Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold182
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: 1166161
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 10
Found at i:92165 original size:21 final size:19
Alignment explanation
Indices: 92122--92167 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 19
92112 TAAATATTTT
*
92122 ATTTATA-ATAAAATTATA
1 ATTTATATATAAAATTAAA
92140 A-TTATATATAAAATTTCAAA
1 ATTTATATATAAAA-TT-AAA
92160 ATTTATAT
1 ATTTATAT
92168 TTATATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 2 0.09
20 3 0.13
21 6 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTATATATAAAATTAAA
Found at i:92182 original size:16 final size:16
Alignment explanation
Indices: 92161--92205 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
92151 AATTTCAAAA
92161 TTTATATTTATATTAT
1 TTTATATTTATATTAT
92177 TTTATATTT-TATTAT
1 TTTATATTTATATTAT
92192 TTT-TATATTATATT
1 TTTATAT-TTATATT
92206 TAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.11
15 11 0.41
16 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATATTTATATTAT
Found at i:92194 original size:8 final size:7
Alignment explanation
Indices: 92161--92212 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
92151 AATTTCAAAA
92161 TTTATAT
1 TTTATAT
92168 TTATATTAT
1 TT-TA-TAT
92177 TTTATAT
1 TTTATAT
92184 TTTATTAT
1 TTTA-TAT
92192 TTT-TAT
1 TTTATAT
*
92198 ATTATAT
1 TTTATAT
*
92205 TTAATAT
1 TTTATAT
92212 T
1 T
92213 ATTAAATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 5 0.13
7 18 0.47
8 10 0.26
9 5 0.13
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTATAT
Found at i:92197 original size:21 final size:22
Alignment explanation
Indices: 92173--92215 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
92163 TATATTTATA
*
92173 TTATTTTATATTT-TATTATTT
1 TTATATTATATTTATATTATTT
92194 TTATATTATATTTAATATTATT
1 TTATATTATATTT-ATATTATT
92216 AAATTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATATTATATTTATATTATTT
Found at i:92198 original size:26 final size:26
Alignment explanation
Indices: 92162--92222 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
92152 ATTTCAAAAT
*
92162 TTATATTTATATTAT-TTTATATTTTA
1 TTATATTTATATTATATTTA-ATATTA
*
92188 TTATTTTTATATTATATTTAATATTA
1 TTATATTTATATTATATTTAATATTA
*
92214 TTAAATTTA
1 TTATATTTA
92223 CATAAATCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATATTTATATTATATTTAATATTA
Found at i:92494 original size:14 final size:14
Alignment explanation
Indices: 92475--92594 Score: 77
Period size: 14 Copynumber: 8.4 Consensus size: 14
92465 ATCTAATTAA
92475 AATATAATATATAT
1 AATATAATATATAT
*
92489 AATATAATATAAAT
1 AATATAATATATAT
* *
92503 AA-ATAATTTTTAT
1 AATATAATATATAT
*
92516 AATATTATATAATAT
1 AATATAATAT-ATAT
*
92531 AAATCATTAATAT-TTT
1 -AAT-A-TAATATATAT
* *
92547 AATAT-TTATATAA
1 AATATAATATATAT
* *
92560 ATATATAATATTTAA
1 A-ATATAATATATAT
92575 AATATAATA-ATAT
1 AATATAATATATAT
92588 AAATATA
1 -AATATA
92595 CAAATTACTA
Statistics
Matches: 81, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
12 3 0.04
13 15 0.19
14 39 0.48
15 13 0.16
16 5 0.06
17 1 0.01
18 5 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATAATATATAT
Found at i:92504 original size:4 final size:5
Alignment explanation
Indices: 92475--92532 Score: 61
Period size: 5 Copynumber: 12.4 Consensus size: 5
92465 ATCTAATTAA
**
92475 AATAT AATAT -ATAT AATAT AATAT AA-AT AA-AT AAT-T TTTAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
*
92521 TATAT AATAT AA
1 AATAT AATAT AA
92533 ATCATTAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 14 0.32
5 30 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
AATAT
Found at i:92516 original size:27 final size:27
Alignment explanation
Indices: 92486--92592 Score: 90
Period size: 27 Copynumber: 3.8 Consensus size: 27
92476 ATATAATATA
92486 TATAATATAATATAAATAAATAATTTT
1 TATAATATAATATAAATAAATAATTTT
* *
92513 TATAATATTATATAATATAAATCATTAATAT
1 TATAATATAATATAA-ATAAATAATT--T-T
* * * *
92544 TTTAATATTTATATAAATATATAATATT
1 TATAATA-TAATATAAATAAATAATTTT
* *
92572 TAAAATATAATA-ATATAAATA
1 TATAATATAATATAAATAAATA
92593 TACAAATTAC
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
26 7 0.11
27 18 0.28
28 15 0.23
29 1 0.02
30 1 0.02
31 14 0.22
32 8 0.12
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
TATAATATAATATAAATAAATAATTTT
Found at i:92531 original size:32 final size:31
Alignment explanation
Indices: 92485--92592 Score: 118
Period size: 32 Copynumber: 3.6 Consensus size: 31
92475 AATATAATAT
*
92485 ATATAATATAATATAAATAAATAATTTTTATA
1 ATAT-ATATAATATAAATAAATAATATTTATA
* *
92517 ATATTATATAATATAAATCATTAATATTT-TA
1 ATA-TATATAATATAAATAAATAATATTTATA
* *
92548 ATAT-T-T-ATATAAATATATAATATTTAAA
1 ATATATATAATATAAATAAATAATATTTATA
92576 ATATA-ATAATATAAATA
1 ATATATATAATATAAATA
92593 TACAAATTAC
Statistics
Matches: 64, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
27 16 0.25
28 6 0.09
29 2 0.03
30 10 0.16
31 5 0.08
32 24 0.38
33 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (31 bp):
ATATATATAATATAAATAAATAATATTTATA
Found at i:92801 original size:21 final size:23
Alignment explanation
Indices: 92777--92821 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
92767 TTTCCAATAA
*
92777 ATTTTTTAAT-TTAAT-TAATTT
1 ATTTTTTAATATCAATATAATTT
92798 ATTTTTTAATATCAATATAATTT
1 ATTTTTTAATATCAATATAATTT
92821 A
1 A
92822 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 4 0.19
23 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTTTAATATCAATATAATTT
Found at i:92954 original size:35 final size:34
Alignment explanation
Indices: 92880--92960 Score: 112
Period size: 35 Copynumber: 2.4 Consensus size: 34
92870 ATATAATTTT
*
92880 TTATTATTTTTAATTATAATTTATTTTTTTATTA
1 TTATTATTTTTAATTATAATATATTTTTTTATTA
92914 TTATTATTTTTACATT-TAAATATATATTTTTTATTA
1 TTATTATTTTTA-ATTAT-AATATAT-TTTTTTATTA
92950 -TATTATTTTTA
1 TTATTATTTTTA
92961 TTTTTATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 13 0.30
35 20 0.47
36 10 0.23
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (34 bp):
TTATTATTTTTAATTATAATATATTTTTTTATTA
Found at i:92966 original size:41 final size:40
Alignment explanation
Indices: 92888--92966 Score: 106
Period size: 41 Copynumber: 1.9 Consensus size: 40
92878 TTTTATTATT
* *
92888 TTTAATTATAATTTATTTTTTTATTATTATTATTTTTACA
1 TTTAAATATAATTTATTTTTATATTATTATTATTTTTACA
*
92928 TTTAAATATATATTT-TTTATTATATTATTTTTATTTTTA
1 TTTAAATATA-ATTTATTT-TTATATTATTATTATTTTTA
92967 TAATAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 12 0.35
41 22 0.65
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (40 bp):
TTTAAATATAATTTATTTTTATATTATTATTATTTTTACA
Found at i:94180 original size:8 final size:8
Alignment explanation
Indices: 94169--94241 Score: 55
Period size: 8 Copynumber: 9.1 Consensus size: 8
94159 TAATTTAATA
94169 ATTTATAT
1 ATTTATAT
94177 ATTTATATT
1 ATTTATA-T
94186 ATATTGATAT
1 AT-TT-ATAT
94196 ATTT-TATT
1 ATTTATA-T
94204 ATTT-TAT
1 ATTTATAT
*
94211 AATTATAT
1 ATTTATAT
*
94219 -TTAATAT
1 ATTTATAT
94226 ATTT-TAT
1 ATTTATAT
*
94233 TTTTATAT
1 ATTTATAT
94241 A
1 A
94242 AATTTTAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
7 17 0.33
8 22 0.42
9 5 0.10
10 5 0.10
11 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (8 bp):
ATTTATAT
Found at i:94189 original size:13 final size:12
Alignment explanation
Indices: 94171--94282 Score: 52
Period size: 12 Copynumber: 8.8 Consensus size: 12
94161 ATTTAATAAT
94171 TTATATATTTATA
1 TTATAT-TTTATA
*
94184 TTATATTGATATATT
1 TTATATT--T-TATA
94199 TTATTATTTTATAA
1 TTA-TATTTTAT-A
94213 TTATATTTAATATA
1 TTATATTT--TATA
*
94227 TTTTATTTT-TA
1 TTATATTTTATA
* *
94238 TATAAATTTTAAA
1 T-TATATTTTATA
*
94251 TTAT-TTATT-TT
1 TTATATT-TTATA
94262 TTATATTTTA-A
1 TTATATTTTATA
94273 TATATATTTT
1 T-TATATTTT
94283 TATCCATATT
Statistics
Matches: 76, Mismatches: 10, Indels: 27
0.67 0.09 0.24
Matches are distributed among these distances:
11 12 0.16
12 22 0.29
13 16 0.21
14 13 0.17
15 9 0.12
16 4 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (12 bp):
TTATATTTTATA
Found at i:94240 original size:22 final size:21
Alignment explanation
Indices: 94142--94232 Score: 67
Period size: 23 Copynumber: 4.1 Consensus size: 21
94132 AAATTTTTAA
*
94142 ATAATTATATTTAAATCTAATTTA
1 ATAATTATATTT-AAT-T-ATTTT
* * *
94166 ATAATT-TATATATTTATATT
1 ATAATTATATTTAATTATTTT
* *
94186 ATATTGATATATTTTATTATTTT
1 ATAAT--TATATTTAATTATTTT
94209 ATAATTATATTTAATATATTTT
1 ATAATTATATTTAAT-TATTTT
94231 AT
1 AT
94233 TTTTATATAA
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
20 7 0.13
21 10 0.19
22 11 0.21
23 18 0.35
24 6 0.12
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (21 bp):
ATAATTATATTTAATTATTTT
Found at i:94285 original size:27 final size:26
Alignment explanation
Indices: 94178--94282 Score: 81
Period size: 30 Copynumber: 3.8 Consensus size: 26
94168 AATTTATATA
* *
94178 TTTATATTATATTGATATATTTTATTAT
1 TTTATATTTTAAT-ATATATTTTATT-T
* *
94206 TTTATAATTATATTTAATATATTTTATTT
1 TTTAT-ATTTTA-AT-ATATATTTTATTT
94235 TTATATAAATTTTAA-AT-TA-TTTATTT
1 TT-TAT--ATTTTAATATATATTTTATTT
94261 TTTATATTTTAATATATATTTT
1 TTTATATTTTAATATATATTTT
94283 TATCCATATT
Statistics
Matches: 67, Mismatches: 3, Indels: 16
0.78 0.03 0.19
Matches are distributed among these distances:
23 7 0.10
24 2 0.03
25 5 0.07
26 12 0.18
27 2 0.03
28 7 0.10
29 9 0.13
30 17 0.25
31 6 0.09
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTATATTTTAATATATATTTTATTT
Found at i:94710 original size:22 final size:23
Alignment explanation
Indices: 94657--94710 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
94647 AAAATTATAT
*
94657 TTAAATA-TAATCATATTTTAAA
1 TTAAATATTAATCATATTATAAA
* * *
94679 TAAAAAATTAATTATA-TATAAA
1 TTAAATATTAATCATATTATAAA
94701 TTAAATATTA
1 TTAAATATTA
94711 TCTATTTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 18 0.72
23 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAAATATTAATCATATTATAAA
Found at i:94735 original size:30 final size:28
Alignment explanation
Indices: 94695--94776 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 28
94685 ATTAATTATA
* *
94695 TATAAATTAAATATTATCTATTTATTTTAG
1 TATAAATTAAA-ATTAT-AATTTATTTGAG
*
94725 TATATATTAAAAATTAATAATTTATTTGAG
1 TATAAATT-AAAATT-ATAATTTATTTGAG
94755 TATAAATTTAAAATTATAATTT
1 TATAAA-TTAAAATTATAATTT
94777 TTTTAAATGT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 7 0.16
30 31 0.69
31 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (28 bp):
TATAAATTAAAATTATAATTTATTTGAG
Found at i:95106 original size:13 final size:14
Alignment explanation
Indices: 95090--95122 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
95080 TTATTTTTTA
*
95090 AAATTAATTATA-T
1 AAATTAATTAAATT
95103 AAATTAATTAAATT
1 AAATTAATTAAATT
95117 AAATTA
1 AAATTA
95123 TCAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTAATTAAATT
Found at i:101039 original size:2 final size:2
Alignment explanation
Indices: 101028--101058 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
101018 TAATTTAAAA
101028 AT AT -T 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
101059 TAAATTATCC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:102647 original size:16 final size:16
Alignment explanation
Indices: 102626--102661 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
102616 GTATGCCCCC
102626 CTGTGTAACGGAGATT
1 CTGTGTAACGGAGATT
102642 CTGTGTAACGGAGATT
1 CTGTGTAACGGAGATT
102658 CTGT
1 CTGT
102662 TGACTGATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.22, C:0.14, G:0.31, T:0.33
Consensus pattern (16 bp):
CTGTGTAACGGAGATT
Found at i:102938 original size:18 final size:17
Alignment explanation
Indices: 102895--102939 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
102885 AGTTATAGTT
102895 TTTTAAAAAAATTTTAAA
1 TTTT-AAAAAATTTTAAA
*
102913 TTCGTAAAAAATTTTAAAA
1 TT-TTAAAAAATTTT-AAA
102932 TTTTAAAA
1 TTTTAAAA
102940 TATATTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTTAAAAAATTTTAAA
Found at i:102961 original size:17 final size:16
Alignment explanation
Indices: 102934--102967 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
102924 TTTTAAAATT
102934 TTAAAATATATTGATA
1 TTAAAATATATTGATA
*
102950 TTAAATATATATTTATA
1 TTAAA-ATATATTGATA
102967 T
1 T
102968 CTAACGACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAAATATATTGATA
Found at i:103560 original size:18 final size:19
Alignment explanation
Indices: 103537--103574 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
103527 ATTAATTTTT
103537 TTTATATGA-TAAAATTAA
1 TTTATATGAGTAAAATTAA
103555 TTTATATGATGTAAAATTAA
1 TTTATATGA-GTAAAATTAA
103575 ATTAGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (19 bp):
TTTATATGAGTAAAATTAA
Found at i:105539 original size:27 final size:27
Alignment explanation
Indices: 105509--105569 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
105499 TATTTAGTTA
*
105509 ATTAAATTTGAATGTTTTTATATTCAT
1 ATTAAATTTGAATGTTTTGATATTCAT
105536 ATTAAATTTGAATGTTTTGATATTCAT
1 ATTAAATTTGAATGTTTTGATATTCAT
*
105563 ATCAAAT
1 ATTAAAT
105570 AACTCGCAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (27 bp):
ATTAAATTTGAATGTTTTGATATTCAT
Found at i:105896 original size:15 final size:16
Alignment explanation
Indices: 105863--105907 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
105853 TTCTTACAAT
105863 ATATTTAATAATATTA
1 ATATTTAATAATATTA
*
105879 ATATTTAA-AATTTTAA
1 ATATTTAATAATATT-A
105895 TATATTTAATAAT
1 -ATATTTAATAAT
105908 TTATATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
17 8 0.32
18 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATTTAATAATATTA
Found at i:107930 original size:26 final size:25
Alignment explanation
Indices: 107898--107948 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
107888 TCACAAATAT
*
107898 TTTTAATT-TCAATTATTAAAATATAA
1 TTTTAATTAT-AAATATT-AAATATAA
107924 TTTTAATTATAAATATTAAATATAA
1 TTTTAATTATAAATATTAAATATAA
107949 AATGCAATCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 14 0.61
27 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTAATTATAAATATTAAATATAA
Found at i:109152 original size:126 final size:126
Alignment explanation
Indices: 108997--109231 Score: 416
Period size: 126 Copynumber: 1.9 Consensus size: 126
108987 AATGAATTAG
*
108997 TTGTGAAAGAGGATGAGGAAGAAGTTATTCCTTCATTTCCTTTATCCGATAAGAAAAAGAAGTCG
1 TTGTGAAAGAGGATGAGGAAGAAGATATTCCTTCATTTCCTTTATCCGATAAGAAAAAGAAGTCG
* **
109062 AAGTCTTCTAAGAAGAGTGGCAATTCCTTCAGTGCAGCATTGCTTGATGAAAACGAATTGA
66 AAGTCTTCTAAAAAGAGCAGCAATTCCTTCAGTGCAGCATTGCTTGATGAAAACGAATTGA
*
109123 TTGTGAAAGAGGATGAGGAAGAAGATATTCCTTCATTTCCTTTATCTGATAAGAAAAAGAAGTCG
1 TTGTGAAAGAGGATGAGGAAGAAGATATTCCTTCATTTCCTTTATCCGATAAGAAAAAGAAGTCG
*
109188 AAGTCTTCTAAAAAGAGCAGTAATTCCTTCAGTGCAGCATTGCT
66 AAGTCTTCTAAAAAGAGCAGCAATTCCTTCAGTGCAGCATTGCT
109232 GGACGATGAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 103 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (126 bp):
TTGTGAAAGAGGATGAGGAAGAAGATATTCCTTCATTTCCTTTATCCGATAAGAAAAAGAAGTCG
AAGTCTTCTAAAAAGAGCAGCAATTCCTTCAGTGCAGCATTGCTTGATGAAAACGAATTGA
Found at i:109523 original size:12 final size:12
Alignment explanation
Indices: 109506--109539 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
109496 AGAATCTTCG
109506 AAGAACAAGAAA
1 AAGAACAAGAAA
*
109518 AAGAACAAGAAG
1 AAGAACAAGAAA
*
109530 AAGAATAAGA
1 AAGAACAAGA
109540 GTGGAAGGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.21, T:0.03
Consensus pattern (12 bp):
AAGAACAAGAAA
Found at i:115124 original size:3 final size:3
Alignment explanation
Indices: 115118--115153 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
115108 TGTTGTTGTG
115118 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
115154 TTAATCCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:116908 original size:1 final size:1
Alignment explanation
Indices: 116902--116927 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
116892 TTGCATCAAT
116902 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
116928 GGGGTTTCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:117384 original size:2 final size:2
Alignment explanation
Indices: 117377--117408 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
117367 AGGGTAAGTT
117377 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
117409 CATAATACAT
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:118536 original size:25 final size:24
Alignment explanation
Indices: 118481--118541 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
118471 ATTATACGAT
*
118481 TTATATTTATATTTTTATTTAAGG
1 TTATATTTATATTTATATTTAAGG
*
118505 TTA-ATTTATAAATTTATATTTGA-G
1 TTATATTTAT--ATTTATATTTAAGG
118529 TTATATTT-TATTT
1 TTATATTTATATTT
118542 TATGATTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.12
23 6 0.19
24 8 0.25
25 14 0.44
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (24 bp):
TTATATTTATATTTATATTTAAGG
Found at i:119016 original size:30 final size:32
Alignment explanation
Indices: 118954--119016 Score: 78
Period size: 34 Copynumber: 2.0 Consensus size: 32
118944 TATCAATATA
118954 TTTGTAAAATCTATGAATTTTGAATTAAATTATG
1 TTTGTAAAATCTAT--ATTTTGAATTAAATTATG
118988 TTTGTAAAATCTAT-TTGTT-AATT-AATTAT
1 TTTGTAAAATCTATATT-TTGAATTAAATTAT
119017 TAATTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
30 6 0.21
31 6 0.21
32 2 0.07
34 14 0.50
ACGTcount: A:0.37, C:0.03, G:0.10, T:0.51
Consensus pattern (32 bp):
TTTGTAAAATCTATATTTTGAATTAAATTATG
Found at i:119236 original size:29 final size:26
Alignment explanation
Indices: 119190--119268 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 26
119180 TAACGGGTAA
*
119190 ATTTAATAATTCATATATTTATATTAT
1 ATTTAATAATT-TTATATTTATATTAT
119217 ATTT-ATATATTTTATTATATTATAATTAT
1 ATTTAATA-ATTTTA-TAT-TTAT-ATTAT
*
119246 GTTTAATAATTTTATATTTATAT
1 ATTTAATAATTTTATATTTATAT
119269 AAATTTTGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
26 7 0.16
27 14 0.31
28 7 0.16
29 14 0.31
30 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
ATTTAATAATTTTATATTTATATTAT
Found at i:119269 original size:29 final size:29
Alignment explanation
Indices: 119190--119270 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
119180 TAACGGGTAA
*
119190 ATTTAATAA-TTCATATATT-TAT-ATTAT
1 ATTTAATAATTTTATAT-TTATATAATTAT
*
119217 ATTT-ATATATTTTAT-TATATTATAATTAT
1 ATTTAATA-ATTTTATATTTA-TATAATTAT
*
119246 GTTTAATAATTTTATATTTATATAA
1 ATTTAATAATTTTATATTTATATAA
119271 ATTTTGATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
26 4 0.09
27 6 0.14
28 7 0.16
29 20 0.47
30 6 0.14
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (29 bp):
ATTTAATAATTTTATATTTATATAATTAT
Found at i:119292 original size:55 final size:56
Alignment explanation
Indices: 119191--119295 Score: 135
Period size: 55 Copynumber: 1.9 Consensus size: 56
119181 AACGGGTAAA
* * *
119191 TTTAATAATTCATATATTTATATTATATTTATATATTTTATTATATTATAATTATG
1 TTTAATAATTCATATATTTATATTAAATTTATATAATTAATTATATTATAATTATG
*
119247 TTTAATAATT-TTATATTTATA-TAAATTT-TGATAATTAATTAATATTATA
1 TTTAATAATTCATATATTTATATTAAATTTAT-ATAATTAATT-ATATTATA
119296 TAAATTTTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
53 1 0.02
54 14 0.33
55 18 0.42
56 10 0.23
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (56 bp):
TTTAATAATTCATATATTTATATTAAATTTATATAATTAATTATATTATAATTATG
Found at i:120773 original size:20 final size:22
Alignment explanation
Indices: 120748--120797 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
120738 TTTATATATA
120748 ATATAAATA-AAATTAT-ATTT
1 ATATAAATATAAATTATCATTT
*
120768 ATAT-AATATAATTTATCATTT
1 ATATAAATATAAATTATCATTT
*
120789 ACATAAATA
1 ATATAAATA
120798 CATAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.16
20 10 0.40
21 7 0.28
22 4 0.16
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAATATAAATTATCATTT
Found at i:122212 original size:13 final size:13
Alignment explanation
Indices: 122179--122217 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
122169 ACTTCGAGTA
*
122179 TAAATAATTGAATT
1 TAAA-AATTAAATT
122193 T-AAAATTAAATT
1 TAAAAATTAAATT
122205 TAAAAATTAAATT
1 TAAAAATTAAATT
122218 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 9 0.39
13 13 0.57
14 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAAAAATTAAATT
Found at i:125221 original size:2 final size:2
Alignment explanation
Indices: 125214--125240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
125204 TTTTTCATTA
125214 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
125241 GATGGAGTGG
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:125714 original size:18 final size:17
Alignment explanation
Indices: 125688--125742 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
125678 CATCATATTT
*
125688 TATTGTATATGTTTATAA
1 TATTTTATAT-TTTATAA
125706 TATTTTATATTTATATAA
1 TATTTTATATTT-TATAA
125724 -ATTTTGATATATTTATAA
1 TATTTT-ATAT-TTTATAA
125742 T
1 T
125743 TTAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
17 7 0.22
18 23 0.72
19 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
TATTTTATATTTTATAA
Found at i:126567 original size:27 final size:28
Alignment explanation
Indices: 126536--126591 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
126526 TATAATTATA
*
126536 TTTAAAATATTTTATATTTAT-TTA-AAT
1 TTTAAAATA-TTAATATTTATATTATAAT
126563 TTTAAAATATTAATATTTATATTATAAT
1 TTTAAAATATTAATATTTATATTATAAT
126591 T
1 T
126592 ATTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.38
27 12 0.46
28 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TTTAAAATATTAATATTTATATTATAAT
Found at i:128331 original size:26 final size:24
Alignment explanation
Indices: 128278--128325 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
128268 CATACTGTGG
128278 CATGTATTTTTAGCTCAAACCAGAT
1 CATGTATTTTTA-CTCAAACCAGAT
128303 CATGTATATTTTA-TCAGAACCAG
1 CATGTAT-TTTTACTCA-AACCAG
128326 TTTCATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 3 0.14
25 13 0.62
26 5 0.24
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (24 bp):
CATGTATTTTTACTCAAACCAGAT
Found at i:130201 original size:19 final size:19
Alignment explanation
Indices: 130138--130218 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 19
130128 TTAATTATTC
130138 AATATAAATATAATTAAATAT
1 AATATAAA-A-AATTAAATAT
*
130159 GATATAAAAAATTAAAATAT
1 AATATAAAAAATT-AAATAT
130179 AATATAAAAAATT-AATAT
1 AATATAAAAAATTAAATAT
*
130197 AAATATATAAATATATAAATAT
1 -AATATA-AAAAAT-TAAATAT
130219 TTTAAAATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
18 5 0.10
19 10 0.19
20 24 0.46
21 8 0.15
22 5 0.10
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (19 bp):
AATATAAAAAATTAAATAT
Found at i:130206 original size:8 final size:8
Alignment explanation
Indices: 130193--130238 Score: 56
Period size: 8 Copynumber: 5.4 Consensus size: 8
130183 TAAAAAATTA
130193 ATATAAAT
1 ATATAAAT
130201 ATATAAAT
1 ATATAAAT
130209 ATATAAAT
1 ATATAAAT
*
130217 ATTTTAAAAT
1 A-TAT-AAAT
130227 ATATATAAT
1 ATATA-AAT
130236 ATA
1 ATA
130239 AATTATTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
8 18 0.55
9 10 0.30
10 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:130214 original size:16 final size:17
Alignment explanation
Indices: 130139--130310 Score: 65
Period size: 16 Copynumber: 9.7 Consensus size: 17
130129 TAATTATTCA
130139 ATATAAATATAATTAAATAT
1 ATATAAATAT-A-TAAA-AT
* *
130159 GATATAAA-AAATTAAA-
1 -ATATAAATATATAAAAT
*
130175 ATAT-AATATAAAAAATT
1 ATATAAATATATAAAA-T
130192 AATATAAATATAT-AAAT
1 -ATATAAATATATAAAAT
*
130209 ATATAAATATTTTAAAAT
1 ATATAAATA-TATAAAAT
* *
130227 ATATATA-ATATAAATT
1 ATATAAATATATAAAAT
*
130243 AT-TAACGTAT-TAAAATTT
1 ATATAA-ATATATAAAA--T
130261 ATATAAA-A-ATAAAAT
1 ATATAAATATATAAAAT
*
130276 ATTTTAAATATAATTATAATAT
1 A-TATAAATAT-A-TA-AA-AT
130298 AATATAAATATAT
1 -ATATAAATATAT
130311 TAATTACTAA
Statistics
Matches: 114, Mismatches: 16, Indels: 43
0.66 0.09 0.25
Matches are distributed among these distances:
14 2 0.02
15 13 0.11
16 26 0.23
17 14 0.12
18 23 0.20
19 11 0.10
20 4 0.04
21 10 0.09
22 10 0.09
23 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
ATATAAATATATAAAAT
Found at i:130233 original size:54 final size:57
Alignment explanation
Indices: 130174--130299 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 57
130164 AAAAAATTAA
*
130174 AATATAATATAAAAAATTAA-TA-T-AAA-TATATAAATATATAAATATTTTAAA-AT
1 AATATAATATAAAAAATTAACTATTAAAATTATATAAAAATA-AAATATTTTAAATAT
**
130227 ATATATAATATAAATTATTAACGTATTAAAATTTATATAAAAATAAAATATTTTAAATAT
1 A-ATATAATATAAAAAATTAAC-TATTAAAA-TTATATAAAAATAAAATATTTTAAATAT
130287 AATTATAATATAA
1 AA-TATAATATAA
130300 TATAAATATA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
53 1 0.02
54 17 0.28
56 2 0.03
57 1 0.02
58 3 0.05
59 13 0.21
60 24 0.39
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.40
Consensus pattern (57 bp):
AATATAATATAAAAAATTAACTATTAAAATTATATAAAAATAAAATATTTTAAATAT
Found at i:130245 original size:26 final size:26
Alignment explanation
Indices: 130170--130245 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
130160 ATATAAAAAA
*
130170 TTAAAATATAATATAA-A-AAATTAAT
1 TTAAAATAT-ATATAATATAAATTATT
* *
130195 AT-AAATATATA-AATATATAAATATT
1 TTAAAATATATATAATATA-AATTATT
130220 TTAAAATATATATAATATAAATTATT
1 TTAAAATATATATAATATAAATTATT
130246 AACGTATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 2 0.05
23 4 0.10
24 7 0.17
25 7 0.17
26 15 0.37
27 6 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TTAAAATATATATAATATAAATTATT
Found at i:132872 original size:38 final size:38
Alignment explanation
Indices: 132821--132895 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
132811 AGTATGTTAG
*
132821 TTTTCACAACATTAACTAAACATAATTTCAATGAATAA
1 TTTTCACAACATTAACTAAACATAATTTAAATGAATAA
132859 TTTTCACAACATTAACTAAACATAATTTAAATGAATA
1 TTTTCACAACATTAACTAAACATAATTTAAATGAATA
132896 GCTTGTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.35
Consensus pattern (38 bp):
TTTTCACAACATTAACTAAACATAATTTAAATGAATAA
Found at i:133376 original size:6 final size:6
Alignment explanation
Indices: 133365--133397 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
133355 TTTAAAAAAT
133365 TTTAAA TTTAAA TTTAAA TTT-AA TTT-AA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
133398 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:133448 original size:22 final size:22
Alignment explanation
Indices: 133366--133448 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
133356 TTAAAAAATT
*
133366 TTAAATTTAAATTTAAATT-TAA
1 TTAAATTTAAA-TAAAATTATAA
* * *
133388 TTTAATTTAATTAAAATTATTAT
1 TTAAATTTAAATAAAATTA-TAA
133411 TTAAAATATT-AA-AAAATTATAA
1 TT-AAAT-TTAAATAAAATTATAA
133433 TTAAATTTAAATAAAA
1 TTAAATTTAAATAAAA
133449 ATTAATCATC
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 2 0.04
21 12 0.25
22 17 0.35
23 11 0.23
24 4 0.08
25 2 0.04
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAATTTAAATAAAATTATAA
Found at i:133796 original size:18 final size:18
Alignment explanation
Indices: 133765--133799 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
133755 AAATTTTTTT
*
133765 TTTTTTAAAGTTTTAATA
1 TTTTTAAAAGTTTTAATA
*
133783 TTTTTAAAATTTTTAAT
1 TTTTTAAAAGTTTTAAT
133800 TAAATAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTTTAAAAGTTTTAATA
Found at i:133861 original size:24 final size:23
Alignment explanation
Indices: 133810--133861 Score: 54
Period size: 23 Copynumber: 2.2 Consensus size: 23
133800 TAAATAAAAT
133810 TATAATTAATAAATTTATTTAAA
1 TATAATTAATAAATTTATTTAAA
*
133833 AATAATTTAA-AAATATTA-TTAATA
1 TATAA-TTAATAAAT-TTATTTAA-A
133857 TATAA
1 TATAA
133862 AATTTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TATAATTAATAAATTTATTTAAA
Found at i:134417 original size:13 final size:13
Alignment explanation
Indices: 134399--134426 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
134389 ATTAAATAAT
134399 AATTATATATTTA
1 AATTATATATTTA
134412 AATTATATATTTA
1 AATTATATATTTA
134425 AA
1 AA
134427 ATTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTATATATTTA
Found at i:134787 original size:11 final size:12
Alignment explanation
Indices: 134766--134799 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
134756 AAAATATTAC
134766 ATAAAAAATAAT
1 ATAAAAAATAAT
*
134778 -TAAAATATAAT
1 ATAAAAAATAAT
134789 ATAAAAAATAA
1 ATAAAAAATAA
134800 ATATGACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:134792 original size:23 final size:23
Alignment explanation
Indices: 134756--134799 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
134746 ACGAAAAATA
*
134756 AAAATATTACATAAAAAATAATT
1 AAAATATAACATAAAAAATAATT
*
134779 AAAATATAATATAAAAAATAA
1 AAAATATAACATAAAAAATAA
134800 ATATGACACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATATAACATAAAAAATAATT
Found at i:134981 original size:36 final size:34
Alignment explanation
Indices: 134914--134983 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 34
134904 AGATTTTTCT
* * *
134914 TTTATTTTTTTTAACATGTAAAAAATTATATAAA
1 TTTATTTTCTTTAACATATAAAAAATAATATAAA
134948 TTTATTTTACTTTAACAATATAAAAAATAATATAAA
1 TTTATTTT-CTTTAAC-ATATAAAAAATAATATAAA
134984 CATGATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
34 8 0.26
35 6 0.19
36 17 0.55
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTATTTTCTTTAACATATAAAAAATAATATAAA
Found at i:135020 original size:12 final size:12
Alignment explanation
Indices: 134964--135022 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
134954 TTACTTTAAC
*
134964 AATATAAAAAAT
1 AATATAAAATAT
134976 AATATAAACATGAT
1 AATATAAA-AT-AT
*
134990 ATTTATAAAA-A-
1 A-ATATAAAATAT
*
135001 AATTTAAAATAT
1 AATATAAAATAT
135013 AATATAAAAT
1 AATATAAAAT
135023 TATATGTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
10 6 0.16
11 2 0.05
12 18 0.49
13 1 0.03
14 4 0.11
15 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:135168 original size:4 final size:4
Alignment explanation
Indices: 135159--135190 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
135149 TTTTTTTATC
135159 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
135191 TTTTTACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:135457 original size:22 final size:20
Alignment explanation
Indices: 135405--135457 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
135395 ATTTTATTTT
135405 TAACATAAAAAATATAAACA
1 TAACATAAAAAATATAAACA
*
135425 TAATATTTAAAAAATATTTAAACA
1 TAACA--TAAAAAATA--TAAACA
*
135449 TGACATAAA
1 TAACATAAA
135458 GATGATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.15
22 13 0.50
24 9 0.35
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (20 bp):
TAACATAAAAAATATAAACA
Found at i:135538 original size:8 final size:10
Alignment explanation
Indices: 135464--135542 Score: 57
Period size: 8 Copynumber: 8.3 Consensus size: 10
135454 TAAAGATGAT
135464 ATAATAT-TA
1 ATAATATATA
135473 ATATATATATA
1 ATA-ATATATA
*
135484 TTATAATATA-C
1 --ATAATATATA
135495 ATAA-ATA-A
1 ATAATATATA
135503 ATAA-AT-TA
1 ATAATATATA
135511 ATTAATATATA
1 A-TAATATATA
135522 ATAATATATA
1 ATAATATATA
135532 A-AA-ATATA
1 ATAATATATA
135540 ATA
1 ATA
135543 TTTTTAAATA
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
8 17 0.29
9 13 0.22
10 16 0.27
11 5 0.08
12 5 0.08
13 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAATATATA
Found at i:137178 original size:11 final size:11
Alignment explanation
Indices: 137164--137190 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
137154 TTAAAATATT
137164 TAAATAATAAA
1 TAAATAATAAA
137175 TAAATAATAAA
1 TAAATAATAAA
137186 TAAAT
1 TAAAT
137191 TTAAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATAATAAA
Found at i:137357 original size:19 final size:21
Alignment explanation
Indices: 137328--137366 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
137318 TTCTGGCTCC
137328 AATTCAAAATAATAT-TTTTA
1 AATTCAAAATAATATATTTTA
137348 AATT-AAAATAATATATTTT
1 AATTCAAAATAATATATTTT
137367 TATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTCAAAATAATATATTTTA
Found at i:137407 original size:20 final size:19
Alignment explanation
Indices: 137371--137410 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
137361 TATTTTTATT
137371 TAAATTTAATTATAAAATA
1 TAAATTTAATTATAAAATA
137390 TAAATATTAA-TATAAAA-A
1 TAAAT-TTAATTATAAAATA
137408 TAA
1 TAA
137411 TTTTTAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAATTTAATTATAAAATA
Found at i:137417 original size:18 final size:19
Alignment explanation
Indices: 137371--137419 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
137361 TATTTTTATT
137371 TAAA-TTTAATTATAAAATA
1 TAAATTTTAA-TATAAAATA
*
137390 TAAATATTAATATAAAA-A
1 TAAATTTTAATATAAAATA
*
137408 TAATTTTTAATA
1 TAAATTTTAATA
137420 CTTTTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 11 0.42
19 11 0.42
20 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TAAATTTTAATATAAAATA
Found at i:140314 original size:11 final size:12
Alignment explanation
Indices: 140272--140320 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
140262 TATATATATT
140272 TATATAAATATAA
1 TATA-AAATATAA
* *
140285 CATAAAAAATAA
1 TATAAAATATAA
140297 T-TAAAATATAA
1 TATAAAATATAA
140308 TATAAATATATAA
1 TATAAA-ATATAA
140321 ATATTATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 10 0.33
12 11 0.37
13 9 0.30
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:140447 original size:20 final size:20
Alignment explanation
Indices: 140383--140447 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
140373 AATAAATATA
* *
140383 AATATTT-TAAATATAATTGT
1 AATATTTATATATAT-ATTAT
**
140403 AATATAAATATATATATTAT
1 AATATTTATATATATATTAT
* * *
140423 CATATTTATATATATTTTTT
1 AATATTTATATATATATTAT
140443 AATAT
1 AATAT
140448 GTAAAAGCTG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 28 0.82
21 6 0.18
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
AATATTTATATATATATTAT
Found at i:141356 original size:20 final size:23
Alignment explanation
Indices: 141309--141360 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 23
141299 AAATATTTTT
*
141309 AATATATTAATAATATACAAATT
1 AATATATTAATAATATACAAATA
*
141332 TATATATTAA-AA-ATA-AAATA
1 AATATATTAATAATATACAAATA
141352 AATATATTA
1 AATATATTA
141361 TATTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 3 0.12
22 2 0.08
23 9 0.35
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATATTAATAATATACAAATA
Found at i:141371 original size:22 final size:23
Alignment explanation
Indices: 141346--141389 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
141336 TATTAAAAAT
141346 AAAA-TAAA-TATATTATATTTAA
1 AAAATTAAATTAT-TTATATTTAA
141368 AAAATTAAATTATTTATATTTA
1 AAAATTAAATTATTTATATTTA
141390 TTTTTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATTAAATTATTTATATTTAA
Found at i:149098 original size:20 final size:19
Alignment explanation
Indices: 149050--149100 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
149040 ATAAATTTTT
*
149050 AAAATTAATT-AAAAATAA
1 AAAATTGATTAAAAAATAA
*
149068 AATA-TGAATTAAAAAATTAA
1 AAAATTG-ATTAAAAAA-TAA
149088 AAAATTGATTAAA
1 AAAATTGATTAAA
149101 TTCGTGAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 1 0.04
18 6 0.23
19 5 0.19
20 12 0.46
21 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAATTGATTAAAAAATAA
Found at i:149334 original size:15 final size:14
Alignment explanation
Indices: 149314--149380 Score: 50
Period size: 14 Copynumber: 4.6 Consensus size: 14
149304 TAAAATATAT
149314 ATTAAATTATAGAAA
1 ATTAAATTATA-AAA
*
149329 ATTAAATTTTAAAA
1 ATTAAATTATAAAA
149343 A-TAAATTA-AAACA
1 ATTAAATTATAAA-A
149356 TATAATAAATATATAAAA
1 -AT--TAAAT-TATAAAA
149374 A-TAAATT
1 ATTAAATT
149381 TTAATTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
12 3 0.07
13 8 0.19
14 10 0.23
15 10 0.23
17 6 0.14
18 3 0.07
19 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (14 bp):
ATTAAATTATAAAA
Found at i:149347 original size:13 final size:15
Alignment explanation
Indices: 149314--149350 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
149304 TAAAATATAT
149314 ATTAAATTATAGAAA
1 ATTAAATTATAGAAA
*
149329 ATTAAATTTTA-AAA
1 ATTAAATTATAGAAA
149343 A-TAAATTA
1 ATTAAATTA
149351 AAACATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 6 0.30
14 4 0.20
15 10 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTAAATTATAGAAA
Found at i:149412 original size:27 final size:25
Alignment explanation
Indices: 149368--149419 Score: 59
Period size: 27 Copynumber: 2.0 Consensus size: 25
149358 TAATAAATAT
**
149368 ATAAAAATAAATTTTAATTATTTATTA
1 ATAAAAATAAATAATAA-TA-TTATTA
*
149395 ATAAATATAAATAATAATATTATTA
1 ATAAAAATAAATAATAATATTATTA
149420 TAATATTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 6 0.27
26 2 0.09
27 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAAAAATAAATAATAATATTATTA
Found at i:158723 original size:2 final size:2
Alignment explanation
Indices: 158716--158756 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
158706 TGATGGACAC
158716 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
158757 TTCATGCCTT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:159045 original size:33 final size:33
Alignment explanation
Indices: 159008--159074 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
158998 TGTCTAATGC
159008 TTGAAATCATCTTCAAGCAGATTCTAACAACAA
1 TTGAAATCATCTTCAAGCAGATTCTAACAACAA
159041 TTGAAATCATCTTCAAGCAGATTCTAACAACAA
1 TTGAAATCATCTTCAAGCAGATTCTAACAACAA
159074 T
1 T
159075 CCAAGGTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.28
Consensus pattern (33 bp):
TTGAAATCATCTTCAAGCAGATTCTAACAACAA
Found at i:159090 original size:3 final size:3
Alignment explanation
Indices: 159084--159118 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
159074 TCCAAGGTTT
159084 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
159119 ATTATTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:162573 original size:202 final size:202
Alignment explanation
Indices: 162222--162627 Score: 785
Period size: 202 Copynumber: 2.0 Consensus size: 202
162212 AATAAACAGG
162222 AATCAAATCAGGGATGGCTCCCAATGCTTGCAAACAAGGACGATTTTAACTATTTCAATATAAAA
1 AATCAAATCAGGGATGGCTCCCAATGCTTGCAAACAAGGACGATTTTAACTATTTCAATATAAAA
162287 AACTTCCAACTTCATCGACTTGCTATCCCATCTAGCAAGAACTGTTTGCATAAAGTATGGAAAGT
66 AACTTCCAACTTCATCGACTTGCTATCCCATCTAGCAAGAACTGTTTGCATAAAGTATGGAAAGT
* *
162352 CCCTAGGCATTCGCATTTCACTTTGTTCCTTCAGAATGCTTTTGAAACAAACCAAATCAATCAAA
131 CCCCAGGCATTCACATTTCACTTTGTTCCTTCAGAATGCTTTTGAAACAAACCAAATCAATCAAA
162417 CCGATCT
196 CCGATCT
162424 AATCAAATCAGGGATGGCTCCCAATGCTTGCAAACAAGGACGATTTTAACTATTTCAATATAAAA
1 AATCAAATCAGGGATGGCTCCCAATGCTTGCAAACAAGGACGATTTTAACTATTTCAATATAAAA
*
162489 AACTTCCAACTTCATCGACTTGCTATCCTATCTAGCAAGAACTGTTTGCATAAAGTATGGAAAGT
66 AACTTCCAACTTCATCGACTTGCTATCCCATCTAGCAAGAACTGTTTGCATAAAGTATGGAAAGT
162554 CCCCAGGCATTCACATTTCACTTTGTTCCTTCAGAATGCTTTTGAAACAAACCAAATCAATCAAA
131 CCCCAGGCATTCACATTTCACTTTGTTCCTTCAGAATGCTTTTGAAACAAACCAAATCAATCAAA
162619 CCGATCT
196 CCGATCT
162626 AA
1 AA
162628 AGGGCTTCTT
Statistics
Matches: 201, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
202 201 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (202 bp):
AATCAAATCAGGGATGGCTCCCAATGCTTGCAAACAAGGACGATTTTAACTATTTCAATATAAAA
AACTTCCAACTTCATCGACTTGCTATCCCATCTAGCAAGAACTGTTTGCATAAAGTATGGAAAGT
CCCCAGGCATTCACATTTCACTTTGTTCCTTCAGAATGCTTTTGAAACAAACCAAATCAATCAAA
CCGATCT
Found at i:163111 original size:44 final size:44
Alignment explanation
Indices: 163048--163136 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
163038 CCTGCATCCG
*
163048 ACATTTACACCTTAGTCCAAGTAATATAGCTCTCAACATTGAGA
1 ACATTTACACCCTAGTCCAAGTAATATAGCTCTCAACATTGAGA
163092 ACATTTACACCCTAGTCCAAGTAATATAGCTCTCAACATTGAGA
1 ACATTTACACCCTAGTCCAAGTAATATAGCTCTCAACATTGAGA
163136 A
1 A
163137 AAGGACAACA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.37, C:0.24, G:0.11, T:0.28
Consensus pattern (44 bp):
ACATTTACACCCTAGTCCAAGTAATATAGCTCTCAACATTGAGA
Found at i:168378 original size:15 final size:16
Alignment explanation
Indices: 168325--168378 Score: 55
Period size: 14 Copynumber: 3.7 Consensus size: 16
168315 TTTTTTTTAA
*
168325 TTTTATGAAT-GTATT
1 TTTTATGAATAATATT
168340 TTTTAT-AA-AATATT
1 TTTTATGAATAATATT
*
168354 TTTTA-AAATAAT-TT
1 TTTTATGAATAATATT
168368 TTTTATGAATA
1 TTTTATGAATA
168379 TACTGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 20 0.61
15 13 0.39
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTTATGAATAATATT
Found at i:168637 original size:24 final size:23
Alignment explanation
Indices: 168593--168665 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
168583 ATTTAAATAA
168593 ATTTTAAAATCTAATTT-ATTTTT
1 ATTTTAAAAT-TAATTTAATTTTT
*
168616 ATTTATAAAATTAATTTAATTTAT
1 ATTT-TAAAATTAATTTAATTTTT
*
168640 -TTTTAAAA--AATTTATTTTTT
1 ATTTTAAAATTAATTTAATTTTT
168660 ATTTTA
1 ATTTTA
168666 TTATATATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 10 0.23
21 5 0.11
22 5 0.11
23 13 0.30
24 11 0.25
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTAAAATTAATTTAATTTTT
Found at i:168662 original size:22 final size:22
Alignment explanation
Indices: 168594--168664 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
168584 TTTAAATAAA
168594 TTTTAAAATCTAATTTATTTTTAT
1 TTTTAAAA--TAATTTATTTTTAT
* *
168618 TTATAAAATTAATTTA-ATTTAT
1 TTTTAAAA-TAATTTATTTTTAT
168640 TTTTAAAA-AATTTATTTTTTAT
1 TTTTAAAATAATTTA-TTTTTAT
168662 TTT
1 TTT
168665 ATTATATATA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 6 0.15
22 20 0.50
23 7 0.17
24 7 0.17
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAAAATAATTTATTTTTAT
Found at i:173593 original size:19 final size:19
Alignment explanation
Indices: 173556--173593 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
173546 ATAACTAAAT
*
173556 TTAAATAAAAATATTTTTA
1 TTAAATAAAAATATATTTA
173575 TTAAATAAATAATA-ATTTA
1 TTAAATAAA-AATATATTTA
173594 AATTAATCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATAAAAATATATTTA
Found at i:177336 original size:2 final size:2
Alignment explanation
Indices: 177329--177355 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
177319 TAGTTTTTAA
177329 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
177356 ATGGGTCAAA
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:177887 original size:21 final size:22
Alignment explanation
Indices: 177863--177904 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
177853 AAGTTTTTTA
177863 AAAAATAAA-TAATATAAAATG
1 AAAAATAAATTAATATAAAATG
*
177884 AAAAATAAATTTATATAAAAT
1 AAAAATAAATTAATATAAAAT
177905 AATTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AAAAATAAATTAATATAAAATG
Found at i:178767 original size:19 final size:18
Alignment explanation
Indices: 178745--178794 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
178735 TTACCCTTTT
178745 AAAACTATTATTTCTATAA
1 AAAACTATTATTTC-ATAA
*
178764 AAAAATATTACTTTCATAA
1 AAAACTATTA-TTTCATAA
*
178783 AACACTATTATT
1 AAAACTATTATT
178795 ATATATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 21 0.78
20 4 0.15
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAACTATTATTTCATAA
Found at i:179018 original size:23 final size:22
Alignment explanation
Indices: 178979--179043 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
178969 TTTTGGATTG
*
178979 TATAAACATAA-ATTAATATAAA
1 TATAAATATAATA-TAATATAAA
* *
179001 TTATAAATATATTATAATTTTAAA
1 -TATAAATATAATATAA-TATAAA
179025 TATAAATATAATATAATAT
1 TATAAATATAATATAATAT
179044 GTGATTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.06
23 27 0.77
24 6 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAAATATAATATAATATAAA
Found at i:179030 original size:6 final size:6
Alignment explanation
Indices: 178979--179040 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
178969 TTTTGGATTG
* * * *
178979 TATAAA CATAAA T-T-AA TATAAA TTATAAA TAT-AT TATAAT TTTAAA
1 TATAAA TATAAA TATAAA TATAAA -TATAAA TATAAA TATAAA TATAAA
179025 TATAAA TAT-AA TATAA
1 TATAAA TATAAA TATAA
179041 TATGTGATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
4 3 0.07
5 11 0.24
6 25 0.56
7 6 0.13
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
TATAAA
Found at i:179034 original size:18 final size:17
Alignment explanation
Indices: 178986--179040 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
178976 TTGTATAAAC
178986 ATAAAT-TAATATAAATT
1 ATAAATATAATAT-AATT
*
179003 ATAAATATATTATAATT
1 ATAAATATAATATAATT
*
179020 TTAAATATAAATATAA-T
1 ATAAATAT-AATATAATT
179037 ATAA
1 ATAA
179041 TATGTGATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 21 0.66
18 11 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATAATT
Found at i:179206 original size:17 final size:18
Alignment explanation
Indices: 179180--179219 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
179170 AATTAAATTA
*
179180 AATTTATATATT-TTAAT
1 AATTTTTATATTATTAAT
179197 AATTTTTATATTATTAAT
1 AATTTTTATATTATTAAT
179215 -ATTTT
1 AATTTT
179220 AATAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTTATATTATTAAT
Found at i:179311 original size:26 final size:25
Alignment explanation
Indices: 179282--179345 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 25
179272 TAAAATCTTA
* *
179282 AATTAATTTATTATTTTTATTATAAT
1 AATTAATATATTATTTTTAATA-AAT
*
179308 AATTAAAAATATTATTTTTAATAAAT
1 AATT-AATATATTATTTTTAATAAAT
179334 AATTAATA-ATTA
1 AATTAATATATTA
179346 AAAAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 4 0.12
25 3 0.09
26 11 0.33
27 15 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTAATATATTATTTTTAATAAAT
Found at i:179440 original size:28 final size:26
Alignment explanation
Indices: 179375--179448 Score: 71
Period size: 28 Copynumber: 2.8 Consensus size: 26
179365 TATTTTTAAT
* *
179375 TTAT-TAAAAAAA-TTCAAACATAAT
1 TTATATAAAAAAATTTAAAACATAAA
179399 TTATATTAATAAAAATTTAAATACAATAAA
1 TTATA-TAA-AAAAATTTAAA-AC-ATAAA
*
179429 TTATATAAAAAAATATAAAA
1 TTATATAAAAAAATTTAAAA
179449 GCAAGTACCA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
24 4 0.10
26 3 0.07
27 6 0.15
28 14 0.34
29 5 0.12
30 9 0.22
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (26 bp):
TTATATAAAAAAATTTAAAACATAAA
Found at i:180956 original size:2 final size:2
Alignment explanation
Indices: 180949--180978 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
180939 TGCCTTTTTA
180949 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
180979 GTTTTCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:183526 original size:17 final size:17
Alignment explanation
Indices: 183501--183548 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
183491 ACTTTTGTTG
*
183501 AAAGTTTGATGGCAACA
1 AAAGCTTGATGGCAACA
183518 AAAGCTTGATGGCAACA
1 AAAGCTTGATGGCAACA
183535 AAAGCTTGATGGCA
1 AAAGCTTGATGGCA
183549 TAAATCATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.21
Consensus pattern (17 bp):
AAAGCTTGATGGCAACA
Found at i:183654 original size:15 final size:15
Alignment explanation
Indices: 183634--183665 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
183624 GTTAAAATCT
183634 AATGTACTTGTTGAC
1 AATGTACTTGTTGAC
183649 AATGTACTTGTTGAC
1 AATGTACTTGTTGAC
183664 AA
1 AA
183666 GTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (15 bp):
AATGTACTTGTTGAC
Found at i:186046 original size:32 final size:32
Alignment explanation
Indices: 186010--186076 Score: 107
Period size: 32 Copynumber: 2.1 Consensus size: 32
186000 ATACATTTCC
* *
186010 AACACATTTTCAAACCTTGATAATGAGGATAT
1 AACACATTTTCAAACCCTGATAATGAAGATAT
*
186042 AACACTTTTTCAAACCCTGATAATGAAGATAT
1 AACACATTTTCAAACCCTGATAATGAAGATAT
186074 AAC
1 AAC
186077 CCTCTAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (32 bp):
AACACATTTTCAAACCCTGATAATGAAGATAT
Found at i:186976 original size:20 final size:19
Alignment explanation
Indices: 186953--186999 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
186943 TTATATTATT
186953 ATTTAAAATAATATTAAATA
1 ATTTAAAATAATATT-AATA
* * *
186973 ATTTATATTAATATTTATA
1 ATTTAAAATAATATTAATA
186992 A-TTAAAAT
1 ATTTAAAAT
187000 TAAATAAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTAAAATAATATTAATA
Found at i:187001 original size:19 final size:20
Alignment explanation
Indices: 186955--187002 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
186945 ATATTATTAT
186955 TTAAAA-TAATATTAAATAA
1 TTAAAATTAATATTAAATAA
* * *
186974 TTTATATTAATATT-TATAA
1 TTAAAATTAATATTAAATAA
186993 TTAAAATTAA
1 TTAAAATTAA
187003 ATAAAATATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAAATTAATATTAAATAA
Found at i:187013 original size:33 final size:32
Alignment explanation
Indices: 186944--187014 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
186934 TTTTAAATTT
* * **
186944 TATATTATTATTTAAAATAATATTAAATAATT
1 TATATTAATATTTAAAATAAAATTAAATAAAA
*
186976 TATATTAATATTTATAATTAAAATTAAATAAAA
1 TATATTAATATTTA-AAATAAAATTAAATAAAA
187009 TATATT
1 TATATT
187015 TTTATTATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
TATATTAATATTTAAAATAAAATTAAATAAAA
Found at i:187031 original size:38 final size:38
Alignment explanation
Indices: 186955--187031 Score: 86
Period size: 38 Copynumber: 2.0 Consensus size: 38
186945 ATATTATTAT
* **
186955 TTAAAATAATATTAAATAATTTATATTAATATTTATAA
1 TTAAAATAATATAAAATAATTTATATTAATATAAATAA
*
186993 TTAAAATTAA-ATAAAATATATTTTTATT-ATATAAATAA
1 TTAAAA-TAATATAAAATA-ATTTATATTAATATAAATAA
187031 T
1 T
187032 AATTTAAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
38 22 0.67
39 11 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (38 bp):
TTAAAATAATATAAAATAATTTATATTAATATAAATAA
Found at i:188049 original size:104 final size:104
Alignment explanation
Indices: 187892--188102 Score: 422
Period size: 104 Copynumber: 2.0 Consensus size: 104
187882 AGAACTCACT
187892 GAAAATTAATTTTTTTATATAAAAAAATTATGAATATAAAGATTTAAATTTTAAATTTTAAATTT
1 GAAAATTAATTTTTTTATATAAAAAAATTATGAATATAAAGATTTAAATTTTAAATTTTAAATTT
187957 ATCGAATATTTTATTTTAAAAAAATTATAAAAATCAATC
66 ATCGAATATTTTATTTTAAAAAAATTATAAAAATCAATC
187996 GAAAATTAATTTTTTTATATAAAAAAATTATGAATATAAAGATTTAAATTTTAAATTTTAAATTT
1 GAAAATTAATTTTTTTATATAAAAAAATTATGAATATAAAGATTTAAATTTTAAATTTTAAATTT
188061 ATCGAATATTTTATTTTAAAAAAATTATAAAAATCAATC
66 ATCGAATATTTTATTTTAAAAAAATTATAAAAATCAATC
188100 GAA
1 GAA
188103 TGAAATTCTT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (104 bp):
GAAAATTAATTTTTTTATATAAAAAAATTATGAATATAAAGATTTAAATTTTAAATTTTAAATTT
ATCGAATATTTTATTTTAAAAAAATTATAAAAATCAATC
Found at i:188745 original size:25 final size:24
Alignment explanation
Indices: 188681--188748 Score: 79
Period size: 23 Copynumber: 2.9 Consensus size: 24
188671 CGATACATTT
*
188681 TTTTAATAATTATATATT-TA-ATA
1 TTTTAATAATT-TATATTATATAAA
*
188704 TATTAATAA-TTATATTATATAAA
1 TTTTAATAATTTATATTATATAAA
188727 TTTTAATATATTTATATTATAT
1 TTTTAATA-ATTTATATTATAT
188749 TATATCATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 6 0.16
22 3 0.08
23 17 0.45
24 1 0.03
25 11 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTAATAATTTATATTATATAAA
Found at i:188748 original size:30 final size:31
Alignment explanation
Indices: 188697--188783 Score: 99
Period size: 30 Copynumber: 2.8 Consensus size: 31
188687 TAATTATATA
* *
188697 TTTAATATATTAATAATTATATTATAT-AAAT
1 TTTAATATATTTAT-ATTATATTATATCAAAG
*
188728 TTTAATATATTTATATTATATTATATCATAG
1 TTTAATATATTTATATTATATTATATCAAAG
*
188759 TTTAAT-TATTT-TTTATATATTATAT
1 TTTAATATATTTATAT-TATATTATAT
188784 TTAAATTATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 2 0.04
30 27 0.54
31 21 0.42
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
TTTAATATATTTATATTATATTATATCAAAG
Found at i:189089 original size:25 final size:27
Alignment explanation
Indices: 189050--189100 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
189040 TTTATAATTA
**
189050 AATTTAAATTTAATT-AA-TAAATAAT
1 AATTTAAATCAAATTAAATTAAATAAT
189075 AATTTAAATCAAATTAAATTAAATAA
1 AATTTAAATCAAATTAAATTAAATAA
189101 ATTACTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 13 0.59
26 2 0.09
27 7 0.32
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTTAAATCAAATTAAATTAAATAAT
Found at i:189103 original size:25 final size:23
Alignment explanation
Indices: 189043--189103 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
189033 TATATATTTT
* **
189043 ATAATTAAATTTAAATTTAATTA
1 ATAAATAAATTTAAATCAAATTA
189066 ATAAATAATAATTTAAATCAAATTAA
1 ATAAAT-A-AATTTAAATCAAATT-A
189092 ATTAAATAAATT
1 A-TAAATAAATT
189104 ACTGACCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 5 0.16
24 1 0.03
25 17 0.55
26 3 0.10
27 5 0.16
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAAATAAATTTAAATCAAATTA
Found at i:189249 original size:11 final size:11
Alignment explanation
Indices: 189231--189295 Score: 78
Period size: 11 Copynumber: 5.7 Consensus size: 11
189221 TCTATAAATT
189231 TAAATATAATA
1 TAAATATAATA
189242 TGAATATATAATA
1 T-AA-ATATAATA
*
189255 TAAAAATAAT-
1 TAAATATAATA
189265 TAAAATATAATA
1 T-AAATATAATA
*
189277 TAAATAAAATA
1 TAAATATAATA
189288 TAAATATA
1 TAAATATA
189296 TTATCATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
10 1 0.02
11 31 0.67
12 5 0.11
13 9 0.20
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
TAAATATAATA
Found at i:189263 original size:24 final size:23
Alignment explanation
Indices: 189223--189296 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
189213 AGAAAATTTC
* *
189223 TATA-AATTTAAATATAATATGAA
1 TATATAATATAAAAATAATAT-AA
189246 TATATAATATAAAAATAAT-TAA
1 TATATAATATAAAAATAATATAA
*
189268 AATATAATATAAATAA-AATATAAA
1 TATATAATATAAA-AATAATAT-AA
189292 TATAT
1 TATAT
189297 TATCATTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
22 17 0.40
23 8 0.19
24 18 0.42
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (23 bp):
TATATAATATAAAAATAATATAA
Found at i:189275 original size:35 final size:33
Alignment explanation
Indices: 189227--189291 Score: 94
Period size: 35 Copynumber: 1.9 Consensus size: 33
189217 AATTTCTATA
* *
189227 AATTTAAATATAATATGAATATATAATATAAAAAT
1 AATTAAAATATAATAT-AA-ATAAAATATAAAAAT
189262 AATTAAAATATAATATAAATAAAATATAAA
1 AATTAAAATATAATATAAATAAAATATAAA
189292 TATATTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 11 0.39
34 2 0.07
35 15 0.54
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (33 bp):
AATTAAAATATAATATAAATAAAATATAAAAAT
Found at i:189332 original size:18 final size:17
Alignment explanation
Indices: 189265--189367 Score: 67
Period size: 16 Copynumber: 6.2 Consensus size: 17
189255 TAAAAATAAT
**
189265 TAAAATAT-AATATAAA
1 TAAAATATAAATATTTA
189281 TAAAATATAAATATATTA
1 TAAAATATAAATAT-TTA
* * *
189299 T-CATTTTAAA-ATTTA
1 TAAAATATAAATATTTA
189314 TAAAATATAAATTATTTA
1 TAAAATATAAA-TATTTA
*
189332 T-ATAT-TAAA-ATTTA
1 TAAAATATAAATATTTA
189346 TATAAATATAAAATATTT-
1 TA-AAATAT-AAATATTTA
189364 TAAA
1 TAAA
189368 TACGATTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.09
15 4 0.06
16 23 0.34
17 17 0.25
18 13 0.19
19 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATATAAATATTTA
Found at i:189363 original size:33 final size:33
Alignment explanation
Indices: 189280--189363 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 33
189270 TATAATATAA
*
189280 ATAAAATAT-AAATATATTATCATTTTAAAATTT
1 ATAAAATATAAAATAT-TTATCATATTAAAATTT
*
189313 ATAAAATATAAATTATTTAT-ATATTAAAATTT
1 ATAAAATATAAAATATTTATCATATTAAAATTT
189345 ATATAAATATAAAATATTT
1 ATA-AAATATAAAATATTT
189364 TAAATACGAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
32 14 0.30
33 27 0.59
34 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (33 bp):
ATAAAATATAAAATATTTATCATATTAAAATTT
Found at i:189728 original size:25 final size:24
Alignment explanation
Indices: 189695--189771 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 24
189685 TATTATATCG
189695 TATTATATTTTAATTATTTTATAAA
1 TATTATA-TTTAATTATTTTATAAA
* *
189720 TATTATATTCATATAATTTTATAAAA
1 TATTATATTTA-ATTATTTTAT-AAA
*
189746 TTATTAAATTTAA-TA-TTTATAAA
1 -TATTATATTTAATTATTTTATAAA
189769 TAT
1 TAT
189772 AATTAAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 8 0.18
25 17 0.39
26 4 0.09
27 9 0.20
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTATATTTAATTATTTTATAAA
Found at i:189764 original size:24 final size:25
Alignment explanation
Indices: 189733--189786 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
189723 TATATTCATA
* *
189733 TAAT-TTTATAAA-ATTATTAAATT
1 TAATATTTATAAATATAATTAAAAT
189756 TAATATTTATAAATATAATTAAAAT
1 TAATATTTATAAATATAATTAAAAT
189781 T-ATATT
1 TAATATT
189787 GAACAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 4 0.15
24 13 0.48
25 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TAATATTTATAAATATAATTAAAAT
Found at i:190269 original size:10 final size:10
Alignment explanation
Indices: 190254--190278 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
190244 TAAATTTAAA
190254 TTTTTTATTT
1 TTTTTTATTT
190264 TTTTTTATTT
1 TTTTTTATTT
190274 TTTTT
1 TTTTT
190279 GAGTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:190317 original size:20 final size:21
Alignment explanation
Indices: 190294--190334 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
190284 AATTTGATTC
190294 AATTTAAAATA-ATATTTTTA
1 AATTTAAAATATATATTTTTA
*
190314 AATTTAAATTATATATTTTTA
1 AATTTAAAATATATATTTTTA
190335 TTTAAATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTAAAATATATATTTTTA
Found at i:190327 original size:19 final size:19
Alignment explanation
Indices: 190294--190342 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
190284 AATTTGATTC
*
190294 AATTTAAAATA-ATATTTTT
1 AATTTAAATTATATA-TTTT
190313 AAATTTAAATTATATATTTT
1 -AATTTAAATTATATATTTT
*
190333 TATTTAAATT
1 AATTTAAATT
190343 TAATTATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 9 0.35
20 14 0.54
21 3 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTAAATTATATATTTT
Found at i:190532 original size:12 final size:13
Alignment explanation
Indices: 190515--190543 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
190505 TCAAGGCCTG
190515 AATTTTTT-TTTA
1 AATTTTTTGTTTA
190527 AATTTTTTGTTTA
1 AATTTTTTGTTTA
190540 AATT
1 AATT
190544 CAAATTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (13 bp):
AATTTTTTGTTTA
Found at i:191946 original size:18 final size:18
Alignment explanation
Indices: 191905--191947 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
191895 TCTTTTTATT
* *
191905 TAAAAAATAACTACTCAC
1 TAAAAAACAACTACTCAA
191923 TAAAAAACAACTACT-AA
1 TAAAAAACAACTACTCAA
*
191940 TATAAAAC
1 TAAAAAAC
191948 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.60, C:0.19, G:0.00, T:0.21
Consensus pattern (18 bp):
TAAAAAACAACTACTCAA
Found at i:193278 original size:2 final size:2
Alignment explanation
Indices: 193271--193297 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
193261 AACTAAACCT
193271 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 T
193298 GTATGTATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:193949 original size:18 final size:18
Alignment explanation
Indices: 193926--193975 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
193916 TTGATTGTTC
193926 ATAAATGTATAATATTTA
1 ATAAATGTATAATATTTA
* *
193944 ATAAATATAAAATAATTTA
1 ATAAATGTATAAT-ATTTA
193963 ATAAA-G-ATAATAT
1 ATAAATGTATAATAT
193976 CTATAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 2 0.07
17 4 0.15
18 11 0.41
19 10 0.37
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (18 bp):
ATAAATGTATAATATTTA
Found at i:193963 original size:19 final size:18
Alignment explanation
Indices: 193926--193972 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
193916 TTGATTGTTC
* *
193926 ATAAATGTATAATATTTA
1 ATAAATATAAAATATTTA
193944 ATAAATATAAAATAATTTA
1 ATAAATATAAAAT-ATTTA
*
193963 ATAAAGATAA
1 ATAAATATAA
193973 TATCTATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (18 bp):
ATAAATATAAAATATTTA
Found at i:194479 original size:7 final size:7
Alignment explanation
Indices: 194469--194502 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
194459 AAAAAATAAA
*
194469 AAATTAT
1 AAATTTT
194476 AAATTTT
1 AAATTTT
*
194483 AAACTTT
1 AAATTTT
194490 AAATTTT
1 AAATTTT
194497 AAATTT
1 AAATTT
194503 ATTAAATACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Done.