
Indices: 1025012--1025153 Score: 84
Period size: 33 Copynumber: 4.5 Consensus size: 32
1025002 ATTCAATAAT
* *
1025012 TTATT-TATTTATATATTTTTATGTA-TTATA
1 TTATTATATTTATATATTTATATATATTTATA
* *
1025042 --ATTATATTTAAAATATTT-TATATTTTTATAAA
1 TTATTATATTT-ATATATTTATATATATTTAT--A
* * ** *
1025074 TTTTTATA-TGATAATAATTTATATTATATAAATT
1 TTATTATATTTAT-AT-ATTTATA-TATATTTATA
1025108 TTATTATATTTATATATTTATATCATATTTATA
1 TTATTATATTTATATATTTATAT-ATATTTATA
1025141 TTATT-T-TTTATAT
1 TTATTATATTTATAT
1025154 TATATAATTA
Statistics
Matches: 84, Mismatches: 15, Indels: 25
0.68 0.12 0.20
Matches are distributed among these distances:
28 3 0.04
29 9 0.11
30 11 0.13
31 7 0.08
32 4 0.05
33 21 0.25
34 18 0.21
35 5 0.06
36 6 0.07
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (32 bp):
TTATTATATTTATATATTTATATATATTTATA
Found at i:1025156 original size:28 final size:27
Alignment explanation
Indices: 1025091--1025160 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 27
1025081 ATGATAATAA
1025091 TTTATATTATATAAATTTTATTATATT
1 TTTATATTATATAAATTTTATTATATT
* *
1025118 TATATATTTATATCATATTTATATTAT-TT
1 TTTATA-TTATAT-AAATTT-TATTATATT
1025147 TTTATATTATATAA
1 TTTATATTATATAA
1025161 TTATGTATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 6 0.17
28 12 0.33
29 12 0.33
30 6 0.17
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTATATTATATAAATTTTATTATATT
Found at i:1026433 original size:13 final size:13
Alignment explanation
Indices: 1026411--1026444 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1026401 TTAAAATTTT
1026411 TTAAAAATAAATA
1 TTAAAAATAAATA
*
1026424 TTAAATATAAATA
1 TTAAAAATAAATA
1026437 TTTAAAAA
1 -TTAAAAA
1026445 AATTAAAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAAAATAAATA
Found at i:1028140 original size:20 final size:19
Alignment explanation
Indices: 1028088--1028141 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1028078 TTATATATTT
1028088 TATAA-TTAAATTTAAATAAA
1 TATAATTTAAA-TT-AATAAA
* *
1028108 TATATTTTTAATTAATAAA
1 TATAATTTAAATTAATAAA
1028127 TAATAATTTAAATTA
1 T-ATAATTTAAATTA
1028142 TTCAAATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 7 0.25
20 17 0.61
21 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATAATTTAAATTAATAAA
Found at i:1028167 original size:2 final size:2
Alignment explanation
Indices: 1028155--1028186 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1028145 AAATCATTAA
1028155 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1028187 AAATTCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1028421 original size:21 final size:20
Alignment explanation
Indices: 1028384--1028424 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1028374 AATTAATTAA
**
1028384 TTTTAAATATTTTTATAATT
1 TTTTAAATATTGATATAATT
1028404 TTTTAAATTATTGATATAATT
1 TTTTAAA-TATTGATATAATT
1028425 AAATTAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTAAATATTGATATAATT
Found at i:1028507 original size:17 final size:18
Alignment explanation
Indices: 1028473--1028520 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1028463 TATACATAAA
1028473 ATTTAAAATATATATTAT
1 ATTTAAAATATATATTAT
* *
1028491 ATTTAAATTAT-TTTTAT
1 ATTTAAAATATATATTAT
1028508 ATTATAATAATAT
1 ATT-TAA-AATAT
1028521 TTTAAATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAAAATATATATTAT
Found at i:1028586 original size:17 final size:16
Alignment explanation
Indices: 1028537--1028582 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1028527 TATTATATAT
1028537 TTATATAAAATTT-AA
1 TTATATAAAATTTAAA
*
1028552 TAATATTAATAATTTAAA
1 TTATA-TAA-AATTTAAA
1028570 TTATATAAAATTT
1 TTATATAAAATTT
1028583 TAAAATATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 8 0.31
17 8 0.31
18 6 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATATAAAATTTAAA
Found at i:1028903 original size:16 final size:17
Alignment explanation
Indices: 1028876--1028932 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
1028866 GGATAATTTT
1028876 AAATATAATATAAATTA
1 AAATATAATATAAATTA
1028893 TAAA-A-AATAT-AATTA
1 -AAATATAATATAAATTA
*
1028908 AAATATAATATAAAATA
1 AAATATAATATAAATTA
*
1028925 ATATATAA
1 AAATATAA
1028933 AAAAATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
14 3 0.09
15 6 0.18
16 10 0.29
17 12 0.35
18 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAATATAAATTA
Found at i:1028912 original size:27 final size:28
Alignment explanation
Indices: 1028882--1028949 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
1028872 TTTTAAATAT
**
1028882 AATATAAATTATAAAA-AATATA-ATTAA
1 AATATAAA-TATAAAATAATATATAAAAA
1028909 AATAT-AATATAAAATAATATATAAAAA
1 AATATAAATATAAAATAATATATAAAAA
1028936 AATATAAATATAAA
1 AATATAAATATAAA
1028950 TTTATATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 7 0.19
26 8 0.22
27 13 0.36
28 8 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (28 bp):
AATATAAATATAAAATAATATATAAAAA
Found at i:1028930 original size:12 final size:12
Alignment explanation
Indices: 1028878--1028941 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 12
1028868 ATAATTTTAA
*
1028878 ATATAATATAA-
1 ATATAAAATAAT
1028889 ATTATAAAA-AAT
1 A-TATAAAATAAT
1028901 ATAATTAAAAT-AT
1 AT-A-TAAAATAAT
1028914 AATATAAAATAAT
1 -ATATAAAATAAT
*
1028927 ATATAAAAAAAT
1 ATATAAAATAAT
1028939 ATA
1 ATA
1028942 AATATAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 4 0.09
12 28 0.64
13 10 0.23
14 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAAAATAAT
Found at i:1028950 original size:12 final size:12
Alignment explanation
Indices: 1028875--1028950 Score: 62
Period size: 11 Copynumber: 6.9 Consensus size: 12
1028865 TGGATAATTT
1028875 TAAATAT-AATA
1 TAAATATAAATA
1028886 TAAAT-TATAA-A
1 TAAATATA-AATA
*
1028897 -AAATATAATTA
1 TAAATATAAATA
1028908 -AAATAT-AATA
1 TAAATATAAATA
1028918 TAAA-ATAATATA
1 TAAATATAA-ATA
1028930 TAAA-A-AAATA
1 TAAATATAAATA
1028940 TAAATATAAAT
1 TAAATATAAAT
1028951 TTATATAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
10 18 0.33
11 22 0.41
12 14 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAAATA
Found at i:1028990 original size:19 final size:19
Alignment explanation
Indices: 1028960--1029020 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 19
1028950 TTTATATAAT
1028960 ATTTTTATTAATATATTAAA
1 ATTTTTA-TAATATATTAAA
1028980 ATTTTTATAATA-ATTTAAA
1 ATTTTTATAATATA-TTAAA
** *
1028999 TATAATTATAATATATAAAA
1 -ATTTTTATAATATATTAAA
1029019 AT
1 AT
1029021 ATACAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
18 1 0.03
19 12 0.34
20 21 0.60
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTTTTATAATATATTAAA
Found at i:1029245 original size:16 final size:17
Alignment explanation
Indices: 1029169--1029245 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 17
1029159 GTCTTTTATA
*
1029169 ATATTATA-ATTATATT
1 ATATTATATTTTATATT
*
1029185 -TAATATATTTTATATTT
1 ATATTATATTTTATA-TT
*
1029202 ATATTA-ATTTTA-A-A
1 ATATTATATTTTATATT
*
1029216 ATATTAATAATTTATATT
1 ATATT-ATATTTTATATT
1029234 ATATTAT-TTTTA
1 ATATTATATTTTA
1029246 AAAATATATT
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
14 5 0.11
15 7 0.15
16 15 0.32
17 11 0.23
18 9 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:1029250 original size:33 final size:35
Alignment explanation
Indices: 1029184--1029292 Score: 102
Period size: 32 Copynumber: 3.1 Consensus size: 35
1029174 ATAATTATAT
1029184 TTAATATATTTTATATTTATATTAATTTTAAAATA
1 TTAATATATTTTATATTTATATTAATTTTAAAATA
*
1029219 TTAATA-A-TTTATA-TTATATTATTTTTAAAA-A
1 TTAATATATTTTATATTTATATTAATTTTAAAATA
* * * *
1029250 TATATTTTATCGTATTATATTTTTATT-ATTTTATAATA
1 T-TAATATAT--T-TTATATTTATATTAATTTTAAAATA
1029288 TTAAT
1 TTAAT
1029293 TCGTATAGTA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
31 2 0.03
32 19 0.32
33 7 0.12
34 1 0.02
35 6 0.10
36 1 0.02
37 15 0.25
38 8 0.14
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (35 bp):
TTAATATATTTTATATTTATATTAATTTTAAAATA
Found at i:1029683 original size:38 final size:37
Alignment explanation
Indices: 1029640--1029749 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 37
1029630 ATGAGTGGTG
* *
1029640 AAAAAAATAAATAAATTTGATA-ATTTTAAATATAATATA
1 AAAAAAATAAATAAATATAATATA-TTT-AATA-AATATA
*
1029679 AAAAATATAATATAAATATAATATATTTAATAAATATA
1 AAAAAAATAA-ATAAATATAATATATTTAATAAATATA
* **
1029717 AAAAATAATAAATAAGGTATAACCTATTTAATA
1 AAAAA-AATAAATAA-ATATAATATATTTAATA
1029750 TATTTTTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
38 15 0.25
39 31 0.52
40 13 0.22
41 1 0.02
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (37 bp):
AAAAAAATAAATAAATATAATATATTTAATAAATATA
Found at i:1029686 original size:14 final size:14
Alignment explanation
Indices: 1029667--1029717 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1029657 TGATAATTTT
1029667 AAATATAATATAAA
1 AAATATAATATAAA
1029681 AAATATAATATAAA
1 AAATATAATATAAA
* *
1029695 TATAATAT-ATTTAAT
1 -A-AATATAATATAAA
1029710 AAATATAA
1 AAATATAA
1029718 AAAATAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 16 0.50
15 6 0.19
16 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATATAATATAAA
Found at i:1029710 original size:25 final size:24
Alignment explanation
Indices: 1029666--1029718 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
1029656 TTGATAATTT
1029666 TAAATATAATATAAAAAATATAATA
1 TAAATATAATATAAAAAATA-AATA
***
1029691 TAAATATAATATATTTAATAAATA
1 TAAATATAATATAAAAAATAAATA
1029715 TAAA
1 TAAA
1029719 AAATAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAATATAATATAAAAAATAAATA
Done.