Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012354.1 Kokia drynarioides strain JFW-HI SEQ_127356, 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: 155757
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3128 original size:35 final size:35
Alignment explanation
Indices: 3082--3151 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
3072 ATTGTCTAAC
3082 TTCAAAATAGAAAAATTTCGATTAAGCAAACATAA
1 TTCAAAATAGAAAAATTTCGATTAAGCAAACATAA
* *
3117 TTCAAAATAGAAAGATTTTGATTAAGCAAACATAA
1 TTCAAAATAGAAAAATTTCGATTAAGCAAACATAA
3152 AAGTAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (35 bp):
TTCAAAATAGAAAAATTTCGATTAAGCAAACATAA
Found at i:3186 original size:18 final size:18
Alignment explanation
Indices: 3165--3208 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
3155 TAAACTAGAT
3165 AAGAAAAACTAAGAA-CTA
1 AAGAAAAACTAA-AATCTA
*
3183 AAGAAAATCTAAAATCTA
1 AAGAAAAACTAAAATCTA
*
3201 AACAAAAA
1 AAGAAAAA
3209 ACTCTGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.68, C:0.11, G:0.07, T:0.14
Consensus pattern (18 bp):
AAGAAAAACTAAAATCTA
Found at i:4949 original size:12 final size:12
Alignment explanation
Indices: 4917--4951 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4907 AAATGCCCAA
4917 ATTATTATTATC
1 ATTATTATTATC
*
4929 ATTACTATTATC
1 ATTATTATTATC
*
4941 ATTGTTATTAT
1 ATTATTATTAT
4952 TTTTTAGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (12 bp):
ATTATTATTATC
Found at i:5679 original size:149 final size:151
Alignment explanation
Indices: 5375--5742 Score: 505
Period size: 149 Copynumber: 2.4 Consensus size: 151
5365 TGATTTTGGA
* * * *
5375 AAAGTTTTGGTTTTTTTAAACAATTTCGAAATAACAGTTTGGA-TTTTAAGTAAAGTAGTGATTT
1 AAAGTTTTGATTTTTTT-AACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
* *
5439 TCATTAAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAAATCTGTTTTTCAGTTATTTTAAA
65 TCATTAAAAAAGAAAGAAAGTTTATATTTTAAAAAATAAAAAATCTGTTTTTCAGTGATTTTAAA
* *
5504 GAAAAAGTTTAAAATTTTGAAT
130 GAAAAAGTTTAAAATTTTAAAC
*
5526 AAAGTTTTGATATTTTTT-ACTATTTTGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATTT
1 AAAGTTTTGAT-TTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
**
5589 TCATT-AAAAAGGGAGAAAGTTTATATTTTAAAAAATAAAAAATCTGCTTTTT-AGTGA-TTTAA
65 TCATTAAAAAAGAAAGAAAGTTTATATTTTAAAAAATAAAAAATCTG-TTTTTCAGTGATTTTAA
*
5651 AGAAAAAAGTTTAAATTTTTAAAC
129 AG-AAAAAGTTTAAAATTTTAAAC
* *
5675 AAAGTTTTGAATTTTTTTTAAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGAT
1 AAAGTTTTG-A-TTTTTTT-AACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGAT
5740 TTT
63 TTT
5743 GTTTTAATTA
Statistics
Matches: 193, Mismatches: 15, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
148 7 0.04
149 69 0.36
150 50 0.26
151 18 0.09
152 35 0.18
153 14 0.07
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (151 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
CATTAAAAAAGAAAGAAAGTTTATATTTTAAAAAATAAAAAATCTGTTTTTCAGTGATTTTAAAG
AAAAAGTTTAAAATTTTAAAC
Found at i:5778 original size:149 final size:146
Alignment explanation
Indices: 5375--5778 Score: 414
Period size: 150 Copynumber: 2.7 Consensus size: 146
5365 TGATTTTGGA
* * * *
5375 AAAGTTTTG-GTTTTTTTAAACAATTTCGAAATAACAGTTTGGATTTTAAGTAAAGTAGTGATTT
1 AAAGTTTTGATTTTTTTTAAACTATTTCGAAATAAAAGTTTAGATTTTAAGTAAAGTAGTGATTT
*
5439 TCA-TTAAAAAAGAAAGAAAGTTTATATTTTTAAAAATAAAAAATCTGTTTTTCAGTTATTTTAA
66 T-ATTTAAAAAAG--A-AAAGTTTATA-TTTT--AAATAAAAAATCTGTTTTTCAGTGATTTTAA
* *
5503 AGAAAAAGTTTAAAATTTTGAAT
124 AGAAAAAGTTTAAAATTTTAAAC
* *
5526 AAAGTTTTGATATTTTTT--ACTATTTTGAAATAAAAGTTTAGATTTTTAAG-AAAGTAGTGATT
1 AAAGTTTTGATTTTTTTTAAACTATTTCGAAATAAAAGTTTAGA-TTTTAAGTAAAGTAGTGATT
*
5588 TTCA-TTAAAAAGGGAGAAAGTTTATATTTTAAAAAATAAAAAATCTGCTTTTT-AGTGA-TTTA
65 TT-ATTTAAAAA-AGA-AAAGTTTATATTTT---AAATAAAAAATCTG-TTTTTCAGTGATTTTA
*
5650 AAGAAAAAAGTTTAAATTTTTAAAC
123 AAG-AAAAAGTTTAAAATTTTAAAC
*
5675 AAAGTTTTGAATTTTTTTTAAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGAT
1 AAAGTTTTG-ATTTTTTTTAAACTATTTCGAAATAAAAGTTTAGATTTT-AAGTAAAGTAGTGAT
* *
5740 TTTGTTTTAATTAAAAGAAAACTTT-TGATTTTAAA-AAAA
64 TTT-ATTTAA--AAAAGAAAAGTTTAT-ATTTTAAATAAAA
5779 TAGAAGAAAA
Statistics
Matches: 220, Mismatches: 18, Indels: 31
0.82 0.07 0.12
Matches are distributed among these distances:
148 11 0.05
149 59 0.27
150 60 0.27
151 24 0.11
152 31 0.14
153 15 0.07
154 15 0.07
155 2 0.01
156 3 0.01
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (146 bp):
AAAGTTTTGATTTTTTTTAAACTATTTCGAAATAAAAGTTTAGATTTTAAGTAAAGTAGTGATTT
TATTTAAAAAAGAAAAGTTTATATTTTAAATAAAAAATCTGTTTTTCAGTGATTTTAAAGAAAAA
GTTTAAAATTTTAAAC
Found at i:6143 original size:17 final size:17
Alignment explanation
Indices: 6113--6148 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
6103 AAGTAATTAC
*
6113 AAGAATATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
*
6130 AAGAAGATGGAAGGTTA
1 AAGAAGATGAAAGGTTA
6147 AA
1 AA
6149 CATTCATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGGTTA
Found at i:13354 original size:18 final size:18
Alignment explanation
Indices: 13333--13371 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
13323 TACAAGTATA
*
13333 ATTT-CATTTATTAAAGAT
1 ATTTGCATTTAATAAA-AT
13351 ATTTGCATTTAATAAAAT
1 ATTTGCATTTAATAAAAT
13369 ATT
1 ATT
13372 ATTAATATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (18 bp):
ATTTGCATTTAATAAAAT
Found at i:40724 original size:13 final size:13
Alignment explanation
Indices: 40706--40730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40696 CCATTATATA
40706 ATTTTTAGCATTC
1 ATTTTTAGCATTC
40719 ATTTTTAGCATT
1 ATTTTTAGCATT
40731 TTATATTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTTTTAGCATTC
Found at i:46594 original size:18 final size:17
Alignment explanation
Indices: 46571--46614 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
46561 TGAGGATGTT
46571 GAAGAAGAAGAGAAAAGA
1 GAAGAAGAAGAGAAAA-A
* *
46589 GAAGAA-AAAAGGAAAA
1 GAAGAAGAAGAGAAAAA
46605 GAAGAAGAAG
1 GAAGAAGAAG
46615 TTGTTTCGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 7 0.32
17 9 0.41
18 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAGAAGAAGAGAAAAA
Found at i:54657 original size:5 final size:5
Alignment explanation
Indices: 54649--54689 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
54639 ATTTAATCAT
*
54649 TTTTA TTTTA TTTTA TTTTA TTTTTA TTTTA GTTTAA TTTT
1 TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTT
54690 GAGATATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 23 0.72
6 9 0.28
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:54673 original size:11 final size:11
Alignment explanation
Indices: 54647--54689 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
54637 TAATTTAATC
54647 ATTTTTATTTT
1 ATTTTTATTTT
54658 A-TTTTATTTT
1 ATTTTTATTTT
54668 ATTTTTATTTT
1 ATTTTTATTTT
* *
54679 AGTTTAATTTT
1 ATTTTTATTTT
54690 GAGATATTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
ATTTTTATTTT
Found at i:55046 original size:12 final size:12
Alignment explanation
Indices: 55029--55053 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55019 TTTTAGCAAC
55029 TGTCCCATTAAT
1 TGTCCCATTAAT
55041 TGTCCCATTAAT
1 TGTCCCATTAAT
55053 T
1 T
55054 ATACCATAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTCCCATTAAT
Found at i:61005 original size:100 final size:101
Alignment explanation
Indices: 60814--61022 Score: 368
Period size: 100 Copynumber: 2.1 Consensus size: 101
60804 AGCTAAACAA
*
60814 TAATTTAAACTATACATAAATGGTTAAGTTTATACTTTAGCTTAAAAAAAATGTAACACATCTAG
1 TAATTTAAACTATACATAAATGGTTAAATTTATACTTTAGCTTAAAAAAAATGTAACACATCTAG
60879 TTAGTCTAAATGATACAACTGATAACCAAGTCTCCT
66 TTAGTCTAAATGATACAACTGATAACCAAGTCTCCT
60915 TAATTTAAA-TGATACATAAATGGTTAAATTTATACTTTAGCTT-AAAAAAATGTAACACATCTA
1 TAATTTAAACT-ATACATAAATGGTTAAATTTATACTTTAGCTTAAAAAAAATGTAACACATCTA
* *
60978 GTTAGTCTAAATGATATAACTGATAACCTAGTCTCCT
65 GTTAGTCTAAATGATACAACTGATAACCAAGTCTCCT
61015 TAATTTAA
1 TAATTTAA
61023 CCATCAATCT
Statistics
Matches: 104, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
100 64 0.62
101 40 0.38
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (101 bp):
TAATTTAAACTATACATAAATGGTTAAATTTATACTTTAGCTTAAAAAAAATGTAACACATCTAG
TTAGTCTAAATGATACAACTGATAACCAAGTCTCCT
Found at i:64910 original size:28 final size:27
Alignment explanation
Indices: 64879--64968 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
64869 AATCCTTAAA
*
64879 CTTAAACCCTAAACATAAAACCCAAAAC
1 CTTAAACCTTAAACATAAAA-CCAAAAC
* * *
64907 CTTAAAACTTAAACCCTAAATA-TAAAAC
1 CTTAAACCTTAAA-CATAAA-ACCAAAAC
**
64935 CTTAAACCTTAAACACTAAAACTTAAAC
1 CTTAAACCTTAAACA-TAAAACCAAAAC
64963 CTTAAA
1 CTTAAA
64969 TGTGAAACCT
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
27 2 0.04
28 43 0.84
29 5 0.10
30 1 0.02
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (27 bp):
CTTAAACCTTAAACATAAAACCAAAAC
Found at i:64917 original size:35 final size:35
Alignment explanation
Indices: 64862--64956 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
64852 TCGATTTTAT
64862 ACCCTAAAATCCTT-AAACTTAAACCCTAAACATAAA
1 ACCC-AAAA-CCTTAAAACTTAAACCCTAAACATAAA
*
64898 ACCCAAAACCTTAAAACTTAAACCCTAAATATAAA
1 ACCCAAAACCTTAAAACTTAAACCCTAAACATAAA
** *
64933 ACCTTAAACCTTAAACACTAAAAC
1 ACCCAAAACCTTAAA-ACTTAAAC
64957 TTAAACCTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
34 4 0.08
35 38 0.72
36 11 0.21
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (35 bp):
ACCCAAAACCTTAAAACTTAAACCCTAAACATAAA
Found at i:64920 original size:21 final size:21
Alignment explanation
Indices: 64896--64968 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
64886 CCTAAACATA
*
64896 AAACCCAAAACCTTAAAACTT
1 AAACCCTAAACCTTAAAACTT
64917 AAACCCTAAA--TATAAAACCTT
1 AAACCCTAAACCT-TAAAA-CTT
*
64938 AAACCTTAAACAC-TAAAACTT
1 AAACCCTAAAC-CTTAAAACTT
*
64959 AAACCTTAAA
1 AAACCCTAAA
64969 TGTGAAACCT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 1 0.02
20 5 0.11
21 34 0.76
22 5 0.11
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCCTAAACCTTAAAACTT
Found at i:64980 original size:21 final size:20
Alignment explanation
Indices: 64909--64989 Score: 81
Period size: 21 Copynumber: 3.9 Consensus size: 20
64899 CCCAAAACCT
* *
64909 TAAAACTTAAACCCTAAATA
1 TAAACCTTAAACCTTAAATA
*
64929 TAAAACCTTAAACCTTAAACA
1 T-AAACCTTAAACCTTAAATA
* *
64950 CTAAAACTTAAACCTTAAATG
1 -TAAACCTTAAACCTTAAATA
*
64971 TGAAACCTTAAACATTAAA
1 T-AAACCTTAAACCTTAAA
64990 ATTTAAATCC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.04
21 47 0.94
22 1 0.02
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAACCTTAAACCTTAAATA
Found at i:65020 original size:14 final size:14
Alignment explanation
Indices: 64903--65021 Score: 71
Period size: 14 Copynumber: 8.5 Consensus size: 14
64893 ATAAAACCCA
*
64903 AAACCTTAAAACTT
1 AAACCCTAAAACTT
*
64917 AAACCCTAAATA-TA
1 AAACCCTAAA-ACTT
* *
64931 AAACCTTAAACCTT
1 AAACCCTAAAACTT
*
64945 AAACACTAAAACTT
1 AAACCCTAAAACTT
* ** *
64959 AAACCTTAAATGTG
1 AAACCCTAAAACTT
*
64973 AAA-CCTTAAACATT
1 AAACCCTAAAAC-TT
*** * *
64987 AAAATTTAAATCCT
1 AAACCCTAAAACTT
65001 AAACCCTAAAACTT
1 AAACCCTAAAACTT
65015 AAACCCT
1 AAACCCT
65022 GAACTATATA
Statistics
Matches: 73, Mismatches: 28, Indels: 8
0.67 0.26 0.07
Matches are distributed among these distances:
13 4 0.05
14 64 0.88
15 5 0.07
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.26
Consensus pattern (14 bp):
AAACCCTAAAACTT
Found at i:65475 original size:18 final size:18
Alignment explanation
Indices: 65437--65476 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
65427 CATCCGATGC
* *
65437 CTCTTGCTCTTGCTCTTG
1 CTCTTGCTCTTGCCCTGG
65455 CTCTTGCTCTTGCCCTGG
1 CTCTTGCTCTTGCCCTGG
65473 CTCT
1 CTCT
65477 GGTTCTAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.38, G:0.17, T:0.45
Consensus pattern (18 bp):
CTCTTGCTCTTGCCCTGG
Found at i:65478 original size:6 final size:6
Alignment explanation
Indices: 65437--65467 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
65427 CATCCGATGC
65437 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG C
1 CTCTTG CTCTTG CTCTTG CTCTTG CTCTTG C
65468 CCTGGCTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.35, G:0.16, T:0.48
Consensus pattern (6 bp):
CTCTTG
Found at i:65991 original size:43 final size:43
Alignment explanation
Indices: 65943--66038 Score: 140
Period size: 43 Copynumber: 2.2 Consensus size: 43
65933 AACTGCACAA
*
65943 TTAATAACATATCACAATATTAACA-AGAGTCAAGTAATATAAT
1 TTAATAACATACCACAATATTAACACAG-GTCAAGTAATATAAT
* *
65986 TTAATAACATGCCACGATATTAACACAGGTCAAGTAATATAAT
1 TTAATAACATACCACAATATTAACACAGGTCAAGTAATATAAT
*
66029 TCAATAACAT
1 TTAATAACAT
66039 GTCAAGGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 46 0.96
44 2 0.04
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (43 bp):
TTAATAACATACCACAATATTAACACAGGTCAAGTAATATAAT
Found at i:67285 original size:21 final size:21
Alignment explanation
Indices: 67261--67306 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
67251 ATAAATTTGT
67261 ATTACTTACTAACAAAATAAA
1 ATTACTTACTAACAAAATAAA
*
67282 ATTACTTACTAACAAAATTAA
1 ATTACTTACTAACAAAATAAA
67303 ATTA
1 ATTA
67307 AATTAAAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTACTTACTAACAAAATAAA
Found at i:71292 original size:185 final size:185
Alignment explanation
Indices: 70975--71350 Score: 734
Period size: 185 Copynumber: 2.0 Consensus size: 185
70965 GAAAAACATT
*
70975 CTTCAAGAGTATGAGATTTGTTCTAGGCAGTGTGTTCAATTTACAAAGTCGTATATTTTTTATAG
1 CTTCCAGAGTATGAGATTTGTTCTAGGCAGTGTGTTCAATTTACAAAGTCGTATATTTTTTATAG
71040 TTCAAATACTCTAAGCAAAGATAGAAGGGACGTTAAGAGCATTCTTGACATGTGTTCGTCGTTCG
66 TTCAAATACTCTAAGCAAAGATAGAAGGGACGTTAAGAGCATTCTTGACATGTGTTCGTCGTTCG
71105 ATATTAAGAGGTATTTAGGTTTGCCTAATTTTGTTGGAAGACGAAAAAGGGCAAC
131 ATATTAAGAGGTATTTAGGTTTGCCTAATTTTGTTGGAAGACGAAAAAGGGCAAC
71160 CTTCCAGAGTATGAGATTTGTTCTAGGCAGTGTGTTCAATTTACAAAGTCGTATATTTTTTATAG
1 CTTCCAGAGTATGAGATTTGTTCTAGGCAGTGTGTTCAATTTACAAAGTCGTATATTTTTTATAG
71225 TTCAAATACTCTAAGCAAAGATAGAAGGGACGTTAAGAGCATTCTTGACATGTGTTCGTCGTTCG
66 TTCAAATACTCTAAGCAAAGATAGAAGGGACGTTAAGAGCATTCTTGACATGTGTTCGTCGTTCG
*
71290 ATATTAAGAGGTATTTAGGTTTGCCTACTTTTGTTGGAAGACGAAAAAGGGCAAC
131 ATATTAAGAGGTATTTAGGTTTGCCTAATTTTGTTGGAAGACGAAAAAGGGCAAC
71345 CTTCCA
1 CTTCCA
71351 ATCAATGAAG
Statistics
Matches: 189, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 189 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (185 bp):
CTTCCAGAGTATGAGATTTGTTCTAGGCAGTGTGTTCAATTTACAAAGTCGTATATTTTTTATAG
TTCAAATACTCTAAGCAAAGATAGAAGGGACGTTAAGAGCATTCTTGACATGTGTTCGTCGTTCG
ATATTAAGAGGTATTTAGGTTTGCCTAATTTTGTTGGAAGACGAAAAAGGGCAAC
Found at i:73415 original size:27 final size:28
Alignment explanation
Indices: 73375--73427 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
73365 AAAAAATAAT
* *
73375 AATAATAATAAAATT-AATAACAAATCA
1 AATAAAAATAAAATTAAAAAACAAATCA
*
73402 AATAAAAATTAAATTAAAAAACAAAT
1 AATAAAAATAAAATTAAAAAACAAAT
73428 AATTTGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 13 0.59
28 9 0.41
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.25
Consensus pattern (28 bp):
AATAAAAATAAAATTAAAAAACAAATCA
Found at i:73721 original size:24 final size:26
Alignment explanation
Indices: 73661--73725 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
73651 TAAATTGACC
73661 TTCTTCTCCTTC-TTCTTTCTTTCTT
1 TTCTTCTCCTTCTTTCTTTCTTTCTT
*
73686 TCTCTTTCTCCTTCTTTCTTTGTTT-TT
1 T-TC-TTCTCCTTCTTTCTTTCTTTCTT
73713 TTCTT-TCCTTCTT
1 TTCTTCTCCTTCTT
73726 CTCCCTTCTC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 8 0.22
25 3 0.08
26 4 0.11
27 12 0.33
28 9 0.25
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (26 bp):
TTCTTCTCCTTCTTTCTTTCTTTCTT
Found at i:73724 original size:20 final size:20
Alignment explanation
Indices: 73673--73725 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
73663 CTTCTCCTTC
73673 TTCTTTCTTTCTTTCTCTTT
1 TTCTTTCTTTCTTTCTCTTT
* * * *
73693 CTCCTTCTTTCTTTGTTTTT
1 TTCTTTCTTTCTTTCTCTTT
*
73713 TTCTTTCCTTCTT
1 TTCTTTCTTTCTT
73726 CTCCCTTCTC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.02, T:0.72
Consensus pattern (20 bp):
TTCTTTCTTTCTTTCTCTTT
Found at i:73802 original size:23 final size:23
Alignment explanation
Indices: 73776--73821 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
73766 TACCTTTCAA
73776 TTACCCTTAATACCAAGGTCTTT
1 TTACCCTTAATACCAAGGTCTTT
73799 TTACCCTTAATACCAAGGTCTTT
1 TTACCCTTAATACCAAGGTCTTT
73822 CCCTCCCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (23 bp):
TTACCCTTAATACCAAGGTCTTT
Found at i:81202 original size:40 final size:40
Alignment explanation
Indices: 81126--81254 Score: 170
Period size: 40 Copynumber: 3.2 Consensus size: 40
81116 CACTGTAGTT
81126 CATACAGGGGCATCG-AGTGCGTACAAGGACATCGAAGTG
1 CATACAGGGGCATCGAAGTGCGTACAAGGACATCGAAGTG
* *
81165 CATACAGGGGCATCGAAGTGCGTACAATGACACCGAAGTG
1 CATACAGGGGCATCGAAGTGCGTACAAGGACATCGAAGTG
* * * * * *
81205 CATATAGGGACATCAAAGTGCATACAGGGGCATCGAAGTG
1 CATACAGGGGCATCGAAGTGCGTACAAGGACATCGAAGTG
*
81245 CGTACAGGGG
1 CATACAGGGG
81255 GCAATAGACA
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
39 15 0.20
40 61 0.80
ACGTcount: A:0.32, C:0.20, G:0.33, T:0.16
Consensus pattern (40 bp):
CATACAGGGGCATCGAAGTGCGTACAAGGACATCGAAGTG
Found at i:81254 original size:20 final size:20
Alignment explanation
Indices: 81107--81254 Score: 147
Period size: 20 Copynumber: 7.5 Consensus size: 20
81097 TCCGACTTAT
* *
81107 ATACAGGGGCA-CTGTAGTTC
1 ATACAGGGGCATC-GAAGTGC
81127 ATACAGGGGCATCG-AGTGC
1 ATACAGGGGCATCGAAGTGC
* * *
81146 GTACAAGGACATCGAAGTGC
1 ATACAGGGGCATCGAAGTGC
81166 ATACAGGGGCATCGAAGTGC
1 ATACAGGGGCATCGAAGTGC
* ** * *
81186 GTACAATGACACCGAAGTGC
1 ATACAGGGGCATCGAAGTGC
* * *
81206 ATATAGGGACATCAAAGTGC
1 ATACAGGGGCATCGAAGTGC
81226 ATACAGGGGCATCGAAGTGC
1 ATACAGGGGCATCGAAGTGC
*
81246 GTACAGGGG
1 ATACAGGGG
81255 GCAATAGACA
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.14
20 88 0.85
21 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.32, T:0.17
Consensus pattern (20 bp):
ATACAGGGGCATCGAAGTGC
Found at i:82143 original size:39 final size:39
Alignment explanation
Indices: 82096--82174 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
82086 ACTAATTTAG
82096 CCTTAATTTTTAACAACCTTATTTCTATTCACCTAATAC
1 CCTTAATTTTTAACAACCTTATTTCTATTCACCTAATAC
82135 CCTTAATTTTTAACAACCTTATTTCTATTCACCTAATAC
1 CCTTAATTTTTAACAACCTTATTTCTATTCACCTAATAC
82174 C
1 C
82175 AAAACCGTCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (39 bp):
CCTTAATTTTTAACAACCTTATTTCTATTCACCTAATAC
Found at i:83630 original size:21 final size:20
Alignment explanation
Indices: 83606--83653 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
83596 ACAGGTCTCA
*
83606 AGACTTGGTTTGTAAGTCTTG
1 AGACTTGGCTT-TAAGTCTTG
* *
83627 AGACCTAGGCTTTAAGTCTTT
1 AGA-CTTGGCTTTAAGTCTTG
83648 AGACTT
1 AGACTT
83654 AGTTGATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 2 0.09
21 14 0.64
22 6 0.27
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (20 bp):
AGACTTGGCTTTAAGTCTTG
Found at i:86204 original size:40 final size:38
Alignment explanation
Indices: 86122--86197 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 38
86112 AAGTCAATAT
*
86122 AATATTTAAAATTTGAAAAAATTCATAAAAAATAAAAAAA
1 AATATTTAAAATTTAAAAAAATTC--AAAAAATAAAAAAA
*
86162 AATATTTAAATTTTTAAAAAAATTC-AAAAATAAAAA
1 AATATTTAAA-ATTTAAAAAAATTCAAAAAATAAAAA
86198 TTAAAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 11 0.33
40 10 0.30
41 12 0.36
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (38 bp):
AATATTTAAAATTTAAAAAAATTCAAAAAATAAAAAAA
Found at i:86205 original size:32 final size:30
Alignment explanation
Indices: 86148--86206 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
86138 AAAAATTCAT
*
86148 AAAAAATAAAAAAAAATATTTAAATTTTTA
1 AAAAAATAAAAAAAAATATTAAAATTTTTA
86178 AAAAAATTCAAAAATAAAA-ATTAAAATTT
1 AAAAAA-T-AAAAA-AAAATATTAAAATTT
86207 GCAAAATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 6 0.24
31 1 0.04
32 14 0.56
33 4 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (30 bp):
AAAAAATAAAAAAAAATATTAAAATTTTTA
Found at i:86521 original size:9 final size:9
Alignment explanation
Indices: 86509--86550 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
86499 TTTTAATCTT
86509 TATAATATA
1 TATAATATA
86518 TATAATAT-
1 TATAATATA
*
86526 TA-AAAATA
1 TATAATATA
*
86534 AATAATATA
1 TATAATATA
86543 TATAATAT
1 TATAATAT
86551 TAAAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
7 4 0.15
8 3 0.11
9 20 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
TATAATATA
Found at i:86542 original size:25 final size:25
Alignment explanation
Indices: 86510--86560 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
86500 TTTAATCTTT
86510 ATAATATATATAATATTAAAAATAA
1 ATAATATATATAATATTAAAAATAA
86535 ATAATATATATAATATTAAAAATAA
1 ATAATATATATAATATTAAAAATAA
86560 A
1 A
86561 AAAGGGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
ATAATATATATAATATTAAAAATAA
Found at i:87663 original size:26 final size:26
Alignment explanation
Indices: 87629--87680 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
87619 AGAAGAGAAT
87629 AGAAAATAAA-GAAAAAAAAAGTTAAA
1 AGAAAATAAAGGAAAAAAAAA-TTAAA
* *
87655 AGAACATAAAGGGAAAAAAAATTAAA
1 AGAAAATAAAGGAAAAAAAAATTAAA
87681 TTACTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.73, C:0.02, G:0.13, T:0.12
Consensus pattern (26 bp):
AGAAAATAAAGGAAAAAAAAATTAAA
Found at i:92003 original size:45 final size:46
Alignment explanation
Indices: 91947--92041 Score: 147
Period size: 45 Copynumber: 2.1 Consensus size: 46
91937 TGGATCTCGT
* * *
91947 GATTGGACCTTGAGGGAAATTGAACTCATTT-CATTATGAGCTTGG
1 GATTGGACCTTGAAGGAAATTGAACCCATTTCCATTATGAGCTTGA
*
91992 GATTGGGCCTTGAAGGAAATTGAACCCATTTCCATTATGAGCTTGA
1 GATTGGACCTTGAAGGAAATTGAACCCATTTCCATTATGAGCTTGA
92038 GATT
1 GATT
92042 AGGTTGTGGA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 28 0.62
46 17 0.38
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (46 bp):
GATTGGACCTTGAAGGAAATTGAACCCATTTCCATTATGAGCTTGA
Found at i:101224 original size:24 final size:25
Alignment explanation
Indices: 101186--101235 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
101176 TGAACAATAA
* *
101186 ACAAATTTGATCTAGTAAAA-AATC
1 ACAAATTTAAACTAGTAAAACAATC
101210 ACAAATTTAAACTAGTAAAACAATC
1 ACAAATTTAAACTAGTAAAACAATC
101235 A
1 A
101236 AACATGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (25 bp):
ACAAATTTAAACTAGTAAAACAATC
Found at i:105100 original size:15 final size:16
Alignment explanation
Indices: 105074--105104 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
105064 TTTAAAGTTT
105074 ATAAAAATATTTAAAA
1 ATAAAAATATTTAAAA
105090 ATAAAAA-ATTTAAAA
1 ATAAAAATATTTAAAA
105105 TTTAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
ATAAAAATATTTAAAA
Found at i:105497 original size:21 final size:22
Alignment explanation
Indices: 105464--105521 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
105454 ATTAATGTTC
105464 TTAAAATAA-TAATTA-CAAGTG
1 TTAAAA-AATTAATTATCAAGTG
* *
105485 TTGAAAAATTAATTTATTAAGTG
1 TTAAAAAATTAA-TTATCAAGTG
*
105508 TTAAAAAATAAATT
1 TTAAAAAATTAATT
105522 TATTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.07
21 8 0.27
22 5 0.17
23 15 0.50
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
TTAAAAAATTAATTATCAAGTG
Found at i:105506 original size:23 final size:23
Alignment explanation
Indices: 105480--105525 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
105470 TAATAATTAC
* *
105480 AAGTGTTGAAAAATTAATTTATT
1 AAGTGTTAAAAAATAAATTTATT
105503 AAGTGTTAAAAAATAAATTTATT
1 AAGTGTTAAAAAATAAATTTATT
105526 TAAAAATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (23 bp):
AAGTGTTAAAAAATAAATTTATT
Found at i:110520 original size:5 final size:6
Alignment explanation
Indices: 110505--110534 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
110495 TATGCTCTAT
110505 TTTTTC TTTTTC TTTTTC TTTTTCC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTT
110535 TTAACATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:118747 original size:56 final size:56
Alignment explanation
Indices: 118687--118794 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
118677 CAGAATCAGG
** * *
118687 ATAACACTCTACCCGAGCTAGAAGTAGAATAATGCTCTACCCGAGTAAGATTCAAT
1 ATAACACTCTACCAAAGCCAGAAGTAGAATAATGCTCTACCCGAGCAAGATTCAAT
* * * *
118743 ATAACGCTCTACCAAAGCCAGAAGTAGATTAATGCTTTACCTGAGCAAGATT
1 ATAACACTCTACCAAAGCCAGAAGTAGAATAATGCTCTACCCGAGCAAGATT
118795 TAGAATGTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 44 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (56 bp):
ATAACACTCTACCAAAGCCAGAAGTAGAATAATGCTCTACCCGAGCAAGATTCAAT
Found at i:142161 original size:52 final size:52
Alignment explanation
Indices: 142090--142276 Score: 245
Period size: 52 Copynumber: 3.6 Consensus size: 52
142080 GCCATAAACG
* * *
142090 AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATGTGAATCCTTTACGAATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
*
142142 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTGTACGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * *
142194 AAGAGGTCCGATGACT-A-TGTCATCGTGATTATATGAATCCCTTGCGGATT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * *
142244 ATA-AGGTCTGGTGGCTATGTGTCATCGTGAGTA
1 A-AGAGGTCCGATGACTAAGTGTCATCGTGAGTA
142277 AACGAAAGAA
Statistics
Matches: 119, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
50 40 0.34
51 2 0.02
52 77 0.65
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (52 bp):
AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:142268 original size:102 final size:104
Alignment explanation
Indices: 142090--142276 Score: 254
Period size: 102 Copynumber: 1.8 Consensus size: 104
142080 GCCATAAACG
* * *
142090 AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATGTGAATCCTTTACGAATTAAGAGGTCCGATG
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGAATTAAGAGGTCCGATG
142155 ACTAAGTGTCATCGTGAGTATATGAATCCTGTACGGATT
66 ACTAAGTGTCATCGTGAGTATATGAATCCTGTACGGATT
* * * * *
142194 AAGAGGTCCGATGACT-A-TGTCATCGTGATTATATGAATCCCTTGCGGATTATA-AGGTCTGGT
1 AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGAATTA-AGAGGTCCGAT
* *
142256 GGCTATGTGTCATCGTGAGTA
65 GACTAAGTGTCATCGTGAGTA
142277 AACGAAAGAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
102 55 0.76
103 2 0.03
104 15 0.21
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (104 bp):
AAGAGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGAATTAAGAGGTCCGATG
ACTAAGTGTCATCGTGAGTATATGAATCCTGTACGGATT
Found at i:148799 original size:162 final size:158
Alignment explanation
Indices: 148439--149105 Score: 561
Period size: 162 Copynumber: 4.2 Consensus size: 158
148429 CATCATACAG
* * * * *
148439 TTCCATTACTAAAGACTTGAGTTGCAAAAAAGGATACAGGGTACTTTCAACAACAATAAAACCTA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACTTA
* * * **
148504 TATGCT-T--TT-GTTCTATATTATCCAGACTCTTCATTTTCCTAAAGAATCCATG--T--CACA
66 TATGCTCTACTTAATTTTATATTA-CCGGACTCTTCATTTTTGTAAAGAATCCATGTCTAACACA
* * **
148561 TATTCAAACATGGAAAAGGAAGTACAATC
130 TATTCAAACATGGATACGGAAGTATGATC
** * * * *
148590 TTCCATTTCTAAAGACTCGAGCTGCAAAAAAGGATGCAAGGTACTTTTAACAGCAGTAAAACTTA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACTTA
* * *
148655 TATGCTCATAATTAATTTTATGTTACTCGGACTCTTCATATTTTGTAAAAGAATCCATGTCTAAT
66 TATGCTC-TACTTAATTTTATATTAC-CGGACTCTTCAT-TTTTGT-AAAGAATCCATGTCTAAC
* * *
148720 ACATATTCAGACATGGATACGAAAGCATGATC
127 ACATATTCAAACATGGATACGGAAGTATGATC
* * * *
148752 TTCCATCACTAAAGACTTGAGCTGCAAAAAAGGATGCAGGGTACTTTTAACAACAATGAAACATA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACTTA
* * * *** *
148817 TATGCTTCTGCTTAACTCTTA-ATTACCTGTACTCTTCATTTTCT-TAAAGAATTTGTGTTTTAA
66 TATGC-TCTACTTAA-TTTTATATTACC-GGACTCTTCATTTT-TGTAAAGAATCCATG-TCTAA
** *
148880 CACATATTCAGGCATGGATACGGAGGTATGATC
126 CACATATTCAAACATGGATACGGAAGTATGATC
* * * * * * * *
148913 TTCCATCATTACATACTTGAGTTGCAAAAAATGAGGCAAGGCACTTTTAACAGCAATAAAGCTTA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACTTA
* * * *** *
148978 CTCATGCTCAACTTCATGTTACCGT-CC--ACTCTTCATTTTTTGTAAAAGAATCCATATCTAAC
66 -T-ATGCTCTACTTAATTTTATATTACCGGACTCTTCA-TTTTTGT-AAAGAATCCATGTCTAAC
* **
149040 ACATATTCAAAAATGGATGTGG-AGATATGATC
127 ACATATTCAAACATGGATACGGAAG-TATGATC
* *
149072 TTCCATCACTAAAGGCTTGAGTTGCAAGAAAGGA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGA
149106 CATAAGGACA
Statistics
Matches: 412, Mismatches: 80, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
151 62 0.15
153 1 0.00
155 3 0.01
156 19 0.05
157 4 0.01
158 22 0.05
159 62 0.15
160 18 0.04
161 96 0.23
162 115 0.28
163 10 0.02
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (158 bp):
TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATGCAAGGTACTTTTAACAACAATAAAACTTA
TATGCTCTACTTAATTTTATATTACCGGACTCTTCATTTTTGTAAAGAATCCATGTCTAACACAT
ATTCAAACATGGATACGGAAGTATGATC
Found at i:149085 original size:320 final size:312
Alignment explanation
Indices: 148439--149105 Score: 720
Period size: 320 Copynumber: 2.1 Consensus size: 312
148429 CATCATACAG
* *
148439 TTCCATTACTAAAGACTTGAGTTGCAAAAAAGGATACAGGGTACTTTCAACAACAATAAAACCTA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATACAGGGTACTTTCAACAACAATAAAACATA
*
148504 TATGCTTTTGTTCTATATTATCCAGACTCTTCATTTTCCTAAAGAATCCATGTCACATATTCAAA
66 TATGCTTCTGTTCTATATTATCCAGACTCTTCATTTTCCTAAAGAATCCATGTCACATATTCAAA
* * *
148569 CATGGAAAAGGAAGTACAATCTTCCATTTCTAAAGACTCGAGCTGCAAAAAAGGATGCAAGGTAC
131 CATGGAAAAGGAAGTACAATCTTCCATATCTAAAGACTCGAGCTGCAAAAAAGGAGGCAAGGCAC
* * *
148634 TTTTAACAGCAGTAAAACTTATATGCTCATAATTAATTTTATGTTACTCGGACTCTTCATATTTT
196 TTTTAACAGCAATAAAACTTATATGCTCATAATTAATGTTACGTTACTC-GACTCTTCATATTTT
* * * *
148699 GTAAAAGAATCCATGTCTAATACATATTCAGACATGGATACGAAAGCATGATC
260 GTAAAAGAATCCATATCTAACACATATTCAAAAATGGATACGAAAGCATGATC
* * * *
148752 TTCCATCACTAAAGACTTGAGCTGCAAAAAAGGATGCAGGGTACTTTTAACAACAATGAAACATA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATACAGGGTACTTTCAACAACAATAAAACATA
* * * ***
148817 TATGCTTCTGCTTAACTCTTAATTA-CCTGTACTCTTCATTTTCTTAAAGAATTTGTGTTTTAAC
66 TATGCTTCTG-TT--CT-AT-ATTATCCAG-ACTCTTCATTTTCCTAAAGAATCCATG---T--C
** * * * ** * * * * *
148881 ACATATTCAGGCATGGATACGGAGGTATGATCTTCCATCAT-TACATACTTGAGTTGCAAAAAAT
120 ACATATTCAAACATGGAAAAGGAAGTACAATCTTCCAT-ATCTAAAGACTCGAGCTGCAAAAAAG
* * *
148945 GAGGCAAGGCACTTTTAACAGCAATAAAGCTTACTCATGCTCA-ACTTCATGTTACCG-T-C-C-
184 GAGGCAAGGCACTTTTAACAGCAATAAAACTTA-T-ATGCTCATAATTAATGTTA-CGTTACTCG
* ** * *
149005 ACTCTTCATTTTTTGTAAAAGAATCCATATCTAACACATATTCAAAAATGGATGTG-GAGATATG
246 ACTCTTCATATTTTGTAAAAGAATCCATATCTAACACATATTCAAAAATGGATACGAAAG-CATG
149069 ATC
310 ATC
* *
149072 TTCCATCACTAAAGGCTTGAGTTGCAAGAAAGGA
1 TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGA
149106 CATAAGGACA
Statistics
Matches: 292, Mismatches: 46, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
313 68 0.23
314 2 0.01
316 2 0.01
317 4 0.01
318 27 0.09
319 2 0.01
320 86 0.29
321 1 0.00
322 1 0.00
323 80 0.27
324 11 0.04
325 8 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (312 bp):
TTCCATCACTAAAGACTTGAGTTGCAAAAAAGGATACAGGGTACTTTCAACAACAATAAAACATA
TATGCTTCTGTTCTATATTATCCAGACTCTTCATTTTCCTAAAGAATCCATGTCACATATTCAAA
CATGGAAAAGGAAGTACAATCTTCCATATCTAAAGACTCGAGCTGCAAAAAAGGAGGCAAGGCAC
TTTTAACAGCAATAAAACTTATATGCTCATAATTAATGTTACGTTACTCGACTCTTCATATTTTG
TAAAAGAATCCATATCTAACACATATTCAAAAATGGATACGAAAGCATGATC
Found at i:149091 original size:159 final size:160
Alignment explanation
Indices: 148685--149105 Score: 410
Period size: 161 Copynumber: 2.6 Consensus size: 160
148675 TGTTACTCGG
* * * * * *
148685 ACTCTTCATATTTTGTAAAAGAATCCATGTCTAATACATATTCAGACATGGATACGAAAGCATGA
1 ACTCTTCATTTTTTGTAAAAGAATCCATATCTAACACATATTCAGACATGGATAGGAGA-TATGA
* * * *
148750 TCTTCCATCACTAAAGACTTGAGCTGCAAAAAAGGATGCAGGGTACTTTTAACAACAATGAAACA
65 TCTTCCATCACTAAAGACTTGAGTTGCAAAAAAGGAGGCAAGGCACTTTTAACAACAATGAAACA
* *
148815 TATATGCTTCTGCTTAACTCTTAATTACCTGT
130 TATA-GCTTCTGCTCAACTCATAATTACCTGT
* *** * * * *
148847 ACTCTTCATTTTCT-T-AAAGAATTTGTGTTTTAACACATATTCAGGCATGGATACGGAGGTATG
1 ACTCTTCATTTTTTGTAAAAGAATCCAT-ATCTAACACATATTCAGACATGGATA-GGAGATATG
* * * * *
148910 ATCTTCCATCATTACATACTTGAGTTGCAAAAAATGAGGCAAGGCACTTTTAACAGCAAT-AAAG
64 ATCTTCCATCACTAAAGACTTGAGTTGCAAAAAAGGAGGCAAGGCACTTTTAACAACAATGAAA-
*
148974 C-T-TA-C-TCATGCTCAACTTCAT-GTTACC-GT
128 CATATAGCTTC-TGCTCAAC-TCATAATTACCTGT
* * *
149003 CCACTCTTCATTTTTTGTAAAAGAATCCATATCTAACACATATTCAAAAATGGATGTGGAGATAT
1 --ACTCTTCATTTTTTGTAAAAGAATCCATATCTAACACATATTCAGACATGGAT-AGGAGATAT
* *
149068 GATCTTCCATCACTAAAGGCTTGAGTTGCAAGAAAGGA
63 GATCTTCCATCACTAAAGACTTGAGTTGCAAAAAAGGA
149106 CATAAGGACA
Statistics
Matches: 207, Mismatches: 42, Indels: 23
0.76 0.15 0.08
Matches are distributed among these distances:
156 4 0.02
157 13 0.06
158 16 0.08
159 62 0.30
160 20 0.10
161 78 0.38
162 14 0.07
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (160 bp):
ACTCTTCATTTTTTGTAAAAGAATCCATATCTAACACATATTCAGACATGGATAGGAGATATGAT
CTTCCATCACTAAAGACTTGAGTTGCAAAAAAGGAGGCAAGGCACTTTTAACAACAATGAAACAT
ATAGCTTCTGCTCAACTCATAATTACCTGT
Found at i:150805 original size:37 final size:38
Alignment explanation
Indices: 150764--150846 Score: 95
Period size: 37 Copynumber: 2.2 Consensus size: 38
150754 TAGAAAATTA
*
150764 ATAAAATTAAAAAATTA-TTAACAA-TT-AATAAAAGTTT
1 ATAAAATTAAAAAATTACTTAA-AATTTCAATAAAA-CTT
150801 ATAAAA-T-AAAAATTATCTTAAAATTTCAATAAAACTT
1 ATAAAATTAAAAAATTA-CTTAAAATTTCAATAAAACTT
150838 ATAAAATTA
1 ATAAAATTA
150847 TAAAGAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
35 8 0.21
36 3 0.08
37 20 0.51
38 8 0.21
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (38 bp):
ATAAAATTAAAAAATTACTTAAAATTTCAATAAAACTT
Found at i:151183 original size:9 final size:9
Alignment explanation
Indices: 151160--151250 Score: 69
Period size: 10 Copynumber: 9.4 Consensus size: 9
151150 CATTTAAATT
151160 TTTTACATAA
1 TTTTA-ATAA
151170 TTTTTAATAA
1 -TTTTAATAA
151180 TTTTAAATATA
1 TTTT-AATA-A
151191 TTTT-ATAA
1 TTTTAATAA
* *
151199 TAATTATTAA
1 T-TTTAATAA
151209 TTTCTAATAA
1 TTT-TAATAA
*
151219 TCTTTTATGAA
1 T-TTTAAT-AA
151230 TTTT-ATAA
1 TTTTAATAA
151238 TTTTAATAA
1 TTTTAATAA
151247 TTTT
1 TTTT
151251 TTACTTAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
8 8 0.12
9 20 0.30
10 24 0.36
11 15 0.22
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:151919 original size:14 final size:14
Alignment explanation
Indices: 151900--151945 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
151890 TTATTTGATT
151900 GAAAATGATTTTTA
1 GAAAATGATTTTTA
*
151914 GAAAATGATTTTCA
1 GAAAATGATTTTTA
*
151928 GAAAATGATTTCTA
1 GAAAATGATTTTTA
151942 GAAA
1 GAAA
151946 TAAATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (14 bp):
GAAAATGATTTTTA
Done.