Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015002.1 Kokia drynarioides strain JFW-HI SEQ_130046, whole genome shotgun sequence
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: 397637
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 163 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:1520 original size:18 final size:18
Alignment explanation
Indices: 1485--1524 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
1475 GAAATATTTA
*
1485 TTTTAATGTTTTTAATAT
1 TTTTAATGTTTATAATAT
1503 TTTTAATGTATTATATATAT
1 TTTTAATGT-TTATA-ATAT
1523 TT
1 TT
1525 AAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTTAATGTTTATAATAT
Found at i:1551 original size:23 final size:23
Alignment explanation
Indices: 1517--1564 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1507 AATGTATTAT
*
1517 ATATATTTAAAAATTATATAAAA
1 ATATATTTAAAAAATATATAAAA
1540 ATAT-TTTCAAAAAATATATAAAA
1 ATATATTT-AAAAAATATATAAAA
1563 AT
1 AT
1565 TTAATATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATATTTAAAAAATATATAAAA
Found at i:10656 original size:26 final size:26
Alignment explanation
Indices: 10626--10687 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 26
10616 TGAATCGTTT
10626 TCAATTCAAATCAT-TTCGAGTTTGAA
1 TCAATTCAAATCATATTCGAG-TTGAA
* *
10652 TCAATT-AATTCATATTTGAGTTGAA
1 TCAATTCAAATCATATTCGAGTTGAA
*
10677 TGAATTCAAAT
1 TCAATTCAAAT
10688 GCTAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 16 0.53
26 14 0.47
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (26 bp):
TCAATTCAAATCATATTCGAGTTGAA
Found at i:16264 original size:17 final size:17
Alignment explanation
Indices: 16242--16277 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
16232 ATACATAATT
16242 ATTATAATT-TTTGTTAA
1 ATTATAATTATTT-TTAA
16259 ATTATAATTATTTTTAA
1 ATTATAATTATTTTTAA
16276 AT
1 AT
16278 GTGAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTATAATTATTTTTAA
Found at i:25062 original size:17 final size:17
Alignment explanation
Indices: 25030--25062 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25020 AAATATAGTA
*
25030 AAATATTATAAAAAAAT
1 AAATATTAAAAAAAAAT
25047 AAATATTAAAAAAAAA
1 AAATATTAAAAAAAAA
25063 AGAGAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATATTAAAAAAAAAT
Found at i:35435 original size:2 final size:2
Alignment explanation
Indices: 35430--35455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35420 TAATTTTTTA
35430 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
35456 TAAGAAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35813 original size:28 final size:27
Alignment explanation
Indices: 35751--35814 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
35741 TTTTTTTTTT
* * *
35751 TGTAAAAAATAAATGAAATATATTTGA
1 TGTAAAAAAAAAATAAAATAAATTTGA
*
35778 TGTTAAAATAAAAATAAAATAAATTATGA
1 TG-TAAAAAAAAAATAAAATAAATT-TGA
35807 -GTAAAAAA
1 TGTAAAAAA
35815 CGAAATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
27 8 0.27
28 19 0.63
29 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (27 bp):
TGTAAAAAAAAAATAAAATAAATTTGA
Found at i:36518 original size:21 final size:21
Alignment explanation
Indices: 36482--36522 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
36472 CTTTTGGTGG
*
36482 TCTAATGAAGGGTTAAATTAAA
1 TCTAATGAAAGGTT-AATTAAA
36504 TCTAA-GAAAGGTTAATTAA
1 TCTAATGAAAGGTTAATTAA
36523 GTTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (21 bp):
TCTAATGAAAGGTTAATTAAA
Found at i:37466 original size:53 final size:51
Alignment explanation
Indices: 37389--37575 Score: 196
Period size: 52 Copynumber: 3.6 Consensus size: 51
37379 AATGAAAAGG
37389 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAAATCCTTAATGGATTTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATG-AATCCTTAATGGA-TTAAA
* * * *
37442 GGTCCGATGACTAAGTGTCATCGTGAGTATATGTATCATTTACGGATTAAGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTAATGGATTAA-A
* ** * * * **
37494 GGTTCGATGACTTTGTGTCATAGTGAGTATACGAATCCCTCGTGGATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTAATGGATTA-AA
* *
37546 GGTCCGATAACTATA-TGTCATCATGAGTAT
1 GGTCCGATGACTA-AGTGTCATCGTGAGTAT
37576 TAAATGAAAT
Statistics
Matches: 110, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
51 4 0.04
52 72 0.65
53 34 0.31
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTAATGGATTAAA
Found at i:38838 original size:27 final size:27
Alignment explanation
Indices: 38766--38862 Score: 140
Period size: 27 Copynumber: 3.5 Consensus size: 27
38756 TAGCTCTTAC
**
38766 GAGCCTAGAATCAGAATAATGCTCTTAC
1 GAGCC-AGAATCAGAATAATGCTCTTTT
*
38794 GAGCCCAGAATCAGAATAACGCTCTTTT
1 GAG-CCAGAATCAGAATAATGCTCTTTT
*
38822 GAGCCAGAATCATAATAATGCTCTTTT
1 GAGCCAGAATCAGAATAATGCTCTTTT
38849 GAGCCAGAATCAGA
1 GAGCCAGAATCAGA
38863 TTACTCCTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
27 35 0.56
28 25 0.40
29 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.25
Consensus pattern (27 bp):
GAGCCAGAATCAGAATAATGCTCTTTT
Found at i:40922 original size:21 final size:22
Alignment explanation
Indices: 40898--40954 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
40888 TGCATGACAA
* *
40898 GTATCGGTAGAAATTA-TACTT
1 GTATCGGTAGAAATTAGCACAT
*
40919 GTATCGGTAG-AACTAGCACAT
1 GTATCGGTAGAAATTAGCACAT
40940 GTATCGGTAGAAATT
1 GTATCGGTAGAAATT
40955 TGTACTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 23 0.77
22 3 0.10
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (22 bp):
GTATCGGTAGAAATTAGCACAT
Found at i:43122 original size:9 final size:9
Alignment explanation
Indices: 43108--43187 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
43098 CAAATGATTT
43108 TTAAAATTA
1 TTAAAATTA
43117 TTAAAATTA
1 TTAAAATTA
43126 TT----TT-
1 TTAAAATTA
43130 TTAAAA-TA
1 TTAAAATTA
*
43138 -TAAAATTG
1 TTAAAATTA
43146 TTAAAATTA
1 TTAAAATTA
*
43155 TTTTTAAATTAA
1 --TTAAAATT-A
43167 TTTAAAATTA
1 -TTAAAATTA
43177 TTAAAATTA
1 TTAAAATTA
43186 TT
1 TT
43188 TTTTTGAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 6 0.11
8 1 0.02
9 29 0.51
10 1 0.02
11 15 0.26
12 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (9 bp):
TTAAAATTA
Found at i:43133 original size:22 final size:22
Alignment explanation
Indices: 43105--43209 Score: 75
Period size: 22 Copynumber: 5.0 Consensus size: 22
43095 CAGCAAATGA
43105 TTTTTAAAATTATTAAAATTAT
1 TTTTTAAAATTATTAAAATTAT
43127 TTTTTAAAA-TA-T-AAA--A-
1 TTTTTAAAATTATTAAAATTAT
* *
43143 TTGTTAAAATTATTTTTAAATTA-
1 TTTTTAAAATTA--TTAAAATTAT
*
43166 -ATTTAAAATTATTAAAATTATT
1 TTTTTAAAATTATTAAAATTA-T
* *
43188 TTTTTGAAA-TAATAAAATTAT
1 TTTTTAAAATTATTAAAATTAT
43209 T
1 T
43210 AAATAATTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 21
0.70 0.07 0.22
Matches are distributed among these distances:
16 8 0.12
17 3 0.05
19 3 0.05
20 10 0.15
21 7 0.11
22 28 0.42
23 7 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTTTAAAATTATTAAAATTAT
Found at i:43165 original size:11 final size:11
Alignment explanation
Indices: 43106--43189 Score: 59
Period size: 11 Copynumber: 7.4 Consensus size: 11
43096 AGCAAATGAT
43106 TTTTAAAATTA
1 TTTTAAAATTA
43117 --TTAAAATTA
1 TTTTAAAATTA
43126 TTTTTTAAAATATAAAA
1 --TTTTAAAAT-T---A
43143 TTGTTAAAATTA
1 TT-TTAAAATTA
*
43155 TTTTTAAATTA
1 TTTTAAAATTA
*
43166 ATTTAAAATTA
1 TTTTAAAATTA
43177 --TTAAAATTA
1 TTTTAAAATTA
43186 TTTT
1 TTTT
43190 TTTGAAATAA
Statistics
Matches: 59, Mismatches: 3, Indels: 22
0.70 0.04 0.26
Matches are distributed among these distances:
9 18 0.31
11 19 0.32
12 3 0.05
13 7 0.12
14 1 0.02
15 3 0.05
16 7 0.12
17 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:43181 original size:31 final size:29
Alignment explanation
Indices: 43107--43190 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 29
43097 GCAAATGATT
*
43107 TTTAAAATTATTAAAATTATTTTTTAAAA
1 TTTAAAATTATTAAAATTATTTTTAAAAA
* *
43136 TATAAAATTGTTAAAATTATTTTTAAATTAA
1 TTTAAAATTATTAAAATTATTTTTAAA--AA
43167 TTTAAAATTATTAAAATTATTTTT
1 TTTAAAATTATTAAAATTATTTTT
43191 TTGAAATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.50
31 24 0.50
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TTTAAAATTATTAAAATTATTTTTAAAAA
Found at i:43204 original size:31 final size:29
Alignment explanation
Indices: 43109--43212 Score: 131
Period size: 31 Copynumber: 3.4 Consensus size: 29
43099 AAATGATTTT
43109 TAAAATTATTAAAATTATTTTTTAAA-ATA
1 TAAAATTATTAAAATTATTTTTTAAATA-A
*
43138 TAAAATTGTTAAAATTA-TTTTTAAATTAA
1 TAAAATTATTAAAATTATTTTTTAAA-TAA
43167 TTTAAAATTATTAAAATTATTTTTTTGAAATAA
1 --TAAAATTATTAAAATTA-TTTTTT-AAATAA
43200 TAAAATTATTAAA
1 TAAAATTATTAAA
43213 TAATTTTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
28 8 0.12
29 17 0.26
30 1 0.02
31 29 0.44
33 8 0.12
34 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAATAA
Found at i:43220 original size:60 final size:60
Alignment explanation
Indices: 43107--43221 Score: 171
Period size: 60 Copynumber: 1.9 Consensus size: 60
43097 GCAAATGATT
* *
43107 TTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTGTTAAAATTATTTTTAAATTAA
1 TTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAAATTAATTTTAAATTAA
*
43167 TTTAAAATTATTAAAATTATTTTTTTGAAATAATAAAATTATT-AAA-TAATTTTAA
1 TTTAAAATTATTAAAATTA-TTTTTTAAAAT-ATAAAATTATTAAAATTAATTTTAA
43222 TTTCCAATTT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
60 27 0.54
61 13 0.26
62 10 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.50
Consensus pattern (60 bp):
TTTAAAATTATTAAAATTATTTTTTAAAATATAAAATTATTAAAATTAATTTTAAATTAA
Found at i:43672 original size:9 final size:9
Alignment explanation
Indices: 43658--43726 Score: 71
Period size: 9 Copynumber: 8.2 Consensus size: 9
43648 ATTTCAAAAA
43658 AATAATTTT
1 AATAATTTT
43667 AATAATTTT
1 AATAATTTT
43676 AAAATAATTTT
1 --AATAATTTT
43687 AATAATTTT
1 AATAATTTT
43696 -AT-ATTTT
1 AATAATTTT
43703 AA-AA----
1 AATAATTTT
43707 AATAATTTT
1 AATAATTTT
43716 AATAATTTT
1 AATAATTTT
43725 AA
1 AA
43727 AATCATTTGC
Statistics
Matches: 51, Mismatches: 0, Indels: 18
0.74 0.00 0.26
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 5 0.10
8 4 0.08
9 29 0.57
11 9 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AATAATTTT
Found at i:43708 original size:29 final size:28
Alignment explanation
Indices: 43658--43725 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
43648 ATTTCAAAAA
43658 AATAATTTTAATAATTTTAAAATAATTTT
1 AATAATTTT-ATAATTTTAAAATAATTTT
43687 AATAATTTTAT-ATTTTAAAAAATAATTTT
1 AATAATTTTATAATTTT--AAAATAATTTT
43716 AATAATTTTA
1 AATAATTTTA
43726 AAATCATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
27 5 0.14
28 2 0.05
29 30 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (28 bp):
AATAATTTTATAATTTTAAAATAATTTT
Found at i:43710 original size:20 final size:22
Alignment explanation
Indices: 43687--43728 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
43677 AAATAATTTT
43687 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
43707 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
43729 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:43721 original size:49 final size:51
Alignment explanation
Indices: 43624--43734 Score: 174
Period size: 49 Copynumber: 2.2 Consensus size: 51
43614 AAATTGGAGA
*
43624 TTAAAATTA-TTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
*
43674 TTAAAATAATTTTAATAATTTTA-TATTT-TAAAAAATAATTTTAATAATT
1 TTAAAATAATTTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
*
43723 TTAAAATCATTT
1 TTAAAATAATTT
43735 GCTGAGTTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
49 31 0.54
50 13 0.23
51 13 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (51 bp):
TTAAAATAATTTTAATAATTTTATTATTTCAAAAAAATAATTTTAATAATT
Found at i:43729 original size:20 final size:20
Alignment explanation
Indices: 43656--43696 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43646 TTATTTCAAA
43656 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
43676 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
43696 A
1 A
43697 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATAATTTTAATAATTTT
Found at i:44765 original size:22 final size:23
Alignment explanation
Indices: 44728--44771 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
44718 TTCCATTTCA
*
44728 ATAATTTTAAGATATTTAAATTT
1 ATAAATTTAAGATATTTAAATTT
44751 ATAAATTT-AGATATTTAAATT
1 ATAAATTTAAGATATTTAAATT
44772 CAAATTCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (23 bp):
ATAAATTTAAGATATTTAAATTT
Found at i:46460 original size:4 final size:4
Alignment explanation
Indices: 46447--46480 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
46437 AACAACAACA
46447 AAAG -AAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
46481 CCAATATGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:48895 original size:23 final size:23
Alignment explanation
Indices: 48869--48914 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
48859 CAAACACTTT
*
48869 TAAATAAACAATTAATAGAATCA
1 TAAAAAAACAATTAATAGAATCA
48892 TAAAAAAACAATTAATAGAATCA
1 TAAAAAAACAATTAATAGAATCA
48915 GTTGGCCGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.04, T:0.24
Consensus pattern (23 bp):
TAAAAAAACAATTAATAGAATCA
Found at i:49250 original size:18 final size:18
Alignment explanation
Indices: 49229--49272 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
49219 AAAAAAAAAA
49229 AAAGGAAAAAAAATTAAG
1 AAAGGAAAAAAAATTAAG
49247 AAAGGAAAAAAAATTAAG
1 AAAGGAAAAAAAATTAAG
*
49265 AAAAGAAA
1 AAAGGAAA
49273 TGTATTGTCG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (18 bp):
AAAGGAAAAAAAATTAAG
Found at i:52778 original size:26 final size:28
Alignment explanation
Indices: 52730--52782 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
52720 TTCCAAAACA
*
52730 TTTTTTCTATTTTTCCTATATTTTCAAG
1 TTTTTTCTATTTTTCCTAAATTTTCAAG
*
52758 TTTTTTTTA-TTTT-CTAAATTTTCAA
1 TTTTTTCTATTTTTCCTAAATTTTCAA
52783 CCAATCTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 11 0.48
27 4 0.17
28 8 0.35
ACGTcount: A:0.21, C:0.11, G:0.02, T:0.66
Consensus pattern (28 bp):
TTTTTTCTATTTTTCCTAAATTTTCAAG
Found at i:55946 original size:21 final size:20
Alignment explanation
Indices: 55908--55948 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
55898 GGTTTTTTAG
*
55908 AAAATTTTAGATTTTTATGA
1 AAAATTTTAGAATTTTATGA
55928 AAAATTTTAAGAATTTTATGA
1 AAAATTTT-AGAATTTTATGA
55949 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (20 bp):
AAAATTTTAGAATTTTATGA
Found at i:56228 original size:19 final size:19
Alignment explanation
Indices: 56191--56230 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
56181 ATTTTCTAAG
*
56191 TTTTAATATTTTTGGGATT
1 TTTTAATATTTTTGAGATT
* *
56210 TTTTTATATTTTTTAGATT
1 TTTTAATATTTTTGAGATT
56229 TT
1 TT
56231 CAATGATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (19 bp):
TTTTAATATTTTTGAGATT
Found at i:56271 original size:10 final size:12
Alignment explanation
Indices: 56240--56269 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56230 TCAATGATTT
56240 AAATTTTTAATA
1 AAATTTTTAATA
56252 AAATTTTTAA-A
1 AAATTTTTAATA
56263 AAATTTT
1 AAATTTT
56270 AACACATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATTTTTAATA
Found at i:61021 original size:71 final size:71
Alignment explanation
Indices: 60905--61044 Score: 271
Period size: 71 Copynumber: 2.0 Consensus size: 71
60895 ACACCTACGA
*
60905 ATCCCATCTCATCATAACTTTCAAACTTTATAGATCTCCCATTGACACACACAAGAAGATGGGTC
1 ATCCCATCTCATCATAACTTTCAAACTTCATAGATCTCCCATTGACACACACAAGAAGATGGGTC
60970 CCCCTC
66 CCCCTC
60976 ATCCCATCTCATCATAACTTTCAAACTTCATAGATCTCCCATTGACACACACAAGAAGATGGGTC
1 ATCCCATCTCATCATAACTTTCAAACTTCATAGATCTCCCATTGACACACACAAGAAGATGGGTC
61041 CCCC
66 CCCC
61045 AAAAGGGACT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 68 1.00
ACGTcount: A:0.31, C:0.33, G:0.10, T:0.26
Consensus pattern (71 bp):
ATCCCATCTCATCATAACTTTCAAACTTCATAGATCTCCCATTGACACACACAAGAAGATGGGTC
CCCCTC
Found at i:64172 original size:30 final size:30
Alignment explanation
Indices: 64133--64201 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
64123 CAAATAATTT
64133 TAAAATTATTAAAATTATTTTTAAAAAATA
1 TAAAATTATTAAAATTATTTTTAAAAAATA
* **
64163 TAATATTATTAAAATTATTTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTAAAAAATA
64193 TAAAATTAT
1 TAAAATTAT
64202 CTTATTCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTAAAAAATA
Found at i:65128 original size:11 final size:9
Alignment explanation
Indices: 65112--65203 Score: 67
Period size: 9 Copynumber: 10.7 Consensus size: 9
65102 GATAATGATT
65112 ATAATTTTAAA
1 ATAATTTT--A
65123 ATAATTTTA
1 ATAATTTTA
65132 ATAATTTT-
1 ATAATTTTA
65140 AT-ATTTTAAAA
1 ATAATTTT---A
65151 ATAATTTTA
1 ATAATTTTA
65160 ATAATTTT-
1 ATAATTTTA
65168 AT-ATTTTA
1 ATAATTTTA
*
65176 A-AA---AA
1 ATAATTTTA
65181 ATAATTTTA
1 ATAATTTTA
65190 ATAATTTTA
1 ATAATTTTA
65199 A-AATT
1 ATAATT
65204 ATTTGCTGAC
Statistics
Matches: 68, Mismatches: 2, Indels: 25
0.72 0.02 0.26
Matches are distributed among these distances:
5 2 0.03
6 2 0.03
7 10 0.15
8 10 0.15
9 29 0.43
11 10 0.15
12 5 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATAATTTTA
Found at i:65183 original size:21 final size:23
Alignment explanation
Indices: 65159--65201 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
65149 AAATAATTTT
65159 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
65180 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
65202 TTATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:65183 original size:30 final size:28
Alignment explanation
Indices: 65110--65198 Score: 144
Period size: 28 Copynumber: 3.1 Consensus size: 28
65100 AGGATAATGA
65110 TTATAATTTT-AAAATAATTTTAATAATT
1 TTAT-ATTTTAAAAATAATTTTAATAATT
65138 TTATATTTTAAAAATAATTTTAATAATT
1 TTATATTTTAAAAATAATTTTAATAATT
65166 TTATATTTTAAAAAAATAATTTTAATAATT
1 TTATATTTT--AAAAATAATTTTAATAATT
65196 TTA
1 TTA
65199 AAATTATTTG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
27 5 0.09
28 31 0.53
30 22 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TTATATTTTAAAAATAATTTTAATAATT
Found at i:74925 original size:18 final size:19
Alignment explanation
Indices: 74904--74946 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
74894 AAATAAGTTT
74904 TTAATTAAAAAATTTT-AA
1 TTAATTAAAAAATTTTAAA
*
74922 TTAATT-GAAAATTTTAAA
1 TTAATTAAAAAATTTTAAA
74940 TTAATTA
1 TTAATTA
74947 CAAATTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TTAATTAAAAAATTTTAAA
Found at i:74932 original size:17 final size:18
Alignment explanation
Indices: 74912--74945 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
74902 TTTTAATTAA
74912 AAAATTTT-AATTAATTG
1 AAAATTTTAAATTAATTG
74929 AAAATTTTAAATTAATT
1 AAAATTTTAAATTAATT
74946 ACAAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAAATTTTAAATTAATTG
Found at i:77988 original size:17 final size:15
Alignment explanation
Indices: 77965--78006 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
77955 CCGTTAGATC
77965 AAAAAATTAATTTATA
1 AAAAAATTAA-TTATA
77981 ATAAAAATT-ATTATA
1 A-AAAAATTAATTATA
77996 AAAATAATTAA
1 AAAA-AATTAA
78007 AAAAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 3 0.13
17 7 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAAATTAATTATA
Found at i:86589 original size:17 final size:17
Alignment explanation
Indices: 86567--86599 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
86557 GTAAAAATTA
86567 AGAAAAAAATTTAATGC
1 AGAAAAAAATTTAATGC
86584 AGAAAAAAATTTAATG
1 AGAAAAAAATTTAATG
86600 GTCTTCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.24
Consensus pattern (17 bp):
AGAAAAAAATTTAATGC
Found at i:87173 original size:287 final size:288
Alignment explanation
Indices: 86645--87221 Score: 980
Period size: 287 Copynumber: 2.0 Consensus size: 288
86635 TCCAAGTGCA
*
86645 GATGATCAGTAAGATTGCCAACTTCTTCATGAAATTCTGGGAACTCAAGTACGGCAACTCCCTTC
1 GATGATCAGTAAGATTGCCAACTTCTTCATGAAATTCTGGGAACTCAAGTACGGCAACTCCCTGC
*
86710 CGAAGTCAATTAAAACATATCACCTACTTATATAAATTGTAAAAATAAACAAAATAAAATAAAAT
66 CGAAGTCAATTAAAACATATCACCTACTTATATAAATTGTAAAAATAAAC---A-AAAATAAAAG
* * *
86775 CCGGATGCATATGAATTCCTTTCTCCTATCTCAGAAAAGAAAACAAGTCAGTACCTACATCAGTT
127 CCGGATGCATATGAATCCCTTTCTCCTACCTCAGAAAAGAAAACAAATCAGTACCTACATCAGTT
86840 GGGAGAACTCTCAGGTGAGGAAAATTGCGGTGTCTCAGGAATGTCTCAGGTAAAGCACCACTTTC
192 GGGAGAACTCTCAGGTGAGGAAAATTGCGGTGTCTCAGGAATGTCTCAGGTAAAGCACCACTTTC
* *
86905 CCGGCGAGAATGACCTATCCTAAAGCCAGTGT
257 CCAGCGAGAATGACATATCCTAAAGCCAGTGT
86937 GATGATCAGTAAGATTGCCAACTTCTTCATGAAATTCTGGGAACTCAAGTACGGCAACTCCCTGC
1 GATGATCAGTAAGATTGCCAACTTCTTCATGAAATTCTGGGAACTCAAGTACGGCAACTCCCTGC
87002 CGAAGTCAATTAAAACATATCAGCCTACTTATATAAATTGTAAAAATAAAC-AAAA-AAAAGCCG
66 CGAAGTCAATTAAAACATATCA-CCTACTTATATAAATTGTAAAAATAAACAAAAATAAAAGCCG
* *
87065 GATGCATATGAATCCCTTTCTCCTACCTCAGAAAAGAAAGCAAATCAGTA-CTCACATCGGTTGG
130 GATGCATATGAATCCCTTTCTCCTACCTCAGAAAAGAAAACAAATCAGTACCT-ACATCAGTTGG
* *
87129 GAGAACTCTCAGGTGAGGAAGATTGCGGTGTCTCAGGGATGTCTCAGGTAAAGCACCACTTTCCC
194 GAGAACTCTCAGGTGAGGAAAATTGCGGTGTCTCAGGAATGTCTCAGGTAAAGCACCACTTTCCC
87194 AGCGAGAATGACATATCCTAAAGCCAGT
259 AGCGAGAATGACATATCCTAAAGCCAGT
87222 AGGTTGAACT
Statistics
Matches: 272, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
286 2 0.01
287 152 0.56
288 4 0.01
292 86 0.32
293 28 0.10
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (288 bp):
GATGATCAGTAAGATTGCCAACTTCTTCATGAAATTCTGGGAACTCAAGTACGGCAACTCCCTGC
CGAAGTCAATTAAAACATATCACCTACTTATATAAATTGTAAAAATAAACAAAAATAAAAGCCGG
ATGCATATGAATCCCTTTCTCCTACCTCAGAAAAGAAAACAAATCAGTACCTACATCAGTTGGGA
GAACTCTCAGGTGAGGAAAATTGCGGTGTCTCAGGAATGTCTCAGGTAAAGCACCACTTTCCCAG
CGAGAATGACATATCCTAAAGCCAGTGT
Found at i:87433 original size:82 final size:82
Alignment explanation
Indices: 87291--87549 Score: 430
Period size: 82 Copynumber: 3.2 Consensus size: 82
87281 TAACTTGAGG
* *
87291 AAAGCTGAAGGCAAGAGGCAAACAATTGAGGCAAATCTAGCTCTCAGA-CGAAACAGTTGAGAGG
1 AAAGCTGAAGGCAAGAAGCAAACAATTGAGGCAAATCTAGCTCTCAGACCG-AACAATTGAGAGG
87355 AAAAGCGAGAGAGAAAGA
65 AAAAGCGAGAGAGAAAGA
* *
87373 AAAGCTCAAGGCAAGAAGCAAACAATTGAGGCAAATCTATCTCTCAGACCGAACAATTGAGAGGA
1 AAAGCTGAAGGCAAGAAGCAAACAATTGAGGCAAATCTAGCTCTCAGACCGAACAATTGAGAGGA
*
87438 AAAGCGAGAGAGATAGA
66 AAAGCGAGAGAGAAAGA
*
87455 AAAGCTGAAGGCGAGAAGCAAACAATTGAGGCAAATCTAGCTCTCAGACCGAACAATTGAGAGGA
1 AAAGCTGAAGGCAAGAAGCAAACAATTGAGGCAAATCTAGCTCTCAGACCGAACAATTGAGAGGA
*
87520 AAAGCGAGAGAGAAAGG
66 AAAGCGAGAGAGAAAGA
*
87537 AAAGTTGAAGGCA
1 AAAGCTGAAGGCA
87550 TCAGACGCGA
Statistics
Matches: 164, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
82 162 0.99
83 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.28, T:0.12
Consensus pattern (82 bp):
AAAGCTGAAGGCAAGAAGCAAACAATTGAGGCAAATCTAGCTCTCAGACCGAACAATTGAGAGGA
AAAGCGAGAGAGAAAGA
Found at i:88103 original size:20 final size:22
Alignment explanation
Indices: 88059--88107 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
88049 ACGTTTCATA
* *
88059 AATATTTATAAATTTTAATATT
1 AATATTTATAAAATTAAATATT
88081 AATATTT-TAAAATTAAATA-T
1 AATATTTATAAAATTAAATATT
88101 AATATTT
1 AATATTT
88108 GAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 8 0.32
21 10 0.40
22 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTATAAAATTAAATATT
Found at i:89535 original size:14 final size:13
Alignment explanation
Indices: 89517--89543 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
89507 ATATAAATTC
89517 GAAAAATAAGTTT
1 GAAAAATAAGTTT
89530 GAAAAATAAGTTT
1 GAAAAATAAGTTT
89543 G
1 G
89544 GACAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (13 bp):
GAAAAATAAGTTT
Found at i:93685 original size:31 final size:28
Alignment explanation
Indices: 93637--93725 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 28
93627 ACCCTAAAAT
93637 TATACATGAATTATGATTTGATATGTAATTA
1 TATACATGAATT-TGATTT--TATGTAATTA
* * *
93668 TATATATGAACTTTGATTTTGTGTAATTT
1 TATACATGAA-TTTGATTTTATGTAATTA
* *
93697 TATACATGAAATTTTGATTTAATGCAATT
1 TATACATG-AA-TTTGATTTTATGTAATT
93726 CTTGTAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 15 0.31
30 16 0.33
31 15 0.31
32 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.12, T:0.48
Consensus pattern (28 bp):
TATACATGAATTTGATTTTATGTAATTA
Found at i:93692 original size:29 final size:30
Alignment explanation
Indices: 93660--93716 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
93650 TGATTTGATA
*
93660 TGTAATTATATATATG-AACTTTGATTTTG
1 TGTAATTATATACATGAAACTTTGATTTTG
* *
93689 TGTAATTTTATACATGAAATTTTGATTT
1 TGTAATTATATACATGAAACTTTGATTT
93717 AATGCAATTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (30 bp):
TGTAATTATATACATGAAACTTTGATTTTG
Found at i:104270 original size:19 final size:20
Alignment explanation
Indices: 104243--104283 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
104233 TTATAAATGA
*
104243 TATTTAAATTATACT-TCAT
1 TATTCAAATTATACTGTCAT
*
104262 TATTCAAATTATCCTGTCAT
1 TATTCAAATTATACTGTCAT
104282 TA
1 TA
104284 AAAAAATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.34, C:0.15, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTCAAATTATACTGTCAT
Found at i:105873 original size:25 final size:25
Alignment explanation
Indices: 105820--105877 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
105810 ACATACACAC
*
105820 ATTTTTTATTTATATTTTTCAAGATA
1 ATTTTTTA-TTATATTTTTCAAGAGA
105846 ATTTTTTA-TATATTTCTTCGAA-AGA
1 ATTTTTTATTATATTT-TTC-AAGAGA
105871 ATTTTTT
1 ATTTTTT
105878 TTAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 7 0.24
25 12 0.41
26 10 0.34
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (25 bp):
ATTTTTTATTATATTTTTCAAGAGA
Found at i:111977 original size:18 final size:18
Alignment explanation
Indices: 111956--112059 Score: 54
Period size: 19 Copynumber: 5.7 Consensus size: 18
111946 TTTTACTAGT
111956 TTTTTAAATTTTTAATAA
1 TTTTTAAATTTTTAATAA
*
111974 TTTTT--ATTTTTTA-AA
1 TTTTTAAATTTTTAATAA
* *
111989 TATTTTAGAATTTCTAATGA
1 T-TTTTA-AATTTTTAATAA
* * **
112009 -TTTTATATATTTTGATTC
1 TTTTTAAAT-TTTTAATAA
*
112027 TTTTTAATATTTTTAAAATA
1 TTTTTAA-ATTTTTAATA-A
*
112047 TTTTTAAGTTTTT
1 TTTTTAAATTTTT
112060 CCTTGATGAT
Statistics
Matches: 62, Mismatches: 15, Indels: 17
0.66 0.16 0.18
Matches are distributed among these distances:
15 3 0.05
16 11 0.18
17 2 0.03
18 15 0.24
19 21 0.34
20 10 0.16
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTTAAATTTTTAATAA
Found at i:112039 original size:9 final size:9
Alignment explanation
Indices: 111956--112053 Score: 55
Period size: 9 Copynumber: 10.8 Consensus size: 9
111946 TTTTACTAGT
111956 TTTTTAA-A
1 TTTTTAATA
111964 TTTTTAATAA
1 TTTTTAAT-A
111974 TTTTT-AT-
1 TTTTTAATA
111981 TTTTTAA-A
1 TTTTTAATA
111989 TATTTTAGA-A
1 T-TTTTA-ATA
*
111999 TTTCTAATGA
1 TTTTTAAT-A
112009 -TTTTATATA
1 TTTTTA-ATA
* * *
112018 TTTTGATTC
1 TTTTTAATA
112027 TTTTTAATA
1 TTTTTAATA
112036 TTTTTAAAATA
1 TTTTT--AATA
112047 TTTTTAA
1 TTTTTAA
112054 GTTTTTCCTT
Statistics
Matches: 70, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
7 5 0.07
8 10 0.14
9 30 0.43
10 16 0.23
11 9 0.13
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTAATA
Found at i:114040 original size:22 final size:21
Alignment explanation
Indices: 114009--114068 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 21
113999 TCTTAATTAA
* *
114009 AATAATATTTTAATAAATTATTT
1 AATATTATTTTAATAAATGA--T
*
114032 AA-ATTATTTTATTAAATGAT
1 AATATTATTTTAATAAATGAT
114052 AATATT-TTTTAATAAAT
1 AATATTATTTTAATAAAT
114069 AGAATTAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 13 0.41
21 3 0.09
22 14 0.44
23 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
AATATTATTTTAATAAATGAT
Found at i:117323 original size:26 final size:26
Alignment explanation
Indices: 117297--117348 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
117287 TTAAATAAAA
* *
117297 TAGGGAATCAAATTAAATAAAACAAAT
1 TAGGG-ATCAAATGAAACAAAACAAAT
*
117324 TAGGGTTCAAATGAAACAAAACAAA
1 TAGGGATCAAATGAAACAAAACAAA
117349 ACAAAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (26 bp):
TAGGGATCAAATGAAACAAAACAAAT
Found at i:118046 original size:2 final size:2
Alignment explanation
Indices: 118039--118063 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
118029 ACCATTCCTT
118039 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
118064 ATTTTGGCCC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:118927 original size:2 final size:2
Alignment explanation
Indices: 118922--118955 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
118912 TACACACGCG
118922 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
118956 TATACAAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:123077 original size:26 final size:27
Alignment explanation
Indices: 123024--123077 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
123014 ATGCTTGGTG
* *
123024 ATAATAAAAGACTACTAATCAATGAAA
1 ATAATAAAAGAATACTAATCAATCAAA
123051 ATAA-AAAAGAATACTAA-CAAGTCAAA
1 ATAATAAAAGAATACTAATCAA-TCAAA
123077 A
1 A
123078 CCCTACTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 3 0.12
26 17 0.71
27 4 0.17
ACGTcount: A:0.63, C:0.11, G:0.07, T:0.19
Consensus pattern (27 bp):
ATAATAAAAGAATACTAATCAATCAAA
Found at i:124392 original size:74 final size:74
Alignment explanation
Indices: 124277--124427 Score: 277
Period size: 74 Copynumber: 2.0 Consensus size: 74
124267 TTTCTATGAA
124277 CCCCTTTTTTTGCTTTATTTTCATTTTTAGTTTGTTTTCGAG-AAAAAAAAAAACAGAAAAAAAA
1 CCCCTTTTTTTGCTTTATTTTCATTTTTAGTTTGTTTTCGAGAAAAAAAAAAAACAGAAAAAAAA
124341 TCATTTTTT
66 TCATTTTTT
124350 CNCCCTTTTTTTGCTTTATTTTCATTTTTAGTTTGTTTTCGAGAAAAAAAAAAAAACAGAAAAAA
1 C-CCCTTTTTTTGCTTTATTTTCATTTTTAGTTTGTTTTCGAG-AAAAAAAAAAAACAGAAAAAA
124415 AATCATTTTTT
64 AATCATTTTTT
124426 CC
1 CC
124428 TAAAATTTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
73 1 0.01
74 41 0.55
75 1 0.01
76 32 0.43
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (74 bp):
CCCCTTTTTTTGCTTTATTTTCATTTTTAGTTTGTTTTCGAGAAAAAAAAAAAACAGAAAAAAAA
TCATTTTTT
Found at i:137404 original size:11 final size:11
Alignment explanation
Indices: 137388--137457 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
137378 CCAAACAATT
137388 AAAATAACAAC
1 AAAATAACAAC
*
137399 AAAATAGCAAC
1 AAAATAACAAC
137410 AAAAATAACAA-
1 -AAAATAACAAC
*
137421 AAAA-AGCAAC
1 AAAATAACAAC
**
137431 AAAAATAACAGG
1 -AAAATAACAAC
*
137443 AAAATAGCAAC
1 AAAATAACAAC
137454 AAAA
1 AAAA
137458 ACAGTAACAA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 4 0.09
10 4 0.09
11 26 0.57
12 12 0.26
ACGTcount: A:0.71, C:0.14, G:0.07, T:0.07
Consensus pattern (11 bp):
AAAATAACAAC
Found at i:137414 original size:12 final size:12
Alignment explanation
Indices: 137388--137472 Score: 72
Period size: 12 Copynumber: 7.5 Consensus size: 12
137378 CCAAACAATT
*
137388 AAAATAACAAC-
1 AAAATAGCAACA
137399 AAAATAGCAACA
1 AAAATAGCAACA
137411 AAAAT---AACA
1 AAAATAGCAACA
*
137420 AAAAAAGCAACA
1 AAAATAGCAACA
* **
137432 AAAATAAC-AGG
1 AAAATAGCAACA
137443 AAAATAGCAACA
1 AAAATAGCAACA
* *
137455 AAAACAGTAACA
1 AAAATAGCAACA
137467 AAAATA
1 AAAATA
137473 ATAGCATAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
9 8 0.14
11 18 0.32
12 31 0.54
ACGTcount: A:0.71, C:0.14, G:0.07, T:0.08
Consensus pattern (12 bp):
AAAATAGCAACA
Found at i:137414 original size:23 final size:22
Alignment explanation
Indices: 137388--137458 Score: 108
Period size: 23 Copynumber: 3.2 Consensus size: 22
137378 CCAAACAATT
137388 AAAATAACAACAAAATAGCAACA
1 AAAATAACAA-AAAATAGCAACA
137411 AAAATAACAAAAAA-AGCAACA
1 AAAATAACAAAAAATAGCAACA
*
137432 AAAATAACAGGAAAATAGCAACA
1 AAAATAACA-AAAAATAGCAACA
137455 AAAA
1 AAAA
137459 CAGTAACAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
21 16 0.36
22 8 0.18
23 21 0.47
ACGTcount: A:0.72, C:0.14, G:0.07, T:0.07
Consensus pattern (22 bp):
AAAATAACAAAAAATAGCAACA
Found at i:137483 original size:26 final size:27
Alignment explanation
Indices: 137445--137496 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
137435 ATAACAGGAA
*
137445 AATAGCAACAAAAACAGTAACAAAAAT
1 AATAGCAACAAAAACAGTAAAAAAAAT
* *
137472 AATAGC-ATAAAAATAGTAAAAAAAA
1 AATAGCAACAAAAACAGTAAAAAAAA
137497 CACCAAAACA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.69, C:0.10, G:0.08, T:0.13
Consensus pattern (27 bp):
AATAGCAACAAAAACAGTAAAAAAAAT
Found at i:137513 original size:21 final size:19
Alignment explanation
Indices: 137489--137547 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 19
137479 TAAAAATAGT
137489 AAAAAAAACACCAAAACAG
1 AAAAAAAACACCAAAACAG
*
137508 CAAAAAAATCGACCAAAACAG
1 -AAAAAAAAC-ACCAAAACAG
*
137529 TAAAAAAAACACAAAAACA
1 -AAAAAAAACACCAAAACA
137548 ATAATATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.71, C:0.20, G:0.05, T:0.03
Consensus pattern (19 bp):
AAAAAAAACACCAAAACAG
Found at i:146883 original size:3 final size:3
Alignment explanation
Indices: 146875--146899 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
146865 TCAATTCTCC
146875 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
146900 AACACTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:148060 original size:15 final size:15
Alignment explanation
Indices: 148042--148081 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
148032 CAAAACTAAG
148042 ATTTTTAAAATA-TC
1 ATTTTTAAAATATTC
*
148056 TATTTTTACAATATTC
1 -ATTTTTAAAATATTC
148072 ATTTTTAAAA
1 ATTTTTAAAA
148082 AAAAATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTTTAAAATATTC
Found at i:164600 original size:28 final size:27
Alignment explanation
Indices: 164564--164621 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
164554 AATTATCCAG
* * *
164564 AAATCATATTTTGACTCTCAAATTTTTA
1 AAATCATATTTTAAC-CTCAAACTTTCA
*
164592 AAATTATATTTTAACCTCAAACTTTCA
1 AAATCATATTTTAACCTCAAACTTTCA
164619 AAA
1 AAA
164622 AATTACATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (27 bp):
AAATCATATTTTAACCTCAAACTTTCA
Found at i:164631 original size:29 final size:27
Alignment explanation
Indices: 164591--164809 Score: 134
Period size: 29 Copynumber: 7.7 Consensus size: 27
164581 TCAAATTTTT
* *
164591 AAAATTATATTTTAACCTCAAACTTTCAA
1 AAAATTACATTTT-ACCCCAAACTTTC-A
* *
164620 AAAATTACATTTTACCACTAAACTTTCC
1 AAAATTACATTTTACC-CCAAACTTTCA
* *
164648 AAAATTCCATTTTGACCCCAAATTTTTTCA
1 AAAATTACATTTT-ACCCCAAA--CTTTCA
* * *
164678 AAAATTACGTTTTTCCCCAAACTTTCC
1 AAAATTACATTTTACCCCAAACTTTCA
** * *
164705 AAAATTTTATTTTTACCCCGAATTTTCCA
1 AAAATTACA-TTTTACCCCAAACTTT-CA
* * *
164734 AAAATTACATTTTGCCCCAGA-TGTCTA
1 AAAATTACATTTTACCCCAAACTTTC-A
* ** *
164761 AAAATTCCATTTTTGACCCTGAACTTTCC
1 AAAATTACA-TTTT-ACCCCAAACTTTCA
164790 AAAATTACCATTTTATCCCC
1 AAAATTA-CATTTTA-CCCC
164810 GGATGTTGAA
Statistics
Matches: 143, Mismatches: 35, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
26 1 0.01
27 21 0.15
28 46 0.32
29 55 0.38
30 20 0.14
ACGTcount: A:0.34, C:0.24, G:0.04, T:0.38
Consensus pattern (27 bp):
AAAATTACATTTTACCCCAAACTTTCA
Found at i:164700 original size:57 final size:56
Alignment explanation
Indices: 164614--164779 Score: 172
Period size: 57 Copynumber: 2.9 Consensus size: 56
164604 AACCTCAAAC
*
164614 TTTCAAAAAATTACATTTTACCACTAAACTTTCCAAAATTCCATTTTGACCCCAAATTT
1 TTTC-AAAAATTACATTTTACC-CCAAACTTTCCAAAATTCCATTTTGACCCCAAA-TT
* * ** * *
164673 TTTCAAAAATTACGTTTTTCCCCAAACTTTCCAAAATTTTATTTTTACCCCGAATT
1 TTTCAAAAATTACATTTTACCCCAAACTTTCCAAAATTCCATTTTGACCCCAAATT
* * * * *
164729 TTCCAAAAATTACATTTTGCCCCAGA-TGTCTAAAAATTCCATTTTTGACCC
1 TTTCAAAAATTACATTTTACCCCAAACTTTC-CAAAATTCCA-TTTTGACCC
164780 TGAACTTTCC
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
55 3 0.03
56 31 0.35
57 36 0.40
58 15 0.17
59 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (56 bp):
TTTCAAAAATTACATTTTACCCCAAACTTTCCAAAATTCCATTTTGACCCCAAATT
Found at i:166078 original size:14 final size:14
Alignment explanation
Indices: 166050--166089 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
166040 TTGAAAGAAT
166050 AATTATATAAAAAA
1 AATTATATAAAAAA
166064 AATTA-ATAAACAAA
1 AATTATATAAA-AAA
*
166078 AAATATATAAAA
1 AATTATATAAAA
166090 TTATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 5 0.22
14 13 0.57
15 5 0.22
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTATATAAAAAA
Found at i:171903 original size:19 final size:21
Alignment explanation
Indices: 171858--171904 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
171848 AAAAAATTCA
171858 TATATATATATATATACACTT
1 TATATATATATATATACACTT
* * *
171879 TGTATATA-ATATA-ATATTT
1 TATATATATATATATACACTT
171898 TATATAT
1 TATATAT
171905 CGTTGTCTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 10 0.45
20 5 0.23
21 7 0.32
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATATATATATATACACTT
Found at i:173289 original size:18 final size:19
Alignment explanation
Indices: 173266--173307 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
173256 CAGTATGATA
173266 AAAAAAAATTAAATCGA-T
1 AAAAAAAATTAAATCGAGT
*
173284 AAAAAAAGTTAAATCGAGT
1 AAAAAAAATTAAATCGAGT
173303 AAAAA
1 AAAAA
173308 TCGATACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (19 bp):
AAAAAAAATTAAATCGAGT
Found at i:177646 original size:3 final size:3
Alignment explanation
Indices: 177638--177662 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
177628 ATCAACTGAG
177638 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
177663 ATCACAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:183833 original size:2 final size:2
Alignment explanation
Indices: 183828--183855 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
183818 ATTTAATTAA
183828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183856 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185409 original size:42 final size:42
Alignment explanation
Indices: 185362--185444 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
185352 ATTACGAGGT
* *
185362 CCGATGATTACGTGTCATTATGAGTATATGAATCCTTTACGA
1 CCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGA
* * *
185404 CCGATGACTATGTGTCATCGTGAGTATATGATTCCTTTACG
1 CCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACG
185445 GAACAAGAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (42 bp):
CCGATGACTACGTGTCATCATGAGTATATGAATCCTTTACGA
Found at i:187552 original size:16 final size:16
Alignment explanation
Indices: 187531--187561 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
187521 TTGTAAATAC
187531 GTTGAAAGCCTTTTTA
1 GTTGAAAGCCTTTTTA
187547 GTTGAAAGCCTTTTT
1 GTTGAAAGCCTTTTT
187562 TTGCAAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.45
Consensus pattern (16 bp):
GTTGAAAGCCTTTTTA
Found at i:187751 original size:10 final size:10
Alignment explanation
Indices: 187707--187759 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
187697 ACAACCATAT
187707 AACAATAACAA
1 AACAATAAC-A
*
187718 AACAATAATA
1 AACAATAACA
** *
187728 TAACAGCAATA
1 -AACAATAACA
187739 AACAATAACA
1 AACAATAACA
187749 AACAATAACA
1 AACAATAACA
187759 A
1 A
187760 TTTCATTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 19 0.54
11 16 0.46
ACGTcount: A:0.68, C:0.17, G:0.02, T:0.13
Consensus pattern (10 bp):
AACAATAACA
Found at i:187758 original size:16 final size:16
Alignment explanation
Indices: 187705--187760 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
187695 AAACAACCAT
187705 ATAACAATAACAAAACA
1 ATAACAATAAC-AAACA
* *
187722 ATAA-TATAAC-AGCA
1 ATAACAATAACAAACA
187736 ATAAACAATAACAAACA
1 AT-AACAATAACAAACA
187753 ATAACAAT
1 ATAACAAT
187761 TTCATTTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 16 0.50
17 9 0.28
ACGTcount: A:0.66, C:0.16, G:0.02, T:0.16
Consensus pattern (16 bp):
ATAACAATAACAAACA
Found at i:193484 original size:114 final size:113
Alignment explanation
Indices: 193264--193467 Score: 270
Period size: 114 Copynumber: 1.8 Consensus size: 113
193254 ATGTTGACTG
* *
193264 TTTCCAGGAGCAGCTTTAGCTGCAGCAGCCATAAGAAGGGACTGTTGCTGTGCTAACATAGCTAG
1 TTTCCAGGAGCAGATTTAGCTGCAGCAGCCATAAGAAGGGACTGTTGCTGAGCTAACATAGCTAG
** ** * *
193329 TTGTTGTTGAGTGGGTATCATTATGCCATTGGATGAAGACTGTTGAGCA
66 TTGTTGTTGAGTGCATATCAAAAGGCCATCGGATG-AGACTGTTGAGCA
* *
193378 TTTCCAGGAGCAGATTTAGCTGCAGCAGCCATGAGAAGGGACTGTTGCTGAGCTAGCGA-AGCTA
1 TTTCCAGGAGCAGATTTAGCTGCAGCAGCCATAAGAAGGGACTGTTGCTGAGCTAAC-ATAGCTA
193442 GTTGTTGTTGA-TGCAT-TGCAAAAGGC
65 GTTGTTGTTGAGTGCATAT-CAAAAGGC
193468 GACGTCGTGT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
112 1 0.01
113 8 0.10
114 69 0.87
115 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (113 bp):
TTTCCAGGAGCAGATTTAGCTGCAGCAGCCATAAGAAGGGACTGTTGCTGAGCTAACATAGCTAG
TTGTTGTTGAGTGCATATCAAAAGGCCATCGGATGAGACTGTTGAGCA
Found at i:195995 original size:18 final size:18
Alignment explanation
Indices: 195968--196020 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
195958 TGTATATAAT
*
195968 ATATGCATATACATACAC
1 ATATGTATATACATACAC
195986 ATATGTATATACATACAC
1 ATATGTATATACATACAC
196004 ATATGTATATACATACA
1 ATATGTATATACATACA
196021 AAGAATGTGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (18 bp):
ATATGTATATACATACAC
Found at i:198655 original size:16 final size:16
Alignment explanation
Indices: 198636--198666 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
198626 TTAAAAAATA
198636 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
198652 ATATAACATTTATAA
1 ATATAAAATTTATAA
198667 ATTGTCCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:199397 original size:24 final size:25
Alignment explanation
Indices: 199353--199399 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
199343 GAATGATAAT
199353 TTTTAAAAAGATTTCCCTAAATTCG
1 TTTTAAAAAGATTTCCCTAAATTCG
*
199378 TTTTGAAAAGA-TTCCCTAAATT
1 TTTTAAAAAGATTTCCCTAAATT
199400 TAAATGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (25 bp):
TTTTAAAAAGATTTCCCTAAATTCG
Found at i:211060 original size:54 final size:54
Alignment explanation
Indices: 210972--211075 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
210962 GGGTGGGAGT
* *
210972 TAAGATGGATGCATCCAACATCTATAGAGGTGATAATGGCAATTCAAAATGATA
1 TAAGATGGATGCATCCAACATCTATAGAGATGATAATAGCAATTCAAAATGATA
*
211026 TAAGATGGATGCATCCAACATCTATGGAGATGATAATAGCAATTCAAAAT
1 TAAGATGGATGCATCCAACATCTATAGAGATGATAATAGCAATTCAAAAT
211076 TATACATTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (54 bp):
TAAGATGGATGCATCCAACATCTATAGAGATGATAATAGCAATTCAAAATGATA
Found at i:211471 original size:2 final size:2
Alignment explanation
Indices: 211428--211458 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
211418 TTCTCTTTTA
211428 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
211459 ATAATTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:212400 original size:6 final size:7
Alignment explanation
Indices: 212380--212431 Score: 50
Period size: 7 Copynumber: 7.0 Consensus size: 7
212370 TTTGGTGAAG
212380 ATTAAAA
1 ATTAAAA
212387 ATTAAAA
1 ATTAAAA
212394 ATTAAAA
1 ATTAAAA
*
212401 GATACAAAA
1 -AT-TAAAA
*
212410 ACTAAAA
1 ATTAAAA
*
212417 ATAATAAA
1 ATTA-AAA
212425 ATTAAAA
1 ATTAAAA
212432 TATAAAGACT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
7 23 0.64
8 9 0.25
9 4 0.11
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (7 bp):
ATTAAAA
Found at i:212436 original size:16 final size:14
Alignment explanation
Indices: 212380--212437 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 14
212370 TTTGGTGAAG
*
212380 ATTAAAAATTAAAA
1 ATTAAAAATAAAAA
212394 ATTAAAAGATACAAAA
1 ATTAAAA-ATA-AAAA
*
212410 ACTAAAAATAATAAA
1 ATTAAAAATAA-AAA
212425 ATTAAAATATAAA
1 ATTAAAA-ATAAA
212438 GACTAAATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 8 0.22
15 15 0.41
16 14 0.38
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
ATTAAAAATAAAAA
Found at i:217601 original size:23 final size:23
Alignment explanation
Indices: 217571--217684 Score: 165
Period size: 23 Copynumber: 4.7 Consensus size: 23
217561 TTTATCTAAA
217571 GAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
*
217594 GAACGGAACGGAATGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
*
217617 GAACGGAATGAAACGGGACGGGTTCACT
1 GAAC-G---G-AACGGAACGGGTTCACT
217645 GAACGGAACGGAACGGGTTCACT
1 GAACGGAACGGAACGGGTTCACT
217668 GAACGGAACGGAACGGG
1 GAACGGAACGGAACGGG
217685 ACGGGAGGGT
Statistics
Matches: 82, Mismatches: 4, Indels: 10
0.85 0.04 0.10
Matches are distributed among these distances:
23 59 0.72
24 2 0.02
27 2 0.02
28 19 0.23
ACGTcount: A:0.32, C:0.19, G:0.37, T:0.12
Consensus pattern (23 bp):
GAACGGAACGGAACGGGTTCACT
Found at i:217642 original size:51 final size:51
Alignment explanation
Indices: 217571--217767 Score: 250
Period size: 51 Copynumber: 3.8 Consensus size: 51
217561 TTTATCTAAA
* *
217571 GAACGGAACGGAACGGGTTCACTGAACGGAACGGAATGGGTTCACTGAACG
1 GAACGGAACGGGACGGGTTCACTGAACGGAACGGAACGGGTTCACTGAACG
* *
217622 GAATGAAACGGGACGGGTTCACTGAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAACGGGACGGGTTCACTGAACGGAACGGAACGGGTTCACTGAACG
* * * *
217673 GAACGGAACGGGACGGGAGGGTTAACTGAACTGAACGGAACGGATTCACTGAACA
1 GAACGGAACGGGAC----GGGTTCACTGAACGGAACGGAACGGGTTCACTGAACG
* * * *
217728 GAGCGGGACGGGACGGGTTCACGGAACTGAACGGAACGGG
1 GAACGGAACGGGACGGGTTCACTGAACGGAACGGAACGGG
217768 ACGGTTTCAC
Statistics
Matches: 127, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
51 82 0.65
55 45 0.35
ACGTcount: A:0.31, C:0.19, G:0.38, T:0.12
Consensus pattern (51 bp):
GAACGGAACGGGACGGGTTCACTGAACGGAACGGAACGGGTTCACTGAACG
Found at i:217676 original size:28 final size:28
Alignment explanation
Indices: 217571--217789 Score: 154
Period size: 28 Copynumber: 8.2 Consensus size: 28
217561 TTTATCTAAA
217571 GAACGGAACGGAACGGGTTCACT-----
1 GAACGGAACGGAACGGGTTCACTGAACG
*
217594 GAACGGAACGGAATGGGTTCACTGAACG
1 GAACGGAACGGAACGGGTTCACTGAACG
* * *
217622 GAATGAAACGGGACGGGTTCACT-----
1 GAACGGAACGGAACGGGTTCACTGAACG
217645 GAACGGAACGGAACGGGTTCACTGAACG
1 GAACGGAACGGAACGGGTTCACTGAACG
* **** * *
217673 GAACGGAACGGGACGGG-AGGGTTAACT
1 GAACGGAACGGAACGGGTTCACTGAACG
* * *
217700 GAACTGAACGGAACGGATTCACTGAACA
1 GAACGGAACGGAACGGGTTCACTGAACG
* * * * *
217728 GAGCGGGACGGGACGGGTTCACGGAACT
1 GAACGGAACGGAACGGGTTCACTGAACG
* * * *
217756 GAACGGAACGGGACGGTTTCACGGAATG
1 GAACGGAACGGAACGGGTTCACTGAACG
217784 GAACGG
1 GAACGG
217790 GTTCACTGAA
Statistics
Matches: 149, Mismatches: 36, Indels: 17
0.74 0.18 0.08
Matches are distributed among these distances:
23 42 0.28
27 18 0.12
28 89 0.60
ACGTcount: A:0.31, C:0.19, G:0.37, T:0.13
Consensus pattern (28 bp):
GAACGGAACGGAACGGGTTCACTGAACG
Found at i:217701 original size:32 final size:33
Alignment explanation
Indices: 217645--217716 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 33
217635 CGGGTTCACT
*
217645 GAACGGAACGGAACGGGTTCACTGAACGGAACG
1 GAACGGAACGGAACGGGTTAACTGAACGGAACG
* * *
217678 GAACGGGACGGGA-GGGTTAACTGAACTGAACG
1 GAACGGAACGGAACGGGTTAACTGAACGGAACG
217710 GAACGGA
1 GAACGGA
217717 TTCACTGAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 23 0.68
33 11 0.32
ACGTcount: A:0.33, C:0.18, G:0.39, T:0.10
Consensus pattern (33 bp):
GAACGGAACGGAACGGGTTAACTGAACGGAACG
Found at i:217766 original size:23 final size:23
Alignment explanation
Indices: 217735--217899 Score: 86
Period size: 23 Copynumber: 7.4 Consensus size: 23
217725 ACAGAGCGGG
*
217735 ACGGGACGGGTTCACGGAACTGA
1 ACGGAACGGGTTCACGGAACTGA
* *
217758 ACGGAACGGG---ACGGTTTCACGGA
1 ACGGAACGGGTTCACGG---AACTGA
*
217781 ATGGAACGGGTTCAC-----TGA
1 ACGGAACGGGTTCACGGAACTGA
217799 ACGGAACGGGTTCAC-----TGA
1 ACGGAACGGGTTCACGGAACTGA
* *
217817 ACGGAACTGGTTCACGGAACGGA
1 ACGGAACGGGTTCACGGAACTGA
* *
217840 ACGGAACTGGTTCACTGAACAGAACGGA
1 ACGGAACGGGTTCAC-G----GAACTGA
*
217868 ACGGAACGGGTTCACTGAACTGA
1 ACGGAACGGGTTCACGGAACTGA
217891 ACGGAACGG
1 ACGGAACGG
217900 AACAGGTTCA
Statistics
Matches: 115, Mismatches: 11, Indels: 32
0.73 0.07 0.20
Matches are distributed among these distances:
18 33 0.29
20 4 0.03
23 54 0.47
24 1 0.01
26 2 0.02
28 21 0.18
ACGTcount: A:0.30, C:0.21, G:0.35, T:0.15
Consensus pattern (23 bp):
ACGGAACGGGTTCACGGAACTGA
Found at i:217807 original size:28 final size:28
Alignment explanation
Indices: 217776--217912 Score: 104
Period size: 28 Copynumber: 4.8 Consensus size: 28
217766 GGACGGTTTC
*
217776 ACGGAATGGAACGGGTTCACTGAACGGA
1 ACGGAACGGAACGGGTTCACTGAACGGA
* *
217804 ACGGGTTCACTGAACGGAACTGGTTCACGGAACGGA
1 AC-GG---A----ACGGAACGGGTTCACTGAACGGA
* *
217840 AC-G---G-AACTGGTTCACTGAACAGA
1 ACGGAACGGAACGGGTTCACTGAACGGA
*
217863 ACGGAACGGAACGGGTTCACTGAACTGA
1 ACGGAACGGAACGGGTTCACTGAACGGA
*
217891 ACGGAACGGAACAGGTTCACTG
1 ACGGAACGGAACGGGTTCACTG
217913 CACATCCTCC
Statistics
Matches: 88, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
23 19 0.22
24 2 0.02
27 1 0.01
28 40 0.45
29 2 0.02
32 1 0.01
34 1 0.01
36 22 0.25
ACGTcount: A:0.31, C:0.21, G:0.32, T:0.15
Consensus pattern (28 bp):
ACGGAACGGAACGGGTTCACTGAACGGA
Found at i:217859 original size:18 final size:18
Alignment explanation
Indices: 217758--217843 Score: 118
Period size: 18 Copynumber: 4.8 Consensus size: 18
217748 ACGGAACTGA
* *
217758 ACGGAACGGGACGGTTTC
1 ACGGAACGGAACGGGTTC
*
217776 ACGGAATGGAACGGGTTC
1 ACGGAACGGAACGGGTTC
*
217794 ACTGAACGGAACGGGTTC
1 ACGGAACGGAACGGGTTC
* *
217812 ACTGAACGGAACTGGTTC
1 ACGGAACGGAACGGGTTC
217830 ACGGAACGGAACGG
1 ACGGAACGGAACGG
217844 AACTGGTTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.28, C:0.21, G:0.36, T:0.15
Consensus pattern (18 bp):
ACGGAACGGAACGGGTTC
Found at i:217864 original size:18 final size:18
Alignment explanation
Indices: 217784--217866 Score: 76
Period size: 18 Copynumber: 4.3 Consensus size: 18
217774 TCACGGAATG
*
217784 GAACGGGTTCACTGAACG
1 GAACGGGTTCACTGAACA
*
217802 GAACGGGTTCACTGAACG
1 GAACGGGTTCACTGAACA
* *
217820 GAACTGGTTCACGGAACGGAA
1 GAACGGGTTCACTGAAC---A
*
217841 CGGAACTGGTTCACTGAACA
1 --GAACGGGTTCACTGAACA
217861 GAACGG
1 GAACGG
217867 AACGGAACGG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
18 38 0.69
20 1 0.02
23 16 0.29
ACGTcount: A:0.30, C:0.22, G:0.33, T:0.16
Consensus pattern (18 bp):
GAACGGGTTCACTGAACA
Found at i:217872 original size:33 final size:28
Alignment explanation
Indices: 217833--217912 Score: 133
Period size: 28 Copynumber: 2.9 Consensus size: 28
217823 CTGGTTCACG
*
217833 GAACGGAACGGAACTGGTTCACTGAACA
1 GAACGGAACGGAACGGGTTCACTGAACA
*
217861 GAACGGAACGGAACGGGTTCACTGAACT
1 GAACGGAACGGAACGGGTTCACTGAACA
*
217889 GAACGGAACGGAACAGGTTCACTG
1 GAACGGAACGGAACGGGTTCACTG
217913 CACATCCTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 49 1.00
ACGTcount: A:0.34, C:0.21, G:0.31, T:0.14
Consensus pattern (28 bp):
GAACGGAACGGAACGGGTTCACTGAACA
Found at i:217912 original size:23 final size:23
Alignment explanation
Indices: 217815--217897 Score: 94
Period size: 23 Copynumber: 3.4 Consensus size: 23
217805 CGGGTTCACT
*
217815 GAACGGAACTGGTTCACGGAACG
1 GAACGGAACTGGTTCACTGAACG
217838 GAACGGAACTGGTTCACTGAACAGAACG
1 GAACGGAACTGGTTCACT-----GAACG
* *
217866 GAACGGAACGGGTTCACTGAACT
1 GAACGGAACTGGTTCACTGAACG
217889 GAACGGAAC
1 GAACGGAAC
217898 GGAACAGGTT
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
23 30 0.58
28 22 0.42
ACGTcount: A:0.34, C:0.22, G:0.31, T:0.13
Consensus pattern (23 bp):
GAACGGAACTGGTTCACTGAACG
Found at i:221404 original size:15 final size:14
Alignment explanation
Indices: 221372--221418 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
221362 TAAAATTTGA
*
221372 AAAAATACAAAAACT
1 AAAAATA-AAAAATT
221387 AAAAATAATAAAATT
1 AAAAATAA-AAAATT
221402 -AAAATAAAAAGATT
1 AAAAATAAAAA-ATT
221416 AAA
1 AAA
221419 TCCATAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.11
14 11 0.39
15 14 0.50
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (14 bp):
AAAAATAAAAAATT
Found at i:222398 original size:19 final size:20
Alignment explanation
Indices: 222359--222438 Score: 87
Period size: 20 Copynumber: 4.1 Consensus size: 20
222349 TATCTAAACT
*
222359 TTTTTATATAATT-TTTAGAA
1 TTTTTATA-AATTATTTTGAA
222379 TTTTTATAAA-TATTTTGAA
1 TTTTTATAAATTATTTTGAA
* *
222398 -TTTAAAAAATTATTTTGAA
1 TTTTTATAAATTATTTTGAA
222417 TTTTTGA-AAATTATTTTGAA
1 TTTTT-ATAAATTATTTTGAA
222437 TT
1 TT
222439 ATTTTGTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
18 8 0.15
19 17 0.33
20 26 0.50
21 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTATAAATTATTTTGAA
Found at i:222734 original size:21 final size:20
Alignment explanation
Indices: 222671--222735 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
222661 AAATAATTAC
* *
222671 AAAAAAATCAGAATAATATT
1 AAAAAATTCAAAATAATATT
* *
222691 TAAAAATTCAAAAAAAT-TAT
1 AAAAAATTCAAAATAATAT-T
*
222711 AAAACAATTGAAAATAATATT
1 AAAA-AATTCAAAATAATATT
222732 AAAA
1 AAAA
222736 TACAAAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
19 1 0.03
20 17 0.49
21 16 0.46
22 1 0.03
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAAATTCAAAATAATATT
Found at i:222783 original size:18 final size:18
Alignment explanation
Indices: 222753--222794 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
222743 AATAAACAAA
222753 TAAAAATGATATA-ATAT
1 TAAAAATGATATAGATAT
* *
222770 TAAAAATGGTTATAGCTAT
1 TAAAAAT-GATATAGATAT
222789 TAAAAA
1 TAAAAA
222795 AATTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
19 9 0.43
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (18 bp):
TAAAAATGATATAGATAT
Found at i:224574 original size:2 final size:2
Alignment explanation
Indices: 224567--224593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
224557 AATGACTAAC
224567 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
224594 TAAATCTTGC
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:227970 original size:24 final size:26
Alignment explanation
Indices: 227943--227990 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
227933 AGAGAAATGT
227943 AAATG-TGATATATGA-A-ATTATGAG
1 AAATGATGA-ATATGAGAGATTATGAG
227967 AAATGATGAATATGAGAGATTATG
1 AAATGATGAATATGAGAGATTATG
227991 CCCATATAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (26 bp):
AAATGATGAATATGAGAGATTATGAG
Found at i:228085 original size:23 final size:23
Alignment explanation
Indices: 228053--228123 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
228043 ACGCTAGTGC
*
228053 GCTTACTGTTCAGCACTGT-GTGT
1 GCTTATTGTTCAGCACT-TCGTGT
**
228076 GCTTATTGTTTTGCACTTCGTGT
1 GCTTATTGTTCAGCACTTCGTGT
*
228099 GCTTATTGTTTC-GCACCTCGTGT
1 GCTTATTG-TTCAGCACTTCGTGT
228122 GC
1 GC
228124 CTACTGATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 38 0.93
24 2 0.05
ACGTcount: A:0.10, C:0.23, G:0.24, T:0.44
Consensus pattern (23 bp):
GCTTATTGTTCAGCACTTCGTGT
Found at i:228144 original size:21 final size:20
Alignment explanation
Indices: 228118--228186 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 20
228108 TTCGCACCTC
228118 GTGTGCCTACTGATTTGCACT
1 GTGTGCCTACTGA-TTGCACT
228139 GTGTGCGCCTACTGATTGCACT
1 GTGT--GCCTACTGATTGCACT
*
228161 GTGTGCCTATTGGATTGCACT
1 GTGTGCCTACT-GATTGCACT
228182 GTGTG
1 GTGTG
228187 TGCTTACTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
20 6 0.14
21 18 0.41
22 11 0.25
23 9 0.20
ACGTcount: A:0.13, C:0.22, G:0.29, T:0.36
Consensus pattern (20 bp):
GTGTGCCTACTGATTGCACT
Found at i:231750 original size:18 final size:21
Alignment explanation
Indices: 231727--231770 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 21
231717 AGAATTGTGA
*
231727 AAAAAAT-TATTTAAA-AT-T
1 AAAAAATAAATTTAAATATAT
231745 AAAAAATAAATTTAAATATAT
1 AAAAAATAAATTTAAATATAT
231766 AAAAA
1 AAAAA
231771 TTCCAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 7 0.32
20 2 0.09
21 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAAATAAATTTAAATATAT
Found at i:231770 original size:22 final size:22
Alignment explanation
Indices: 231697--231770 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
231687 CATAAAAATT
**
231697 ATATATATTAAAATAAATTTAGA
1 ATATATAAAAAAATAAATTTA-A
* *
231720 AT-TGTGAAAAAAAT-TATTTAA
1 ATATAT-AAAAAAATAAATTTAA
231741 A-AT-T-AAAAAATAAATTTAA
1 ATATATAAAAAAATAAATTTAA
231760 ATATATAAAAA
1 ATATATAAAAA
231771 TTCCAAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 3 0.08
21 4 0.10
22 11 0.28
23 8 0.20
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATATAAAAAAATAAATTTAA
Found at i:233470 original size:18 final size:18
Alignment explanation
Indices: 233447--233483 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
233437 ACAATTCATA
233447 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
233465 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
233483 T
1 T
233484 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:233817 original size:17 final size:18
Alignment explanation
Indices: 233783--233818 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
233773 TGAATTTCTA
233783 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
233801 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
233818 T
1 T
233819 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:234298 original size:2 final size:2
Alignment explanation
Indices: 234293--234317 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
234283 TTTTTTATGT
234293 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
234318 TAGTTAGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:238079 original size:18 final size:18
Alignment explanation
Indices: 238058--238100 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
238048 TCCGGTGAGA
238058 ATGATGAGGAGTTATCAG
1 ATGATGAGGAGTTATCAG
** * *
238076 ATGATGCTGAGTTTTCGG
1 ATGATGAGGAGTTATCAG
238094 ATGATGA
1 ATGATGA
238101 AAAGGAGGCC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (18 bp):
ATGATGAGGAGTTATCAG
Found at i:244166 original size:28 final size:28
Alignment explanation
Indices: 244123--244221 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 28
244113 CTTGAACAAC
*
244123 AGATAGCCACAAAGGCATCCATAAGCAA
1 AGATAGCCACAAAGGCATCCATAAGAAA
* * *
244151 AGATGGCCACATAGGCTTCCATAAGAAA
1 AGATAGCCACAAAGGCATCCATAAGAAA
* *
244179 AGATAGTCATACAA--CATCCATAA-ACAA
1 AGATAGCCACA-AAGGCATCCATAAGA-AA
*
244206 AGATAGCCACGAAGGC
1 AGATAGCCACAAAGGC
244222 TTTTCCATTA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
26 3 0.05
27 18 0.33
28 33 0.60
29 1 0.02
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.14
Consensus pattern (28 bp):
AGATAGCCACAAAGGCATCCATAAGAAA
Found at i:246107 original size:23 final size:23
Alignment explanation
Indices: 246080--246225 Score: 145
Period size: 23 Copynumber: 6.3 Consensus size: 23
246070 AGGAACACTA
*
246080 GTGTGCTCTCCGATTAGCACTGT
1 GTGTGCTCTCTGATTAGCACTGT
*
246103 GTGTGCTCT-TAGATTAGTACTGT
1 GTGTGCTCTCT-GATTAGCACTGT
* * *
246126 GTGTGCTCTCCGTTTAGCACTTT
1 GTGTGCTCTCTGATTAGCACTGT
* *
246149 GTGTGCTCTCTGTTTTGCAC-GT
1 GTGTGCTCTCTGATTAGCACTGT
* *
246171 CTTGTGCTCTCTGTTTAGCACT-T
1 -GTGTGCTCTCTGATTAGCACTGT
* *
246194 CATGTGCTCTCTGATTAGCACTTT
1 -GTGTGCTCTCTGATTAGCACTGT
246218 GTGTGCTC
1 GTGTGCTC
246226 AGTACTTTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
22 1 0.01
23 102 0.98
24 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (23 bp):
GTGTGCTCTCTGATTAGCACTGT
Found at i:246145 original size:46 final size:45
Alignment explanation
Indices: 246080--246225 Score: 161
Period size: 46 Copynumber: 3.2 Consensus size: 45
246070 AGGAACACTA
* *
246080 GTGTGCTCTCCGATTAGCACTGTGTGTGCTCT-TAGATTAGTACTGT
1 GTGTGCTCTCCGTTTAGCACT-TGTGTGCTCTCT-GATTAGCACTGT
* *
246126 GTGTGCTCTCCGTTTAGCACTTTGTGTGCTCTCTGTTTTGCAC-GT
1 GTGTGCTCTCCGTTTAGCAC-TTGTGTGCTCTCTGATTAGCACTGT
* * * *
246171 CTTGTGCTCTCTGTTTAGCACTTCATGTGCTCTCTGATTAGCACTTT
1 -GTGTGCTCTCCGTTTAGCACTT-GTGTGCTCTCTGATTAGCACTGT
246218 GTGTGCTC
1 GTGTGCTC
246226 AGTACTTTGT
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
45 4 0.05
46 77 0.92
47 3 0.04
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.42
Consensus pattern (45 bp):
GTGTGCTCTCCGTTTAGCACTTGTGTGCTCTCTGATTAGCACTGT
Found at i:247516 original size:29 final size:29
Alignment explanation
Indices: 247477--247598 Score: 111
Period size: 29 Copynumber: 4.2 Consensus size: 29
247467 ACACTCTCAC
* * *
247477 ATAACACAATCAGCTACAAAAGCTCACAT
1 ATAACAGAATCAACCACAAAAGCTCACAT
* * *
247506 ATAACAGAATCAACCACACAGGCTCTCAT
1 ATAACAGAATCAACCACAAAAGCTCACAT
* *
247535 ATAATAGAATCATCCACAAACA-CTCACAT
1 ATAACAGAATCAACCACAAA-AGCTCACAT
* * * * *
247564 ATAACAGATTCAACCATAAAGGCGCTCAT
1 ATAACAGAATCAACCACAAAAGCTCACAT
247593 ATAACA
1 ATAACA
247599 AATGCAGTCA
Statistics
Matches: 73, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.19
Consensus pattern (29 bp):
ATAACAGAATCAACCACAAAAGCTCACAT
Found at i:247612 original size:58 final size:58
Alignment explanation
Indices: 247472--247598 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 58
247462 GTGTTACACT
* * * * * *
247472 CTCACATAACACAATCAGCTACAAA-AGCTCACATATAACAGAATCAACCACACAGGCT
1 CTCATATAACAGAATCATCCACAAACA-CTCACATATAACAGAATCAACCACAAAGGCG
* * *
247530 CTCATATAATAGAATCATCCACAAACACTCACATATAACAGATTCAACCATAAAGGCG
1 CTCATATAACAGAATCATCCACAAACACTCACATATAACAGAATCAACCACAAAGGCG
247588 CTCATATAACA
1 CTCATATAACA
247599 AATGCAGTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 57 0.98
59 1 0.02
ACGTcount: A:0.45, C:0.28, G:0.08, T:0.19
Consensus pattern (58 bp):
CTCATATAACAGAATCATCCACAAACACTCACATATAACAGAATCAACCACAAAGGCG
Found at i:254721 original size:14 final size:15
Alignment explanation
Indices: 254702--254731 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
254692 TAGTTTTATT
254702 ATATTTTTAAA-AAA
1 ATATTTTTAAATAAA
254716 ATATTTTTAAATAAA
1 ATATTTTTAAATAAA
254731 A
1 A
254732 ATAATCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATATTTTTAAATAAA
Found at i:256355 original size:21 final size:21
Alignment explanation
Indices: 256291--256355 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
256281 AATATTCAAA
*
256291 CTTAAA-TATTTTAATTTAAT
1 CTTAAATTATTTCAATTTAAT
* *
256311 CATAAAATT-TTTCAA--TACT
1 C-TTAAATTATTTCAATTTAAT
*
256330 TTTAAATTATTTCAATTTAAT
1 CTTAAATTATTTCAATTTAAT
256351 CTTAA
1 CTTAA
256356 TTTTTTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 6 0.18
19 9 0.27
20 1 0.03
21 16 0.48
22 1 0.03
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (21 bp):
CTTAAATTATTTCAATTTAAT
Found at i:257060 original size:15 final size:15
Alignment explanation
Indices: 257040--257069 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
257030 CATTTACAAG
257040 ATTAAGGCTGTGTCA
1 ATTAAGGCTGTGTCA
257055 ATTAAGGCTGTGTCA
1 ATTAAGGCTGTGTCA
257070 GCCTTGAAAA
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:0.27, C:0.13, G:0.27, T:0.33
Consensus pattern (15 bp):
ATTAAGGCTGTGTCA
Found at i:266773 original size:55 final size:55
Alignment explanation
Indices: 266697--266807 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
266687 AAAGAGTACC
266697 ATGGAAGTTTTTACTGAAAGAATTAAATTATATTTTGCTTGCTTTACAAAAAAAT
1 ATGGAAGTTTTTACTGAAAGAATTAAATTATATTTTGCTTGCTTTACAAAAAAAT
* * *
266752 ATGGAAGTTTTTA-TAGGAAGAATTAAATTATATTTTGTTTGCTTTATAAAAAAAT
1 ATGGAAGTTTTTACT-GAAAGAATTAAATTATATTTTGCTTGCTTTACAAAAAAAT
266807 A
1 A
266808 AATAATTTAA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 1 0.02
55 51 0.98
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (55 bp):
ATGGAAGTTTTTACTGAAAGAATTAAATTATATTTTGCTTGCTTTACAAAAAAAT
Found at i:273175 original size:22 final size:21
Alignment explanation
Indices: 273143--273193 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
273133 ATCTTAGCTC
*
273143 AAAT-TTAAATTAAATAATTA
1 AAATATTAAATTAAATAATAA
* *
273163 AAATATTATAATTTAATTATAA
1 AAATATTA-AATTAAATAATAA
273185 AAATATTAA
1 AAATATTAA
273194 CATAAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 18 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAATATTAAATTAAATAATAA
Found at i:273773 original size:2 final size:2
Alignment explanation
Indices: 273762--273791 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
273752 TGCTTCATCA
273762 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
273792 GTGGGATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:275823 original size:29 final size:30
Alignment explanation
Indices: 275791--276090 Score: 306
Period size: 30 Copynumber: 10.1 Consensus size: 30
275781 AAAAATTATG
275791 TTTTGACCCTCAAAC-TTCCAAAAATTCCAT
1 TTTTGACCCTCAAACTTTCC-AAAATTCCAT
* * *
275821 TTTTAACCCTAAAAC-TTCTAAAATTTACCA-
1 TTTTGACCCTCAAACTTTCCAAAA-TT-CCAT
*
275851 TTTT-ACCCCCAAAC-TTCCAAAAATTCCA-
1 TTTTGACCCTCAAACTTTCC-AAAATTCCAT
*
275879 TTTT-AACCTCAAAACTTTCCAAAATTCCAT
1 TTTTGACCCTC-AAACTTTCCAAAATTCCAT
275909 TTTTGA-CCTCAAAACTTTCCAAAATTCCATT
1 TTTTGACCCTC-AAACTTTCCAAAATTCCA-T
*
275940 TTTTTACCCT-AAACTTTCCAAAATTCCAT
1 TTTTGACCCTCAAACTTTCCAAAATTCCAT
*
275969 TTTTAACCC-CAAAACTTTCCAAAATTCCAT
1 TTTTGACCCTC-AAACTTTCCAAAATTCCAT
275999 TTTT-ACCCTCAAA-TTTCCAAAAATTCCAT
1 TTTTGACCCTCAAACTTTCC-AAAATTCCAT
276028 TTTTGACCC-CAAAACTTTCCAAAATTCCAT
1 TTTTGACCCTC-AAACTTTCCAAAATTCCAT
* * *
276058 TTTT-ATCCACGAAC-TTCCAAAAATTCCAT
1 TTTTGACCCTCAAACTTTCC-AAAATTCCAT
276087 TTTT
1 TTTT
276091 TTAGCTCGAA
Statistics
Matches: 240, Mismatches: 12, Indels: 37
0.83 0.04 0.13
Matches are distributed among these distances:
28 20 0.08
29 81 0.34
30 121 0.50
31 15 0.06
32 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.01, T:0.36
Consensus pattern (30 bp):
TTTTGACCCTCAAACTTTCCAAAATTCCAT
Found at i:275869 original size:59 final size:60
Alignment explanation
Indices: 275791--276062 Score: 341
Period size: 59 Copynumber: 4.6 Consensus size: 60
275781 AAAAATTATG
*
275791 TTTTGACCCTC-AAAC-TTCCAAAAATTCCATTTTTAACCCTAAAAC-TTCTAAAATTTACCA-
1 TTTTGACCC-CAAAACTTTCC-AAAATTCCATTTTTAACCCTAAAACTTTCCAAAA-TT-CCAT
*
275851 TTTT-ACCCCCAAAC-TTCCAAAAATTCCA-TTTTAA-CCTCAAAACTTTCCAAAATTCCAT
1 TTTTGACCCCAAAACTTTCC-AAAATTCCATTTTTAACCCT-AAAACTTTCCAAAATTCCAT
* *
275909 TTTTGACCTCAAAACTTTCCAAAATTCCATTTTTTTACCCT-AAACTTTCCAAAATTCCAT
1 TTTTGACCCCAAAACTTTCCAAAATTCCA-TTTTTAACCCTAAAACTTTCCAAAATTCCAT
* *
275969 TTTTAACCCCAAAACTTTCCAAAATTCCATTTTT-ACCCTCAAA-TTTCCAAAAATTCCAT
1 TTTTGACCCCAAAACTTTCCAAAATTCCATTTTTAACCCTAAAACTTTCC-AAAATTCCAT
276028 TTTTGACCCCAAAACTTTCCAAAATTCCATTTTTA
1 TTTTGACCCCAAAACTTTCCAAAATTCCATTTTTA
276063 TCCACGAACT
Statistics
Matches: 193, Mismatches: 7, Indels: 24
0.86 0.03 0.11
Matches are distributed among these distances:
57 6 0.03
58 28 0.15
59 97 0.50
60 54 0.28
61 5 0.03
62 3 0.02
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (60 bp):
TTTTGACCCCAAAACTTTCCAAAATTCCATTTTTAACCCTAAAACTTTCCAAAATTCCAT
Found at i:276091 original size:119 final size:117
Alignment explanation
Indices: 275791--276242 Score: 385
Period size: 119 Copynumber: 3.8 Consensus size: 117
275781 AAAAATTATG
* * *
275791 TTTTGACCCTCAAAC-TTCCAAAAATTCCATTTTTAACCCTAAAACTTCTAAAATTTACCA-TTT
1 TTTTGACCC-CAAACTTTCC-AAAATTCCATTTTTATCCCT-AAACTTCCAAAAATT-CCATTTT
* *
275854 T-ACCCCCAAAC-TTCCAAAAATT-CCATTTTAACCTCAAAACTTTCC-AAAATTCCAT
62 TAACCCCAAAACTTTCC-AAAATTACCATTTTACCCTC-AAA-TTTCCAAAAATTCCAT
* *
275909 TTTTGACCTCAAAACTTTCCAAAATTCCATTTTTTTACCCTAAACTTTCC-AAAATTCCATTTTT
1 TTTTGACC-CCAAACTTTCCAAAATTCCATTTTTAT-CCCTAAAC-TTCCAAAAATTCCATTTTT
275973 AACCCCAAAACTTTCCAAAATT-CCATTTTTACCCTCAAATTTCCAAAAATTCCAT
63 AACCCCAAAACTTTCCAAAATTACCA-TTTTACCCTCAAATTTCCAAAAATTCCAT
*
276028 TTTTGACCCCAAAACTTTCCAAAATTCCATTTTTATCCAC-GAACTTCCAAAAATTCCATTTTTT
1 TTTTGACCCC-AAACTTTCCAAAATTCCATTTTTATCC-CTAAACTTCCAAAAATTCCA-TTTTT
* * * * * * * * * * *
276092 TAGCTCGAAGCTTTCAAAAATTACCATTTTACCCCCAGATGTCCAAAATTTCCTT
63 AACCCCAAAACTTTCCAAAATTACCATTTTACCCTCAAATTTCCAAAAATTCCAT
* * * * *
276147 TTTTGATCCC-GACTTTTCTCAAAATTAC-TGTTTT-TCCCCTGAA-TGT-CTAAAATTCCATTT
1 TTTTGACCCCAAAC-TTTC-CAAAATTCCAT-TTTTAT-CCCTAAACT-TCCAAAAATTCCA-TT
* *
276207 TTTAA-CTCTAAACTTTCCAAAATTACCATTTTACCC
60 TTTAACCCCAAAACTTTCCAAAATTACCATTTTACCC
276243 CCGAGAGTCC
Statistics
Matches: 285, Mismatches: 29, Indels: 41
0.80 0.08 0.12
Matches are distributed among these distances:
117 37 0.13
118 84 0.29
119 148 0.52
120 16 0.06
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.37
Consensus pattern (117 bp):
TTTTGACCCCAAACTTTCCAAAATTCCATTTTTATCCCTAAACTTCCAAAAATTCCATTTTTAAC
CCCAAAACTTTCCAAAATTACCATTTTACCCTCAAATTTCCAAAAATTCCAT
Done.