Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015319.1 Kokia drynarioides strain JFW-HI SEQ_130365, 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: 446018
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 477 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4667 original size:31 final size:31
Alignment explanation
Indices: 4631--4708 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
4621 CATAAAACAC
* *
4631 TTTAAA-AACTTAAATAGAATTATAAATGATA
1 TTTAAATAA-TTAAATAGAATGATAAATAATA
* *
4662 TTTAAATAATTCAATATAATGATAAATAATA
1 TTTAAATAATTAAATAGAATGATAAATAATA
*
4693 TTTAAATAATTTAATA
1 TTTAAATAATTAAATA
4709 CAATAATATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
31 39 0.95
32 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (31 bp):
TTTAAATAATTAAATAGAATGATAAATAATA
Found at i:5648 original size:31 final size:31
Alignment explanation
Indices: 5610--5746 Score: 160
Period size: 31 Copynumber: 4.5 Consensus size: 31
5600 TTAATATAAT
5610 ATTTGGTACCTAAACTTGACATTTTTTTCTA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTA
* * *
5641 ATTTGGTACTTAAA--T-A-TTTTTTTGTCCA
1 ATTTGGTACCTAAACTTGACATTTTTT-TCTA
*
5669 ATTTGGTA-CTCAAACTTGACATTTTTTCCTA
1 ATTTGGTACCT-AAACTTGACATTTTTTTCTA
5700 ATTTGGTACCTAAACTTGACATTTTTTT-TA
1 ATTTGGTACCTAAACTTGACATTTTTTTCTA
* *
5730 AGTTGGTACTTAAACTT
1 ATTTGGTACCTAAACTT
5747 TTTGGAGTCC
Statistics
Matches: 89, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
27 7 0.08
28 15 0.17
29 1 0.01
30 18 0.20
31 40 0.45
32 8 0.09
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.48
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTA
Found at i:5762 original size:89 final size:90
Alignment explanation
Indices: 5610--5801 Score: 266
Period size: 89 Copynumber: 2.1 Consensus size: 90
5600 TTAATATAAT
* *** *
5610 ATTTGGTACCTAAACTTGACATTTTTTTCTAATTTGGTACTTAAATATTTTTTTGTCCAATTTGG
1 ATTTGGTACCTAAACTTGACATTTTTTTCTAAGTTGGTACTTAAATATTTTGGAGTCCAATTTGA
5675 TA-CTCAAACTTGACAT-TTTTTCCTA
66 TACCT-AAACTTGAC-TCTTTTTCCTA
5700 ATTTGGTACCTAAACTTGACATTTTTTT-TAAGTTGGTACTTAAACT-TTTTGGAGTCCAATTTG
1 ATTTGGTACCTAAACTTGACATTTTTTTCTAAGTTGGTACTTAAA-TATTTTGGAGTCCAATTTG
* *
5763 ATACCTGAACTTGACTCTTTTTTCTA
65 ATACCTAAACTTGACTCTTTTTCCTA
5789 ATTTGGTACCTAA
1 ATTTGGTACCTAA
5802 TATTTTATAA
Statistics
Matches: 92, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
88 1 0.01
89 60 0.65
90 31 0.34
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACATTTTTTTCTAAGTTGGTACTTAAATATTTTGGAGTCCAATTTGA
TACCTAAACTTGACTCTTTTTCCTA
Found at i:6017 original size:31 final size:31
Alignment explanation
Indices: 5982--6064 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 31
5972 AAAAAGTTGG
* *
5982 GGTACCAAATTAGC-AAAACATGTCAAGTTTA
1 GGTACCAAATTAGCAAAAAC-TGTCAAGCTCA
*
6013 GGTACCAAATTAGGAAAAACTGTCAAGCTCA
1 GGTACCAAATTAGCAAAAACTGTCAAGCTCA
*
6044 GGTATCAAATTGAGTCAAAAA
1 GGTACCAAATT-AG-CAAAAA
6065 AAATTTTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 32 0.73
32 7 0.16
33 5 0.11
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (31 bp):
GGTACCAAATTAGCAAAAACTGTCAAGCTCA
Found at i:6683 original size:30 final size:30
Alignment explanation
Indices: 6647--6708 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
6637 ATTTATTTTA
6647 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
*
6677 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTATTATTTTAGAGGCAT
6707 TT
1 TT
6709 ATTTGTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGGCAT
Found at i:13118 original size:41 final size:41
Alignment explanation
Indices: 13054--13140 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
13044 GTGGTGGAAA
*
13054 AACCCTATTTTTTACAAATTGCCCATCATGTACATTACCAT
1 AACCCTATTTTTTACAAACTGCCCATCATGTACATTACCAT
* *
13095 AACCTTATTTTTTACAAACTGCCCATCATGTACGTTACCAT
1 AACCCTATTTTTTACAAACTGCCCATCATGTACATTACCAT
13136 AACCC
1 AACCC
13141 ATATACCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (41 bp):
AACCCTATTTTTTACAAACTGCCCATCATGTACATTACCAT
Found at i:15992 original size:29 final size:28
Alignment explanation
Indices: 15950--16006 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
15940 TATGGTTTAA
15950 TGTGTAATTGTATACATAAATTATGATTT
1 TGTGTAATTGTATACA-AAATTATGATTT
* *
15979 TGTGTAATTTTATACAAAATTTTGATTT
1 TGTGTAATTGTATACAAAATTATGATTT
16007 GATCCAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 11 0.42
29 15 0.58
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (28 bp):
TGTGTAATTGTATACAAAATTATGATTT
Found at i:29619 original size:23 final size:23
Alignment explanation
Indices: 29587--29632 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
29577 GCTGGGGAAA
29587 CAATAAGCACACACAGTGCAATC
1 CAATAAGCACACACAGTGCAATC
*
29610 CAATAGGCACACACAGTGCAATC
1 CAATAAGCACACACAGTGCAATC
29633 AGTAGGCGCA
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:0.41, C:0.30, G:0.15, T:0.13
Consensus pattern (23 bp):
CAATAAGCACACACAGTGCAATC
Found at i:29644 original size:22 final size:22
Alignment explanation
Indices: 29593--29720 Score: 89
Period size: 23 Copynumber: 5.7 Consensus size: 22
29583 GAAACAATAA
*
29593 GCACACACAGTGCAATCCAATAG
1 GCACACACAGTGCAAT-CAGTAG
29616 GCACACACAGTGCAATCAGTAG
1 GCACACACAGTGCAATCAGTAG
* * * *
29638 GCGCACATAGCGCAAATCAGTAA
1 GCACACACAGTGC-AATCAGTAG
* *
29661 GCACACGA-AGTGCGAAACAGTAA
1 GCACAC-ACAGTGC-AATCAGTAG
* * * *
29684 GAACACAAAGTGCGAAACAGTAA
1 GCACACACAGTGC-AATCAGTAG
*
29707 G-ACACAAAGTGCAA
1 GCACACACAGTGCAA
29721 AACAGTAAGT
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
21 2 0.02
22 27 0.29
23 62 0.67
24 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.22, T:0.11
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:29681 original size:23 final size:22
Alignment explanation
Indices: 29655--29729 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 22
29645 TAGCGCAAAT
*
29655 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAG-ACACAAAGTGCGAAA
29678 CAGTAAGAACACAAAGTGCGAAA
1 CAGTAAG-ACACAAAGTGCGAAA
*
29701 CAGTAAGACACAAAGTGCAAAA
1 CAGTAAGACACAAAGTGCGAAA
29723 CAGTAAG
1 CAGTAAG
29730 TGTGCTAGCG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 21 0.43
23 28 0.57
ACGTcount: A:0.49, C:0.19, G:0.23, T:0.09
Consensus pattern (22 bp):
CAGTAAGACACAAAGTGCGAAA
Found at i:35606 original size:28 final size:26
Alignment explanation
Indices: 35539--35611 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
35529 CGAAGTACTT
* *
35539 AACAGTAAGCACACAAGAGCTGGGGA
1 AACAATAAGCACACAAGTGCTGGGGA
35565 AACAATAAGCACACAAGTGCTGGGGA
1 AACAATAAGCACACAAGTGCTGGGGA
35591 AACAATAAGCACACACAGTGC
1 AACAATAAGCACACA-AGTGC
35612 AATCCAGTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
26 39 0.89
27 5 0.11
ACGTcount: A:0.44, C:0.22, G:0.25, T:0.10
Consensus pattern (26 bp):
AACAATAAGCACACAAGTGCTGGGGA
Found at i:35629 original size:23 final size:22
Alignment explanation
Indices: 35599--35642 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
35589 GAAACAATAA
35599 GCACACACAGTGCAATCCAGTAG
1 GCACACACAGTGCAAT-CAGTAG
35622 GCACACACAGTGCAATCAGTA
1 GCACACACAGTGCAATCAGTA
35643 AGTGCACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.36, C:0.30, G:0.20, T:0.14
Consensus pattern (22 bp):
GCACACACAGTGCAATCAGTAG
Found at i:35687 original size:23 final size:23
Alignment explanation
Indices: 35655--35714 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
35645 TGCACATAAC
* * *
35655 GCAAATCAGTATGCACACGAAGT
1 GCAAAACAGTAAGCACACAAAGT
35678 G-AGAAACAGTAAGCACACAAAGT
1 GCA-AAACAGTAAGCACACAAAGT
35701 GCAAAACAGTAAGC
1 GCAAAACAGTAAGC
35715 GCGCTAGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.12
Consensus pattern (23 bp):
GCAAAACAGTAAGCACACAAAGT
Found at i:37983 original size:21 final size:21
Alignment explanation
Indices: 37941--37983 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
37931 TCAACAAAAT
**
37941 AAAAAATTTTAAAATATTTAA
1 AAAAAATTTTAAAATAACTAA
**
37962 AAAAAATTTTAATTTAACTAA
1 AAAAAATTTTAAAATAACTAA
37983 A
1 A
37984 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAAATTTTAAAATAACTAA
Found at i:38889 original size:15 final size:15
Alignment explanation
Indices: 38865--38905 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
38855 TTATATTATT
*
38865 TTAATAATTAATTAA
1 TTAATTATTAATTAA
*
38880 TTAATTATTAATTAT
1 TTAATTATTAATTAA
38895 TTATATTATTA
1 TTA-ATTATTA
38906 TTTTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTATTAATTAA
Found at i:38893 original size:19 final size:19
Alignment explanation
Indices: 38854--38907 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
38844 TATTTTATCG
*
38854 ATTATATTATTTTAATAATTA
1 ATTATATTA--TTATTAATTA
38875 ATTA-ATTAATTATTAATTA
1 ATTATATT-ATTATTAATTA
*
38894 TTTATATTATTATT
1 ATTATATTATTATT
38908 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 18 0.62
20 6 0.21
21 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATATTATTATTAATTA
Found at i:50098 original size:16 final size:18
Alignment explanation
Indices: 50072--50104 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50062 CTGATATAAA
50072 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
50089 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
50105 CCTAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:53723 original size:6 final size:6
Alignment explanation
Indices: 53684--53721 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
53674 CAAGTCATAT
*
53684 GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC GGACTC GG
1 GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC GG
53722 ACGAGCCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.03, C:0.32, G:0.50, T:0.16
Consensus pattern (6 bp):
GGGCTC
Found at i:70783 original size:9 final size:9
Alignment explanation
Indices: 70765--70817 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
70755 GTCAGTAAAT
70765 AATT-TTAA
1 AATTATTAA
70773 AATTATTAA
1 AATTATTAA
70782 AATTATT--
1 AATTATTAA
70789 --TT-TTAA
1 AATTATTAA
70795 AA-TA-TAA
1 AATTATTAA
70802 AATTATTAA
1 AATTATTAA
70811 AATTATT
1 AATTATT
70818 TTAAAATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.16
8 6 0.16
9 21 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:70812 original size:29 final size:27
Alignment explanation
Indices: 70770--70826 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 27
70760 TAAATAATTT
70770 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTA--TTTTAAAATA
70799 TAAAATTATTAAAATTATTTTAAAATA
1 TAAAATTATTAAAATTATTTTAAAATA
70826 T
1 T
70827 CATCATCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 11 0.39
29 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAAATTATTAAAATTATTTTAAAATA
Found at i:70824 original size:20 final size:20
Alignment explanation
Indices: 70761--70817 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
70751 TCACGTCAGT
*
70761 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
70781 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
70801 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
70818 TTAAAATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:72308 original size:22 final size:22
Alignment explanation
Indices: 72283--72327 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
72273 GAAAACCGAG
* * *
72283 TAATTAAACTCCATTTTCTTTT
1 TAATAAAAATCCATGTTCTTTT
72305 TAATAAAAATCCATGTTCTTTT
1 TAATAAAAATCCATGTTCTTTT
72327 T
1 T
72328 CATTCCAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.02, T:0.51
Consensus pattern (22 bp):
TAATAAAAATCCATGTTCTTTT
Found at i:76003 original size:15 final size:14
Alignment explanation
Indices: 75983--76024 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
75973 ATATTAAATT
75983 ATATTTTGAAATAAA
1 ATATTTT-AAATAAA
*
75998 ATATTTTACATTAAA
1 ATATTTTA-AATAAA
76013 ATATTTTAAATA
1 ATATTTTAAATA
76025 TTTTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (14 bp):
ATATTTTAAATAAA
Found at i:77076 original size:15 final size:15
Alignment explanation
Indices: 77056--77140 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 15
77046 ATAAAATTAC
77056 AATTAAATATAATTT
1 AATTAAATATAATTT
* *
77071 AATTAAAAATAATAAAT
1 AATTAAATATAAT--TT
* * *
77088 ATTTTAATCATATTTT
1 AATTAAAT-ATAATTT
*
77104 AATT--ATATTA-TT
1 AATTAAATATAATTT
77116 -ATTAAATATAATTT
1 AATTAAATATAATTT
77130 AA-TAAATATAA
1 AATTAAATATAA
77141 AAATATATAA
Statistics
Matches: 52, Mismatches: 11, Indels: 15
0.67 0.14 0.19
Matches are distributed among these distances:
11 3 0.06
12 2 0.04
13 7 0.13
14 13 0.25
15 13 0.25
16 4 0.08
17 6 0.12
18 4 0.08
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATAATTT
Found at i:77152 original size:24 final size:24
Alignment explanation
Indices: 77121--77206 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
77111 TTATTATTAA
77121 ATATAATTTAATAAATATAAAAAT
1 ATATAATTTAATAAATATAAAAAT
*
77145 ATATAATTTAATAATATTATTAAAAT
1 ATATAATTTAATAA-A-TATAAAAAT
*
77171 AT-GAA-TTAATAAA-ATAAAAAT
1 ATATAATTTAATAAATATAAAAAT
77192 ATATAATATTAATAA
1 ATATAAT-TTAATAA
77207 TTAAAACAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
21 9 0.17
22 2 0.04
23 1 0.02
24 28 0.53
25 3 0.06
26 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (24 bp):
ATATAATTTAATAAATATAAAAAT
Found at i:77179 original size:59 final size:57
Alignment explanation
Indices: 77056--77179 Score: 135
Period size: 59 Copynumber: 2.1 Consensus size: 57
77046 ATAAAATTAC
* * * *
77056 AATTAAATATAATTTAATTAAAAATAATAAATATTTTAATCATATTTTAATTATATT
1 AATTAAATATAATTTAATTAAAAATAAAAAATATTTTAATAATATTTTAATAATATG
*
77113 ATTATTAAATATAATTTAA-TAAATATAAAAATATATAATTTAATAATATTATTAA-AATATG
1 A--ATTAAATATAATTTAATTAAAAATAAAAA-ATAT--TTTAATAATATT-TTAATAATATG
77174 AATTAA
1 AATTAA
77180 TAAAATAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
57 1 0.02
58 10 0.18
59 25 0.45
61 16 0.29
62 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (57 bp):
AATTAAATATAATTTAATTAAAAATAAAAAATATTTTAATAATATTTTAATAATATG
Found at i:77188 original size:47 final size:49
Alignment explanation
Indices: 77101--77207 Score: 157
Period size: 48 Copynumber: 2.2 Consensus size: 49
77091 TTAATCATAT
*
77101 TTTAATTATATTATTATTAAATATAATTTAATAAATATAAAAATATATAA
1 TTTAATAATATTATTA-TAAATATAATTTAATAAATATAAAAATATATAA
77151 TTTAATAATATTATTA-AAATATGAA-TTAATAAA-ATAAAAATATATAA
1 TTTAATAATATTATTATAAATAT-AATTTAATAAATATAAAAATATATAA
77198 TATTAATAAT
1 T-TTAATAAT
77208 TAAAACAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
47 15 0.28
48 22 0.41
49 2 0.04
50 15 0.28
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (49 bp):
TTTAATAATATTATTATAAATATAATTTAATAAATATAAAAATATATAA
Found at i:78944 original size:20 final size:20
Alignment explanation
Indices: 78920--78959 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
78910 GTATCTTATA
78920 AAAAATTAAAAAAATATAAAT
1 AAAAA-TAAAAAAATATAAAT
* *
78941 AAAAATATATAAATATAAA
1 AAAAATAAAAAAATATAAA
78960 CAGATAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAATAAAAAAATATAAAT
Found at i:78945 original size:14 final size:14
Alignment explanation
Indices: 78926--78955 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
78916 TATAAAAAAT
78926 TAAAAAAATATAAA
1 TAAAAAAATATAAA
*
78940 TAAAAATATATAAA
1 TAAAAAAATATAAA
78954 TA
1 TA
78956 TAAACAGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAAAAAATATAAA
Found at i:93418 original size:22 final size:22
Alignment explanation
Indices: 93392--93443 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
93382 ACCAATACAA
93392 AACCCATATCCCTAAAACACAC
1 AACCCATATCCCTAAAACACAC
*
93414 AACCCATATCCCTAAAACACAT
1 AACCCATATCCCTAAAACACAC
93436 AACCCATA
1 AACCCATA
93444 ATCTTGAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.15
Consensus pattern (22 bp):
AACCCATATCCCTAAAACACAC
Found at i:93535 original size:14 final size:14
Alignment explanation
Indices: 93518--93545 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
93508 ACCCGAATCT
93518 TGTAACCTTAAACC
1 TGTAACCTTAAACC
93532 TGTAACCTTAAACC
1 TGTAACCTTAAACC
93546 CGTCATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TGTAACCTTAAACC
Found at i:95238 original size:29 final size:29
Alignment explanation
Indices: 95176--95244 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
95166 AAAAAGGTAT
*
95176 TTTTTAATATTTTAATATTTAATATTATAG
1 TTTTT-ATTTTTTAATATTTAATATTATAG
95206 TTTTCTATTTTTTAA-ATTTAA-ATTTAATA-
1 TTTT-TATTTTTTAATATTTAATA-TT-ATAG
95235 TTTTTATTTT
1 TTTTTATTTT
95245 AGTTGCCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
28 7 0.20
29 12 0.34
30 15 0.43
31 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (29 bp):
TTTTTATTTTTTAATATTTAATATTATAG
Found at i:103086 original size:2 final size:2
Alignment explanation
Indices: 103079--103134 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
103069 TGTAAAAAGA
*
103079 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
103121 AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG
103135 TGAGTAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:132472 original size:23 final size:25
Alignment explanation
Indices: 132446--132492 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
132436 ACTATTAAAA
*
132446 TTTAAAAAA-A-AAAAAACAAATTT
1 TTTAAAAAATAGAAAAAAAAAATTT
132469 TTTAAAAAATAGAAAAAAAAAATT
1 TTTAAAAAATAGAAAAAAAAAATT
132493 ATAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 1 0.05
25 11 0.52
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (25 bp):
TTTAAAAAATAGAAAAAAAAAATTT
Found at i:133604 original size:31 final size:29
Alignment explanation
Indices: 133566--133644 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 29
133556 ATTTTAAAAT
133566 TATATATGAA-TTATGGATTAATATATAATTG
1 TATATATGAACTT-T-GATT-ATATATAATTG
* * *
133597 TATATATGAACTTTGATTTTATGTAATTT
1 TATATATGAACTTTGATTATATATAATTG
*
133626 TATATATGAAGTTTTGATT
1 TATATATGAA-CTTTGATT
133645 TGATTCAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 18 0.43
30 11 0.26
31 11 0.26
32 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.13, T:0.51
Consensus pattern (29 bp):
TATATATGAACTTTGATTATATATAATTG
Found at i:136949 original size:86 final size:86
Alignment explanation
Indices: 136848--137074 Score: 303
Period size: 86 Copynumber: 2.6 Consensus size: 86
136838 TTATGAGGAA
*
136848 AAACGCCGTTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGGT
* *
136913 CTTTAGCGGCGTTTTTCCAAC
66 CTTTAACGGCGCTTTTCCAAC
* * * *
136934 AAACGTCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCGCAAACGCCGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGGT
*
136999 CTTTAACGGTGCTTTTCCAAC
66 CTTTAACGGCGCTTTTCCAAC
* * ** ** *
137020 AAACGCCGCTAAAGAGCAT-AGTCTTTAACAACATTTTTCTCACAAACGCCACTAA
1 AAACGCCGCTAAAGAACATGA-TCTTTAGCGGCGCTTTTCCCACAAACGCCACTAA
137075 TATTAACAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
86 121 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAACATGGT
CTTTAACGGCGCTTTTCCAAC
Found at i:137048 original size:43 final size:43
Alignment explanation
Indices: 136848--137046 Score: 290
Period size: 43 Copynumber: 4.6 Consensus size: 43
136838 TTATGAGGAA
* * *
136848 AAACGCCGTTAAAGAACATGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAAC
* *
136891 AAACGCCACTAAAGAACATGGTCTTTAGCGGCGTTTTTCCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAAC
* **
136934 AAACGTCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCCGC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAAC
* *
136977 AAACGCCGCTAAAGAACATGGTCTTTAACGGTGCTTTTCCAAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAAC
* *
137020 AAACGCCGCTAAAGAGCATAGTCTTTA
1 AAACGCCGCTAAAGAACATGGTCTTTA
137047 ACAACATTTT
Statistics
Matches: 139, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 139 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCCAAC
Found at i:137398 original size:20 final size:20
Alignment explanation
Indices: 137373--137410 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
137363 AATTCTTAAC
137373 AAAATTGAAACAAAAAGTAT
1 AAAATTGAAACAAAAAGTAT
* *
137393 AAAATTTAGACAAAAAGT
1 AAAATTGAAACAAAAAGT
137411 TTCTATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (20 bp):
AAAATTGAAACAAAAAGTAT
Found at i:138595 original size:2 final size:2
Alignment explanation
Indices: 138588--138620 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
138578 GAGAAAAATG
138588 AT 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 AT A
138621 AATCACGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:139550 original size:22 final size:23
Alignment explanation
Indices: 139524--139567 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
139514 TAAAATGCTG
*
139524 CATTAGTAGAATAT-CAAAGCAA
1 CATTAGTAAAATATCCAAAGCAA
139546 CATTAGTAAAATATCCAAAGCA
1 CATTAGTAAAATATCCAAAGCA
139568 GGCACAAATC
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:0.50, C:0.16, G:0.11, T:0.23
Consensus pattern (23 bp):
CATTAGTAAAATATCCAAAGCAA
Found at i:140388 original size:41 final size:41
Alignment explanation
Indices: 140325--140511 Score: 232
Period size: 41 Copynumber: 4.6 Consensus size: 41
140315 GTGTTTTTAT
* *
140325 CATAAACGCCGCTAATGCTCTGAGCTTTAGCGGCGCTTGCC
1 CATAAACGCCGCTATTGATCTGAGCTTTAGCGGCGCTTGCC
* * * *
140366 CATAAATGCTGCTATTGATCTGACCTTTAGTGGCGCTTGCC
1 CATAAACGCCGCTATTGATCTGAGCTTTAGCGGCGCTTGCC
* * *
140407 CATAAGCGCCGTTATTGATCTGAGCTTTAGTGGCGCTTGCC
1 CATAAACGCCGCTATTGATCTGAGCTTTAGCGGCGCTTGCC
* * **
140448 CATAAGCGCCGCTATTGCTCTGAATTTTAGCGGCGCTTGCC
1 CATAAACGCCGCTATTGATCTGAGCTTTAGCGGCGCTTGCC
*
140489 CA-AAACCGCCGCTATTGCTCTGA
1 CATAAA-CGCCGCTATTGATCTGA
140512 CCTCAGCTAT
Statistics
Matches: 128, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 2 0.02
41 126 0.98
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (41 bp):
CATAAACGCCGCTATTGATCTGAGCTTTAGCGGCGCTTGCC
Found at i:140897 original size:28 final size:29
Alignment explanation
Indices: 140865--140922 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
140855 GTGGCGATTT
140865 CAAATGAACAATAAGTGATGAGCTC-TTA
1 CAAATGAACAATAAGTGATGAGCTCATTA
* *
140893 CAAATGCACAGTAAGTGATGAGCTCATTA
1 CAAATGAACAATAAGTGATGAGCTCATTA
140922 C
1 C
140923 TGTGGTGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (29 bp):
CAAATGAACAATAAGTGATGAGCTCATTA
Found at i:142070 original size:20 final size:21
Alignment explanation
Indices: 142036--142077 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
142026 AATCAAAGTC
*
142036 TATTATTTATTTATTCTTTGG
1 TATTATTTATATATTCTTTGG
142057 TATT-TTTATATATTCTTTGG
1 TATTATTTATATATTCTTTGG
142077 T
1 T
142078 TTTAGTATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.19, C:0.05, G:0.10, T:0.67
Consensus pattern (21 bp):
TATTATTTATATATTCTTTGG
Found at i:142910 original size:16 final size:16
Alignment explanation
Indices: 142889--142938 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
142879 TTCTTAATAT
142889 AATTATTTTTATATTA
1 AATTATTTTTATATTA
*
142905 AATTATATTTTGA-AATA
1 AATTAT-TTTT-ATATTA
*
142922 AAATA-TTTTATATTA
1 AATTATTTTTATATTA
142937 AA
1 AA
142939 AGATTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
14 1 0.04
15 9 0.32
16 6 0.21
17 11 0.39
18 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
AATTATTTTTATATTA
Found at i:156279 original size:18 final size:19
Alignment explanation
Indices: 156256--156299 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
156246 GTTCAAAGTG
*
156256 TAATTAAATTAAAATT-TT
1 TAATTAAACTAAAATTATT
*
156274 TAATT-AACTAAATTTATT
1 TAATTAAACTAAAATTATT
156292 TAATTAAA
1 TAATTAAA
156300 AAATCTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 12 0.55
19 2 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TAATTAAACTAAAATTATT
Found at i:162432 original size:24 final size:24
Alignment explanation
Indices: 162364--162435 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
162354 TTAAGTTATA
*
162364 ATTAAAAT-TAATTATAAATATGAA-
1 ATTAAAATATATTTATAAA-AT-AAT
*
162388 ATTAAAA-A-ATTTAATTGAAATAAT
1 ATTAAAATATATTT-A-TAAAATAAT
162412 ATTAAAATATATTTATAAAATAAT
1 ATTAAAATATATTTATAAAATAAT
162436 TATATAATAC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
23 5 0.13
24 25 0.64
25 5 0.13
26 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (24 bp):
ATTAAAATATATTTATAAAATAAT
Found at i:171337 original size:6 final size:6
Alignment explanation
Indices: 171326--171386 Score: 65
Period size: 6 Copynumber: 10.7 Consensus size: 6
171316 GACTTTAAGA
* * * *
171326 TAAATT TAAATT TAAA-T TAAATT TAAA-A TAAATT TAGACT TAAA-A
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
171371 TAAATT TAAATT TAAA
1 TAAATT TAAATT TAAA
171387 ATAAATCCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 13 0.29
6 32 0.71
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:171345 original size:11 final size:11
Alignment explanation
Indices: 171326--171392 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
171316 GACTTTAAGA
171326 TAAATTTAAATT
1 TAAA-TTAAATT
171338 TAAATTAAATT
1 TAAATTAAATT
*
171349 TAAAATAAATT
1 TAAATTAAATT
* *
171360 TAGACTTAAA-A
1 TA-AATTAAATT
171371 TAAATTTAAATT
1 TAAA-TTAAATT
*
171383 TAAAATAAAT
1 TAAATTAAAT
171393 CCAATTTGGT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.02
11 31 0.69
12 13 0.29
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:171346 original size:17 final size:17
Alignment explanation
Indices: 171326--171392 Score: 91
Period size: 17 Copynumber: 3.9 Consensus size: 17
171316 GACTTTAAGA
*
171326 TAAATTTAAATTTAAA-T
1 TAAATTTAAA-ATAAATT
171343 TAAATTTAAAATAAATT
1 TAAATTTAAAATAAATT
* *
171360 TAGACTTAAAATAAATT
1 TAAATTTAAAATAAATT
171377 TAAATTTAAAATAAAT
1 TAAATTTAAAATAAAT
171393 CCAATTTGGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
16 4 0.09
17 40 0.91
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAAATAAATT
Found at i:171359 original size:28 final size:28
Alignment explanation
Indices: 171319--171380 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
171309 TAATTTGGAC
* * *
171319 TTTAAGATAAATTTAAATTTAAATTAAA
1 TTTAAAATAAATTTAAACTTAAAATAAA
*
171347 TTTAAAATAAATTTAGACTTAAAATAAA
1 TTTAAAATAAATTTAAACTTAAAATAAA
171375 TTTAAA
1 TTTAAA
171381 TTTAAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.40
Consensus pattern (28 bp):
TTTAAAATAAATTTAAACTTAAAATAAA
Found at i:172672 original size:25 final size:24
Alignment explanation
Indices: 172643--172699 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
172633 ATAATAAAAT
172643 AAAAAATTCAGAA-AAAAAAAAAGA
1 AAAAAATTCA-AAGAAAAAAAAAGA
* *
172667 AGAAAAATTCAAAGAACATAAAAGA
1 A-AAAAATTCAAAGAAAAAAAAAGA
172692 AAAAAATT
1 AAAAAATT
172700 AAATTTCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.74, C:0.05, G:0.09, T:0.12
Consensus pattern (24 bp):
AAAAAATTCAAAGAAAAAAAAAGA
Found at i:182623 original size:21 final size:21
Alignment explanation
Indices: 182599--182698 Score: 102
Period size: 21 Copynumber: 4.9 Consensus size: 21
182589 ATTCACATAA
*
182599 AAATTATAAAAAATATTAATT
1 AAATTATAAAAAATATTAAAT
182620 AAATTAT--AAAATA--AAAT
1 AAATTATAAAAAATATTAAAT
* *
182637 AAAATAATTAAAAATATTAAAT
1 -AAATTATAAAAAATATTAAAT
*
182659 AAATTATAAAAAAAATTAAAT
1 AAATTATAAAAAATATTAAAT
*
182680 AATATTA-AAAAAAAATTAA
1 AA-ATTATAAAAAATATTAA
182699 CTCTTACCAT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.04
18 6 0.09
19 6 0.09
20 6 0.09
21 39 0.57
22 8 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATTATAAAAAATATTAAAT
Found at i:182652 original size:39 final size:38
Alignment explanation
Indices: 182598--182683 Score: 127
Period size: 39 Copynumber: 2.2 Consensus size: 38
182588 TATTCACATA
* *
182598 AAAATTATAAAAAATATTAATTAAATTATAAAATAAAAT
1 AAAATAATAAAAAATATTAAATAAATTATAAAA-AAAAT
*
182637 AAAATAATTAAAAATATTAAATAAATTATAAAAAAAAT
1 AAAATAATAAAAAATATTAAATAAATTATAAAAAAAAT
*
182675 TAAATAATA
1 AAAATAATA
182684 TTAAAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 12 0.29
39 30 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (38 bp):
AAAATAATAAAAAATATTAAATAAATTATAAAAAAAAT
Found at i:184858 original size:56 final size:56
Alignment explanation
Indices: 184791--184904 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
184781 GAGCTACCAT
184791 TTAGCGAAGTCAATGATCCTCTCCAATTCTTTACACTTGATCAAACATTTACTTTA
1 TTAGCGAAGTCAATGATCCTCTCCAATTCTTTACACTTGATCAAACATTTACTTTA
* *
184847 TTAGCGAAGTCAGTGATCCTCTCCAATTCTTTACACTTGATCAAACCTTTACTTTA
1 TTAGCGAAGTCAATGATCCTCTCCAATTCTTTACACTTGATCAAACATTTACTTTA
184903 TT
1 TT
184905 TAAATACTCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (56 bp):
TTAGCGAAGTCAATGATCCTCTCCAATTCTTTACACTTGATCAAACATTTACTTTA
Found at i:188931 original size:17 final size:17
Alignment explanation
Indices: 188892--188931 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
188882 CTGTAGTATA
*
188892 ATTGTCCTTGCATTATT
1 ATTGTCATTGCATTATT
* *
188909 AATGTCATTGCATTTTT
1 ATTGTCATTGCATTATT
188926 ATTGTC
1 ATTGTC
188932 GCTGCATCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (17 bp):
ATTGTCATTGCATTATT
Found at i:191420 original size:21 final size:21
Alignment explanation
Indices: 191394--191436 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
191384 TCGATATCCG
*
191394 ATAGAATTATCTATCAATTAT
1 ATAGAATTATCTATCAACTAT
191415 ATAGAATTATCTATCAACTAT
1 ATAGAATTATCTATCAACTAT
191436 A
1 A
191437 CTTGCATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.40
Consensus pattern (21 bp):
ATAGAATTATCTATCAACTAT
Found at i:193701 original size:9 final size:9
Alignment explanation
Indices: 193681--193717 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
193671 TTTAAAATTC
193681 AAAAATAT-
1 AAAAATATA
193689 AAAAATATA
1 AAAAATATA
*
193698 AAAAAAATA
1 AAAAATATA
193707 AAAAAT-TA
1 AAAAATATA
193715 AAA
1 AAA
193718 GTATTATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
8 13 0.50
9 13 0.50
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAATATA
Found at i:193716 original size:17 final size:19
Alignment explanation
Indices: 193681--193717 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
193671 TTTAAAATTC
193681 AAAAATATAAAAATATAAA
1 AAAAATATAAAAATATAAA
193700 AAAAATA-AAAAAT-TAAA
1 AAAAATATAAAAATATAAA
193717 A
1 A
193718 GTATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAATATAAAAATATAAA
Found at i:193838 original size:2 final size:2
Alignment explanation
Indices: 193833--193867 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
193823 ATATATATAT
193833 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
193868 ATTACAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:203257 original size:17 final size:17
Alignment explanation
Indices: 203237--203272 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
203227 AACATTATTC
203237 TAGTATT-TATATTATAG
1 TAGTATTATATATT-TAG
203254 TAGTATTATATATTTAG
1 TAGTATTATATATTTAG
203271 TA
1 TA
203273 TGAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (17 bp):
TAGTATTATATATTTAG
Found at i:205704 original size:15 final size:14
Alignment explanation
Indices: 205673--205703 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
205663 TTATACTATC
205673 TTTGGGATGTTTTT
1 TTTGGGATGTTTTT
205687 TTTGGGATGTTTTT
1 TTTGGGATGTTTTT
205701 TTT
1 TTT
205704 TTGTTAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.26, T:0.68
Consensus pattern (14 bp):
TTTGGGATGTTTTT
Found at i:209506 original size:90 final size:86
Alignment explanation
Indices: 209368--209569 Score: 239
Period size: 90 Copynumber: 2.3 Consensus size: 86
209358 CCAACTTAAA
* *
209368 AAAAAAAGGCAATTAAGCCCCT-CTTTTTTTTACACTCATTTGGGTACTTAAACTTTCAAAATGC
1 AAAAAAA-GCAATTAAGCCCCTACTTTTTTTTACACTCAATTGGATACTTAAACTTTCAAAATGC
* *
209432 ATTAAAAAGGTCC-TCAAACCTTTT
65 ATCAAAAA-GACCTTCAAA-C-TTT
* * * * *
209456 CAAAAAAAGCAATTAAGCCTCTACTTTCTTTTTGCACTTAATTGGATACTTTAACTTTTAAAATG
1 -AAAAAAAGCAATTAAGCCCCTACTTT-TTTTTACACTCAATTGGATACTTAAACTTTCAAAATG
209521 CATCAAAAAGACCTTCAAACTTT
64 CATCAAAAAGACCTTCAAACTTT
*
209544 AAAAAAA-AAATTAAGCCCCTACTTTT
1 AAAAAAAGCAATTAAGCCCCTACTTTT
209570 ATTAAAAAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
85 1 0.01
86 16 0.16
87 7 0.07
88 16 0.16
89 15 0.15
90 44 0.44
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (86 bp):
AAAAAAAGCAATTAAGCCCCTACTTTTTTTTACACTCAATTGGATACTTAAACTTTCAAAATGCA
TCAAAAAGACCTTCAAACTTT
Found at i:209652 original size:19 final size:19
Alignment explanation
Indices: 209619--209700 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
209609 TAAATATTAT
*
209619 TAAAAATTAGAAAAAAAATA
1 TAAAAATT-GTAAAAAAATA
*
209639 TAAAAATTGTAAAAATATA
1 TAAAAATTGTAAAAAAATA
***
209658 -AAAAATTGTAAAATTTTA
1 TAAAAATTGTAAAAAAATA
* *
209676 TAAAAATCGTAAAAAATTA
1 TAAAAATTGTAAAAAAATA
209695 TAAAAA
1 TAAAAA
209701 ATATAGAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
18 16 0.30
19 30 0.56
20 8 0.15
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (19 bp):
TAAAAATTGTAAAAAAATA
Found at i:209660 original size:28 final size:27
Alignment explanation
Indices: 209606--209775 Score: 119
Period size: 28 Copynumber: 5.9 Consensus size: 27
209596 CCAATAAAGG
* *
209606 TTATAAATATTATTAAAAATTAGAAAAAAA
1 TTATAAAAATTA-TAAAAA-TA-TAAAAAA
* *
209636 ATATAAAAATTGTAAAAATATAAAAAA
1 TTATAAAAATTATAAAAATATAAAAAA
* * *
209663 TTGTAAAATTTTATAAAAATCGTAAAAAA
1 TTATAAAA-ATTATAAAAAT-ATAAAAAA
* *
209692 TTATAAAAAATATAGAAATATAAAAAAA
1 TTATAAAAATTATAAAAATAT-AAAAAA
* *
209720 TTAT-AAAATTTTATAAAGTCATAAGAAAA
1 TTATAAAAATTATA-AAAAT-ATAA-AAAA
209749 TTATACAAAA-TATAAAGAAATATAAAA
1 TTATA-AAAATTAT-AA-AAATATAAAA
209776 TTCGTAAAAA
Statistics
Matches: 110, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
27 20 0.18
28 34 0.31
29 32 0.29
30 16 0.15
31 8 0.07
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (27 bp):
TTATAAAAATTATAAAAATATAAAAAA
Found at i:209680 original size:57 final size:57
Alignment explanation
Indices: 209606--209736 Score: 158
Period size: 56 Copynumber: 2.3 Consensus size: 57
209596 CCAATAAAGG
* * *
209606 TTATAAATATTATTA-AAAATTAGAAAAAAAATATAAAAATTGTAAAAATAT-AAAAAA
1 TTATAAA-ATT-TTATAAAAATAGAAAAAAAATATAAAAAATATAAAAATATAAAAAAA
* * * * *
209663 TTGTAAAATTTTATAAAAATCGTAAAAAATTATAAAAAATATAGAAATATAAAAAAA
1 TTATAAAATTTTATAAAAATAGAAAAAAAATATAAAAAATATAAAAATATAAAAAAA
209720 TTATAAAATTTTATAAA
1 TTATAAAATTTTATAAA
209737 GTCATAAGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
55 3 0.05
56 32 0.51
57 28 0.44
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (57 bp):
TTATAAAATTTTATAAAAATAGAAAAAAAATATAAAAAATATAAAAATATAAAAAAA
Found at i:209749 original size:57 final size:57
Alignment explanation
Indices: 209630--209775 Score: 179
Period size: 56 Copynumber: 2.5 Consensus size: 57
209620 AAAAATTAGA
* * * * * *
209630 AAAAAAATATAAAAATTGTAAAAATAT-AAAAAATTGTAAAATTTTATAAAAATCGT
1 AAAAAATTATAAAAAATATAGAAATATAAAAAAATTATAAAATTTTATAAAAATCAT
*
209686 AAAAAATTATAAAAAATATAGAAATATAAAAAAATTATAAAATTTTAT-AAAGTCAT
1 AAAAAATTATAAAAAATATAGAAATATAAAAAAATTATAAAATTTTATAAAAATCAT
*
209742 AAGAAAATTATACAAAATATAAAGAAATATAAAA
1 AA-AAAATTATA-AAAA-ATATAGAAATATAAAA
209776 TTCGTAAAAA
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
56 31 0.40
57 28 0.36
58 4 0.05
59 15 0.19
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (57 bp):
AAAAAATTATAAAAAATATAGAAATATAAAAAAATTATAAAATTTTATAAAAATCAT
Found at i:209784 original size:57 final size:55
Alignment explanation
Indices: 209651--209784 Score: 155
Period size: 57 Copynumber: 2.3 Consensus size: 55
209641 AAAATTGTAA
* *
209651 AAATATAAAAAATTGTAAAATTTTATAAAAATCGTAAAAAATTATAAAAAATATAG
1 AAATAT-AAAAATTGTAAAATTTTATAAAAATCATAAAAAATTATAAAAAATAAAG
* *
209707 AAATATAAAAAAATTATAAAATTTTAT-AAAGTCATAAGAAAATTATACAAAATATAAAG
1 AAATAT--AAAAATTGTAAAATTTTATAAAAATCATAA-AAAATTATA-AAAA-ATAAAG
209766 AAATAT-AAAATTCGTAAAA
1 AAATATAAAAATT-GTAAAA
209785 AAAATTATAA
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
56 20 0.29
57 33 0.49
58 4 0.06
59 11 0.16
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (55 bp):
AAATATAAAAATTGTAAAATTTTATAAAAATCATAAAAAATTATAAAAAATAAAG
Found at i:209796 original size:10 final size:10
Alignment explanation
Indices: 209614--209801 Score: 78
Period size: 10 Copynumber: 19.5 Consensus size: 10
209604 GGTTATAAAT
*
209614 ATTATTAAAA
1 ATTATAAAAA
*
209624 ATTAGAAAAA
1 ATTATAAAAA
*
209634 A-AATATAAAA
1 ATTATA-AAAA
*
209644 ATTGT-AAAA
1 ATTATAAAAA
209653 A-TATAAAAA
1 ATTATAAAAA
* *
209662 ATTGTAAAAT
1 ATTATAAAAA
*
209672 TTTAT-AAAA
1 ATTATAAAAA
**
209681 ATCGTAAAAA
1 ATTATAAAAA
209691 ATTATAAAAA
1 ATTATAAAAA
*
209701 A-TAT-AGAA
1 ATTATAAAAA
209709 A-TATAAAAAA
1 ATTAT-AAAAA
209719 ATTAT--AAA
1 ATTATAAAAA
* *
209727 ATTTTATAAA
1 ATTATAAAAA
* *
209737 GTCATAAGAAA
1 ATTATAA-AAA
*
209748 ATTATACAAA
1 ATTATAAAAA
209758 A-TATAAAGAA
1 ATTATAAA-AA
209768 A-TAT-AAAA
1 ATTATAAAAA
* *
209776 TTCGTAAAAAAA
1 AT--TATAAAAA
209788 ATTAT-AAAA
1 ATTATAAAAA
209797 ATTAT
1 ATTAT
209802 CATACCAAAA
Statistics
Matches: 130, Mismatches: 32, Indels: 33
0.67 0.16 0.17
Matches are distributed among these distances:
8 18 0.14
9 36 0.28
10 58 0.45
11 13 0.10
12 5 0.04
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:210116 original size:19 final size:20
Alignment explanation
Indices: 210071--210123 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
210061 TTTTAATAAA
*
210071 TTCTAAAGTTT-TTATATTT
1 TTCTAAAATTTATTATATTT
*
210090 TTATTAAAATTTATTA-ATTT
1 TT-CTAAAATTTATTATATTT
210110 TTCTAAAATTTATT
1 TTCTAAAATTTATT
210124 TTTTATAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 13 0.45
20 13 0.45
21 3 0.10
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (20 bp):
TTCTAAAATTTATTATATTT
Found at i:210311 original size:92 final size:92
Alignment explanation
Indices: 210155--210361 Score: 301
Period size: 92 Copynumber: 2.3 Consensus size: 92
210145 TTTTAATAAG
* * *
210155 AGCAAGAGCTTAATTG-TTTTTTTGAAAAATTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCA
1 AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCA
*
210219 AGTACCCAATTGAAT-GGAGAAAAAAAA
66 AGTACCCAATTGAATACGA-AAAAAAAA
* *
210246 AGCAAGGGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGATCTTTTTTATGCATTTTGAAAGTTCA
1 AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCA
* *
210311 AGTGCTCAATTGAATACGAAAAAAAAA
66 AGTACCCAATTGAATACGAAAAAAAAA
* *
210338 AGGAGGGGCTTAATTGCTTTTTTT
1 AGCAAGGGCTTAATTGCTTTTTTT
210362 TTAAGTTTGA
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
91 15 0.14
92 87 0.84
93 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (92 bp):
AGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCA
AGTACCCAATTGAATACGAAAAAAAAA
Found at i:214152 original size:58 final size:59
Alignment explanation
Indices: 214043--214153 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 59
214033 AATTGGACCT
* *
214043 AAAAAAATTTAAGTACCAACATAAAAAAATAGTATCAAATTCAGATACCAAATTGAATA
1 AAAAAAATTTAAATACCAACATAAAAAAATAGTATCAAATTCAAATACCAAATTGAATA
* * *
214102 AAAAAAATTTTAAATACTAA-ATTAAAAAAA-A-TATCAAATTTAAATTCCAAAT
1 AAAAAAA-TTTAAATACCAACA-TAAAAAAATAGTATCAAATTCAAATACCAAAT
214154 ATTATATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 18 0.40
59 9 0.20
60 18 0.40
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (59 bp):
AAAAAAATTTAAATACCAACATAAAAAAATAGTATCAAATTCAAATACCAAATTGAATA
Found at i:219612 original size:18 final size:18
Alignment explanation
Indices: 219597--219641 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
219587 TTCCTCTTCT
219597 TCTTCTTCTTCTTCTTTC
1 TCTTCTTCTTCTTCTTTC
219615 TCTTCTTCTTCTTCTTTC
1 TCTTCTTCTTCTTCTTTC
219633 TCTTCTTCT
1 TCTTCTTCT
219642 CGTAATTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTCTTCTTCTTCTTTC
Found at i:219653 original size:3 final size:3
Alignment explanation
Indices: 219585--219641 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
219575 CTTTGTTTGC
*
219585 TCT TCC TCT TCT TCT TCT TCT TCT TCT T-T CTCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT TCT
219630 T-T CTCT TCT TCT
1 TCT -TCT TCT TCT
219642 CGTAATTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 2 0.04
3 44 0.92
4 2 0.04
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:226893 original size:45 final size:45
Alignment explanation
Indices: 226844--227002 Score: 203
Period size: 45 Copynumber: 3.5 Consensus size: 45
226834 AAGTGGTGTC
* *
226844 ATAGTATGTTTCAACTATGGTCTTATTCATTTTTGATGTATTGCT
1 ATAGTATCTTTCAACTATGGTCTTGTTCATTTTTGATGTATTGCT
* * ** *
226889 ATAGTATCTTTTAACTATTGTCTTGTTCATTTCCGATGTATTGCC
1 ATAGTATCTTTCAACTATGGTCTTGTTCATTTTTGATGTATTGCT
* * * *
226934 ATAGTATCTTTCAACCATGGTCTTGTTCATTTTTGGTATAGTG-T
1 ATAGTATCTTTCAACTATGGTCTTGTTCATTTTTGATGTATTGCT
226978 CATAGTATCTTTCAACTATGGTCTT
1 -ATAGTATCTTTCAACTATGGTCTT
227003 TCTTGTTTCA
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 96 1.00
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.48
Consensus pattern (45 bp):
ATAGTATCTTTCAACTATGGTCTTGTTCATTTTTGATGTATTGCT
Found at i:227017 original size:45 final size:45
Alignment explanation
Indices: 226839--227048 Score: 168
Period size: 45 Copynumber: 4.7 Consensus size: 45
226829 TCCTGAAGTG
* * *
226839 GTGTCATAGTATGTTTCAACTATGGTCTTATTCATTTTTGATGTAT-
1 GTGTCATAGTATCTTTCAACTATGGTC-T-TTCATTTTTCAGGTATA
* * * *
226885 -TG-CTATAGTATCTTTTAACTATTGTCTTGTTCA-TTTCCGATGTAT-
1 GTGTC-ATAGTATCTTTCAACTATGGTC-T-TTCATTTTTC-AGGTATA
* *
226930 -TGCCATAGTATCTTTCAACCATGGTCTTGTTCATTTTT--GGTATA
1 GTGTCATAGTATCTTTCAACTATGGTC-T-TTCATTTTTCAGGTATA
226974 GTGTCATAGTATCTTTCAACTATGGTCTTTC-TTGTTTCAGGTATA
1 GTGTCATAGTATCTTTCAACTATGGTCTTTCATT-TTTCAGGTATA
* * *
227019 ATGTCATAATATCTTTCAACCATGGTCTTT
1 GTGTCATAGTATCTTTCAACTATGGTCTTT
227049 TTTTTCGTTT
Statistics
Matches: 139, Mismatches: 16, Indels: 19
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.01
43 10 0.07
44 5 0.04
45 118 0.85
46 4 0.03
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (45 bp):
GTGTCATAGTATCTTTCAACTATGGTCTTTCATTTTTCAGGTATA
Found at i:227032 original size:90 final size:90
Alignment explanation
Indices: 226840--227047 Score: 240
Period size: 90 Copynumber: 2.3 Consensus size: 90
226830 CCTGAAGTGG
* * * * *
226840 TGTCATAGTATGTTTCAACTATGGTCTTATTCATTTTTGATGTATTGCTATAGTATCTTTTAACT
1 TGTCATAGTATCTTTCAACCATGGTCTTATTCATTTTTGATATAGTGCTATAGTATCTTTCAACT
* * * *
226905 ATTGTCTTGTTCATTTCCGATGTAT
66 ATGGTCTTGTTCATTTCAGATATAA
* * *
226930 TGCCATAGTATCTTTCAACCATGGTCTTGTTCATTTTTGGTATAGTG-TCATAGTATCTTTCAAC
1 TGTCATAGTATCTTTCAACCATGGTCTTATTCATTTTTGATATAGTGCT-ATAGTATCTTTCAAC
** *
226994 TATGGTCTT-TCTTGTTTCAGGTATAA
65 TATGGTCTTGT-TCATTTCAGATATAA
*
227020 TGTCATAATATCTTTCAACCATGGTCTT
1 TGTCATAGTATCTTTCAACCATGGTCTT
227048 TTTTTTCGTT
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
89 2 0.02
90 97 0.98
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.48
Consensus pattern (90 bp):
TGTCATAGTATCTTTCAACCATGGTCTTATTCATTTTTGATATAGTGCTATAGTATCTTTCAACT
ATGGTCTTGTTCATTTCAGATATAA
Found at i:228928 original size:17 final size:17
Alignment explanation
Indices: 228888--228930 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
228878 TGTTGCTAAT
* *
228888 ATTTTACTTTGTTTAAA
1 ATTTTAATTTATTTAAA
* *
228905 ATATTAATTTATTTATA
1 ATTTTAATTTATTTAAA
228922 ATTTTAATT
1 ATTTTAATT
228931 CAATATACTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAATTTATTTAAA
Found at i:238505 original size:24 final size:24
Alignment explanation
Indices: 238446--238510 Score: 114
Period size: 23 Copynumber: 2.8 Consensus size: 24
238436 GTATACTGGT
*
238446 TAACCATTCTGGGCTCATAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
238470 TAA-CATTCTGGGCTCGTAAGAGC
1 TAACCATTCTGGGCTCGTAAGAGC
238493 TAACCATTCTGGGCTCGT
1 TAACCATTCTGGGCTCGT
238511 GTGAGTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (24 bp):
TAACCATTCTGGGCTCGTAAGAGC
Found at i:243535 original size:52 final size:52
Alignment explanation
Indices: 243452--243699 Score: 297
Period size: 52 Copynumber: 4.8 Consensus size: 52
243442 GCCATAAATG
*
243452 AAGAGGTCCT-ATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAGAGGT-CTGATGATTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
243504 AAGAGGTCTGATGATTAAGTGTCATCATGAGTATATGAATCCTTTACCGATT
1 AAGAGGTCTGATGATTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
243556 AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTCACGGATT
1 AAGAGGTCTGATGATTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * * * *
243608 AATAGGTCCGATAACTT-TGTGTCATCGTGAGTATATGAATCCCTTGCGGATT
1 AAGAGGTCTGATGA-TTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * * *
243660 ATA-ATGTCTGGT-CTCTATGTGTCATCGTGAGTATATGAAT
1 A-AGAGGTCTGATGAT-TAAGTGTCATCGTGAGTATATGAAT
243700 AAAGTGAAAT
Statistics
Matches: 172, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 3 0.02
52 166 0.97
53 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (52 bp):
AAGAGGTCTGATGATTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:244631 original size:15 final size:14
Alignment explanation
Indices: 244613--244642 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
244603 TTTGTATAAT
244613 ATAATGATAAGATGA
1 ATAATGATAA-ATGA
244628 ATAATGATAAATGA
1 ATAATGATAAATGA
244642 A
1 A
244643 CAGTAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.27
Consensus pattern (14 bp):
ATAATGATAAATGA
Found at i:250260 original size:51 final size:52
Alignment explanation
Indices: 250178--250372 Score: 223
Period size: 52 Copynumber: 3.8 Consensus size: 52
250168 GCCATAAACG
* *
250178 AAGAGCTTTGATGACTAAGTGTCATCGTGAGTA-ATGAATCCTTTATGGATT
1 AAGAGGTTTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * *
250229 AATAGGTTTGATGACTAAGTGTCATCATGAGTATACGAATCCTTTACGGATT
1 AAGAGGTTTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * ** * *
250281 AAGAGGTCTAATGACTCTGTGTCATCGTGAGTATATGAATCCCTTGCGGATT
1 AAGAGGTTTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
** * * *
250333 ATA-AGGTCCGATGGCTATGTGTCATTGTGAGTATATGAAT
1 A-AGAGGTTTGATGACTAAGTGTCATCGTGAGTATATGAAT
250373 GAAGTGAAAT
Statistics
Matches: 123, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
51 30 0.24
52 92 0.75
53 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.34
Consensus pattern (52 bp):
AAGAGGTTTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:252874 original size:13 final size:13
Alignment explanation
Indices: 252856--252893 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
252846 TATTCCTTTG
252856 TTCTTCTCTTCTA
1 TTCTTCTCTTCTA
*
252869 TTCTTCTCTTCTG
1 TTCTTCTCTTCTA
*
252882 TTCTTCTTTTCT
1 TTCTTCTCTTCT
252894 CCTTCTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.03, C:0.29, G:0.03, T:0.66
Consensus pattern (13 bp):
TTCTTCTCTTCTA
Found at i:257906 original size:51 final size:52
Alignment explanation
Indices: 257777--258040 Score: 192
Period size: 51 Copynumber: 5.2 Consensus size: 52
257767 AAAAAGGTCT
* **
257777 GATGACTACGTGTCATCATGAGTATATGAATCC-TTTACTTA-TATGAGGTTC
1 GATGACTA-GTGTCATCATGAGAATATGAATCCTTTTACGAATTATGAGGTTC
* ** * * *
257828 GATGACAACGCATTATCGTGA-ATATATGAATCCTTTTACGAATTATAAGGTTC
1 GATGACTA-GTGTCATCATGAGA-ATATGAATCCTTTTACGAATTATGAGGTTC
* *
257881 GATGACT-GTGTCATCATGAGAATATGAAT--GTTTACGGATTATGAGG-TC
1 GATGACTAGTGTCATCATGAGAATATGAATCCTTTTACGAATTATGAGGTTC
* * * *
257929 TGATGACTACGTGTCATCGTGAGTATATGAATCC-TTTATGGATTATGAGG-TC
1 -GATGACTA-GTGTCATCATGAGAATATGAATCCTTTTACGAATTATGAGGTTC
* * * * *
257981 TGATTACTATGTGTCATTATGAGTATAAGAATCC--TTAC-AGATTATGAGGTCC
1 -GATGACTA-GTGTCATCATGAGAATATGAATCCTTTTACGA-ATTATGAGGTTC
258033 GATGACTA
1 GATGACTA
258041 TATGTTATCG
Statistics
Matches: 173, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
48 2 0.01
49 21 0.12
51 81 0.47
52 54 0.31
53 15 0.09
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (52 bp):
GATGACTAGTGTCATCATGAGAATATGAATCCTTTTACGAATTATGAGGTTC
Found at i:257962 original size:102 final size:101
Alignment explanation
Indices: 257770--258086 Score: 304
Period size: 103 Copynumber: 3.1 Consensus size: 101
257760 GTAAATGAAA
**
257770 AAGGTCTGATGACTACGTGTCATCATGAGTATATGAATCCTTTACTTA-TATGAGGT-TCGATGA
1 AAGGTCTGATGACT--GTGTCATCATGAGTATATGAAT-CTTTACAGATTATGAGGTCT-GATGA
* **
257833 CAACGCATTATCGTGAATATATGAATCCTTTTACGAATTAT
62 CTACGTGTTATCGTGAATATATGAATCC-TTTACGAATTAT
* * *
257874 AAGGT-TCGATGACTGTGTCATCATGAGAATATGAATGTTTACGGATTATGAGGTCTGATGACTA
1 AAGGTCT-GATGACTGTGTCATCATGAGTATATGAATCTTTACAGATTATGAGGTCTGATGACTA
* * * *
257938 CGTGTCATCGTGAGTATATGAATCCTTTATGGATTAT
65 CGTGTTATCGTGAATATATGAATCCTTTACGAATTAT
* * * * * *
257975 GAGGTCTGATTACTATGTGTCATTATGAGTATAAGAATCCTTACAGATTATGAGGTCCGATGACT
1 AAGGTCTGATGAC--TGTGTCATCATGAGTATATGAATCTTTACAGATTATGAGGTCTGATGACT
** * *
258040 ATATGTTATCGTGATTATATG-ATCCCTCTAC-AGATTA-
64 ACGTGTTATCGTGAATATATGAAT-CCTTTACGA-ATTAT
258077 AAGGTCTGAT
1 AAGGTCTGAT
258087 AACTCTGTGC
Statistics
Matches: 177, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
101 25 0.14
102 69 0.39
103 71 0.40
104 12 0.07
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (101 bp):
AAGGTCTGATGACTGTGTCATCATGAGTATATGAATCTTTACAGATTATGAGGTCTGATGACTAC
GTGTTATCGTGAATATATGAATCCTTTACGAATTAT
Found at i:261707 original size:52 final size:51
Alignment explanation
Indices: 261582--261766 Score: 221
Period size: 52 Copynumber: 3.6 Consensus size: 51
261572 TGGAAAAAAG
** *
261582 GGTTCGATGACTATGTGTCATCGTTTGTATATGAATCCTTTTATGGA-TTGA
1 GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCC-TTTATAGATTTGA
* * *
261633 GG-TCTAATGACTATGAGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
1 GGTTC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTATAGATT-TGA
* *
261685 GGTTCGATGACTATGTGTCATCGTGAGTATATGGATCCTATTATAGATTTAA
1 GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCT-TTATAGATTTGA
* * *
261737 GGTCCGATGACTTTGTGTCATTGTGAGTAT
1 GGTTCGATGACTATGTGTCATCGTGAGTAT
261767 TAAATGGGAA
Statistics
Matches: 115, Mismatches: 14, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
50 8 0.07
51 32 0.28
52 65 0.57
53 10 0.09
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (51 bp):
GGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATAGATTTGA
Found at i:263520 original size:21 final size:21
Alignment explanation
Indices: 263482--263521 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
263472 ATAATGAAAA
* * *
263482 GAGATTTATTTTTTAATCAAT
1 GAGATTAATGTTTAAATCAAT
263503 GAGATTAATGTTTAAATCA
1 GAGATTAATGTTTAAATCA
263522 TAATCCGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (21 bp):
GAGATTAATGTTTAAATCAAT
Found at i:266594 original size:51 final size:52
Alignment explanation
Indices: 266517--266649 Score: 162
Period size: 51 Copynumber: 2.6 Consensus size: 52
266507 GAAAAAAAAG
* * *
266517 GGTCCAATGACTATGTGTCATTGTGAGTATATGAAT-CT-TTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTATTACGGATT-TAA
* * *
266568 GGTCCGATGACTATGTGTCATCGTGAGTAAATGGATCCTATTACTGATTTAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTATTACGGATTTAA
* * *
266620 GATCCGTTGACTTTGTGTCATCGTGAGTAT
1 GGTCCGATGACTATGTGTCATCGTGAGTAT
266650 TAAATGAGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 32 0.46
52 30 0.43
53 8 0.11
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTATTACGGATTTAA
Found at i:266639 original size:52 final size:51
Alignment explanation
Indices: 266523--266648 Score: 155
Period size: 52 Copynumber: 2.5 Consensus size: 51
266513 AAAGGGTCCA
* * * *
266523 ATGACTATGTGTCATTGTGAGTATATGAATCTTTACGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTAAATGAATCTTTACGGATTATAAGATCCG
* *
266574 ATGACTATGTGTCATCGTGAGTAAATGGATCCTATTACTGATT-TAAGATCCG
1 ATGACTATGTGTCATCGTGAGTAAATGAAT-CT-TTACGGATTATAAGATCCG
* *
266626 TTGACTTTGTGTCATCGTGAGTA
1 ATGACTATGTGTCATCGTGAGTA
266649 TTAAATGAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
51 27 0.42
52 30 0.46
53 8 0.12
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.37
Consensus pattern (51 bp):
ATGACTATGTGTCATCGTGAGTAAATGAATCTTTACGGATTATAAGATCCG
Found at i:273129 original size:52 final size:52
Alignment explanation
Indices: 273051--273291 Score: 331
Period size: 52 Copynumber: 4.6 Consensus size: 52
273041 TAAATGAAAA
*
273051 AGGTCTGATGACTACGTGTCATCGTGAGTATATGAAT-CTTCTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTT-TACGGATTATG
* * *
273103 AGGTCCGATGACTATGTGTTATCGTGAGTATATAAATCCTTTACGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
273155 AGGTTCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * * * * *
273207 AGGTCTGGTGACTACATGTCATCGTAACTATAAGAATCCTTTACGGATTATA
1 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
273259 AGGTCCGATGATTATGTGTCATCGTGAGTATAT
1 AGGTCCGATGACTACGTGTCATCGTGAGTATAT
273292 TATCCCTCTA
Statistics
Matches: 162, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
52 159 0.98
53 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (52 bp):
AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:275850 original size:42 final size:42
Alignment explanation
Indices: 275803--275887 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
275793 CAAATATATC
*
275803 AATAACTTTTAAAATGAGAATATGATAATTTGAATGTTTTTA
1 AATAACTTTTAAAATGAGAATATGATAATTTAAATGTTTTTA
275845 AATAACTTTTAAAATGAGAATATGATAATTTAAATGTTTTTA
1 AATAACTTTTAAAATGAGAATATGATAATTTAAATGTTTTTA
275887 A
1 A
275888 TCTTTACATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (42 bp):
AATAACTTTTAAAATGAGAATATGATAATTTAAATGTTTTTA
Found at i:276921 original size:87 final size:87
Alignment explanation
Indices: 276775--276949 Score: 350
Period size: 87 Copynumber: 2.0 Consensus size: 87
276765 AATGATGTGA
276775 CGCGCTAGCCTTGGAAAGTGGGGGACACGTTGCAATGACCATGGAAGAAAATTTGGTATTTGTGG
1 CGCGCTAGCCTTGGAAAGTGGGGGACACGTTGCAATGACCATGGAAGAAAATTTGGTATTTGTGG
276840 GATAAATCATAAATGGACGACC
66 GATAAATCATAAATGGACGACC
276862 CGCGCTAGCCTTGGAAAGTGGGGGACACGTTGCAATGACCATGGAAGAAAATTTGGTATTTGTGG
1 CGCGCTAGCCTTGGAAAGTGGGGGACACGTTGCAATGACCATGGAAGAAAATTTGGTATTTGTGG
276927 GATAAATCATAAATGGACGACC
66 GATAAATCATAAATGGACGACC
276949 C
1 C
276950 TTAAAGGTAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.23
Consensus pattern (87 bp):
CGCGCTAGCCTTGGAAAGTGGGGGACACGTTGCAATGACCATGGAAGAAAATTTGGTATTTGTGG
GATAAATCATAAATGGACGACC
Found at i:280427 original size:16 final size:15
Alignment explanation
Indices: 280390--280428 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
280380 GTTGCAATTA
280390 AATTTTAATTTTTAT
1 AATTTTAATTTTTAT
* *
280405 TAGTTTATATTTTTAT
1 AATTTTA-ATTTTTAT
280421 AATTTTAA
1 AATTTTAA
280429 GAAAATTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 2
0.76 0.16 0.08
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (15 bp):
AATTTTAATTTTTAT
Found at i:283466 original size:18 final size:18
Alignment explanation
Indices: 283443--283481 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
283433 TCTGGGGAAC
*
283443 TTTAAATCCTTCTAGGAT
1 TTTAAATCCTTCAAGGAT
*
283461 TTTAAATCTTTCAAGGAT
1 TTTAAATCCTTCAAGGAT
283479 TTT
1 TTT
283482 TATATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTAAATCCTTCAAGGAT
Found at i:290255 original size:32 final size:32
Alignment explanation
Indices: 290214--290278 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
290204 ATGTCCCGAT
290214 TGTCAGCTTGTGTGAGCATTATTTCCTATGTA
1 TGTCAGCTTGTGTGAGCATTATTTCCTATGTA
290246 TGTCAGCTTGTGTGAGCATTATTTCCTATGTA
1 TGTCAGCTTGTGTGAGCATTATTTCCTATGTA
290278 T
1 T
290279 CCAAAGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.22, T:0.45
Consensus pattern (32 bp):
TGTCAGCTTGTGTGAGCATTATTTCCTATGTA
Found at i:296561 original size:26 final size:22
Alignment explanation
Indices: 296515--296559 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 22
296505 TTTTTAATAA
296515 ATTTATTATTTTTCATTTTTAC
1 ATTTATTATTTTTCATTTTTAC
296537 ATTTATTTATTTATTCACTTTTT
1 ATTTA-TTATTT-TTCA-TTTTT
296560 TATTATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 6 0.30
24 4 0.20
25 5 0.25
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTATTATTTTTCATTTTTAC
Found at i:297869 original size:15 final size:15
Alignment explanation
Indices: 297849--297881 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
297839 AATCTTTTAA
297849 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
297864 AAATTATTAAAAATT
1 AAATTATTAAAAATT
297879 AAA
1 AAA
297882 ATTTAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:308591 original size:28 final size:28
Alignment explanation
Indices: 308558--308646 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
308548 TTTCTTCATG
* *
308558 GCTTCATTGTTATAGCTCGTACTTCGCA
1 GCTTCATTGTAATAGCTCGCACTTCGCA
* *
308586 GCTTCACTGTAATAGCTCGCACTTCGTA
1 GCTTCATTGTAATAGCTCGCACTTCGCA
* * * *
308614 GCATCATTGTACA-AGTTTGCACATCGCA
1 GCTTCATTGTA-ATAGCTCGCACTTCGCA
308642 GCTTC
1 GCTTC
308647 GCTGCTCCCC
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 48 0.98
29 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (28 bp):
GCTTCATTGTAATAGCTCGCACTTCGCA
Found at i:308704 original size:18 final size:18
Alignment explanation
Indices: 308683--308731 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
308673 CCACTTCATG
**
308683 TGAGCTTGCCAATTTGAA
1 TGAGCTTGCCAAACTGAA
* * *
308701 TGAGCTCGCTAAACTGGA
1 TGAGCTTGCCAAACTGAA
308719 TGAGCTTGCCAAA
1 TGAGCTTGCCAAA
308732 ACAATTCACC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (18 bp):
TGAGCTTGCCAAACTGAA
Found at i:310567 original size:23 final size:22
Alignment explanation
Indices: 310534--310584 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
310524 CTTTATTTGA
310534 TAAAATA-TTTTGATATAACAAAT
1 TAAAATATTTTTGA-AT-ACAAAT
* *
310557 TAAAATGTTTTTGAATACAAGT
1 TAAAATATTTTTGAATACAAAT
310579 TAAAAT
1 TAAAAT
310585 TGACAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 11 0.44
23 8 0.32
24 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (22 bp):
TAAAATATTTTTGAATACAAAT
Found at i:310581 original size:22 final size:24
Alignment explanation
Indices: 310541--310584 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
310531 TGATAAAATA
310541 TTTTGATATAACAAATTAAAATGT
1 TTTTGATATAACAAATTAAAATGT
*
310565 TTTTGA-AT-ACAAGTTAAAAT
1 TTTTGATATAACAAATTAAAAT
310585 TGACAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 2 0.11
24 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAATGT
Found at i:312069 original size:14 final size:14
Alignment explanation
Indices: 312050--312077 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
312040 AGACTATTGA
312050 TAACATTAGGAATG
1 TAACATTAGGAATG
312064 TAACATTAGGAATG
1 TAACATTAGGAATG
312078 ACACCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
TAACATTAGGAATG
Found at i:319605 original size:21 final size:21
Alignment explanation
Indices: 319567--319606 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
319557 GGTTAACTCC
*
319567 AAGGACAAGAAAAGAAAGAGG
1 AAGGACAAGAAAAAAAAGAGG
319588 AAGGACAA-AAAGAAAAAGA
1 AAGGACAAGAAA-AAAAAGA
319607 AGTACAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.68, C:0.05, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGACAAGAAAAAAAAGAGG
Found at i:319608 original size:18 final size:19
Alignment explanation
Indices: 319576--319619 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
319566 CAAGGACAAG
*
319576 AAAAGAAAGAGGAAGGACA
1 AAAAGAAAGAAGAAGGACA
*
319595 AAAAGAAA-AAGAAGTACA
1 AAAAGAAAGAAGAAGGACA
319613 AAGAAGA
1 AA-AAGA
319620 GCACCCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.68, C:0.05, G:0.25, T:0.02
Consensus pattern (19 bp):
AAAAGAAAGAAGAAGGACA
Found at i:319755 original size:17 final size:17
Alignment explanation
Indices: 319716--319769 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
319706 ATGCATCTCA
* *
319716 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCA-T
319734 TTTATTTGTCACTGCAT
1 TTTATTTGTCACTGCAT
* *
319751 TTTATTTGTTACTACAT
1 TTTATTTGTCACTGCAT
319768 TT
1 TT
319770 ACATTGTAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.56
18 14 0.44
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (17 bp):
TTTATTTGTCACTGCAT
Found at i:326775 original size:23 final size:23
Alignment explanation
Indices: 326745--326790 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
326735 AAAAAGCCTG
326745 ATAAGCATGATTTTCTTGGCTTT
1 ATAAGCATGATTTTCTTGGCTTT
326768 ATAAGCATGATTTTCTTGGCTTT
1 ATAAGCATGATTTTCTTGGCTTT
326791 CATTTACAAA
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:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (23 bp):
ATAAGCATGATTTTCTTGGCTTT
Found at i:329255 original size:22 final size:23
Alignment explanation
Indices: 329205--329255 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
329195 CTTTATTTGA
* *
329205 TAAAATATTTTGTTATAATAAAT
1 TAAAATATTTTGTTAAAACAAAT
*
329228 TAAAATATTTT-TTAAAACAAGT
1 TAAAATATTTTGTTAAAACAAAT
329250 TAAAAT
1 TAAAAT
329256 TGACAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAAATATTTTGTTAAAACAAAT
Found at i:332767 original size:27 final size:27
Alignment explanation
Indices: 332736--332788 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
332726 GTTTTTCTTT
* * *
332736 TAACATAGATAGCCATAGAGGCGTCCC
1 TAACAAAGATAGCCACAAAGGCGTCCC
*
332763 TAACAAAGATAGTCACAAAGGCGTCC
1 TAACAAAGATAGCCACAAAGGCGTCC
332789 ATTCATAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (27 bp):
TAACAAAGATAGCCACAAAGGCGTCCC
Found at i:349477 original size:28 final size:28
Alignment explanation
Indices: 349416--349536 Score: 134
Period size: 28 Copynumber: 4.2 Consensus size: 28
349406 TGGTGTTGAT
* *
349416 ATTTCAACAAAATCTAGCCACAAAGGCTC
1 ATTTTAACAGAATC-AGCCACAAAGGCTC
* * *
349445 ATTTTAACAGAATCAACTACAAAGGCAC
1 ATTTTAACAGAATCAGCCACAAAGGCTC
* * *
349473 CTTTTAATAGAATCAGCCATAAAGGCTC
1 ATTTTAACAGAATCAGCCACAAAGGCTC
*
349501 ATTTTAACAAAATCAGCCACAAAGGCTTC
1 ATTTTAACAGAATCAGCCACAAAGGC-TC
349530 ACTTTTA
1 A-TTTTA
349537 CGGAAACTAG
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
28 55 0.73
29 15 0.20
30 5 0.07
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (28 bp):
ATTTTAACAGAATCAGCCACAAAGGCTC
Found at i:350182 original size:5 final size:5
Alignment explanation
Indices: 350166--350213 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
350156 AGAAGTCAAG
* ** *
350166 CCCGA GCCCGA CCCGA CCTGA CCCGA CTTGA CCCGA CCCGA CCTGA CC
1 CCCGA -CCCGA CCCGA CCCGA CCCGA CCCGA CCCGA CCCGA CCCGA CC
350214 AATATTAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
5 30 0.86
6 5 0.14
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (5 bp):
CCCGA
Found at i:350192 original size:15 final size:15
Alignment explanation
Indices: 350166--350213 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
350156 AGAAGTCAAG
*
350166 CCCGAGCCCGACCCGA
1 CCCGA-CCCGACCTGA
* *
350182 CCTGACCCGACTTGA
1 CCCGACCCGACCTGA
350197 CCCGACCCGACCTGA
1 CCCGACCCGACCTGA
350212 CC
1 CC
350214 AATATTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (15 bp):
CCCGACCCGACCTGA
Found at i:350481 original size:12 final size:12
Alignment explanation
Indices: 350464--350529 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
350454 ATAACATCCA
350464 AACAACAAAAAT
1 AACAACAAAAAT
350476 AACAACCAAAACAGT
1 AACAA-CAAAA-A-T
*
350491 AGCAA-AAAAAT
1 AACAACAAAAAT
* *
350502 AGCAAGAAAAAT
1 AACAACAAAAAT
* *
350514 AACAATAAAAAC
1 AACAACAAAAAT
350526 AACA
1 AACA
350530 TCGAAATAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 6 0.13
12 25 0.54
13 9 0.20
14 1 0.02
15 5 0.11
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:350608 original size:44 final size:43
Alignment explanation
Indices: 350555--350638 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 43
350545 AAATAACACC
* *
350555 AAAAAAGCAACCAAAACAATAAAAATACAACACCAAAACAGTA
1 AAAAAAGCAACCAAAACAACAAAAAAACAACACCAAAACAGTA
*
350598 AAAAATAGCAACCAAAACAACAAAAAAACAGCACCAAAACA
1 AAAAA-AGCAACCAAAACAACAAAAAAACAACACCAAAACA
350639 ACAATATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 5 0.14
44 32 0.86
ACGTcount: A:0.68, C:0.23, G:0.05, T:0.05
Consensus pattern (43 bp):
AAAAAAGCAACCAAAACAACAAAAAAACAACACCAAAACAGTA
Found at i:350640 original size:22 final size:23
Alignment explanation
Indices: 350555--350642 Score: 94
Period size: 22 Copynumber: 4.0 Consensus size: 23
350545 AAATAACACC
*
350555 AAAAA-AGCAACCAAAACAATAA
1 AAAAACAGCAACCAAAACAACAA
* * **
350577 AAATACAAC-ACCAAAAC-AGTA
1 AAAAACAGCAACCAAAACAACAA
*
350598 AAAAATAGCAACCAAAACAACAA
1 AAAAACAGCAACCAAAACAACAA
350621 AAAAACAGC-ACCAAAACAACAA
1 AAAAACAGCAACCAAAACAACAA
350643 TATAATTTTC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
21 8 0.15
22 33 0.62
23 12 0.23
ACGTcount: A:0.68, C:0.23, G:0.05, T:0.05
Consensus pattern (23 bp):
AAAAACAGCAACCAAAACAACAA
Found at i:355539 original size:11 final size:12
Alignment explanation
Indices: 355518--355543 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
355508 TTAAATTTTT
355518 AAAATTAAAAAA
1 AAAATTAAAAAA
355530 AAAATTAAAAAA
1 AAAATTAAAAAA
355542 AA
1 AA
355544 CTATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATTAAAAAA
Found at i:360320 original size:26 final size:26
Alignment explanation
Indices: 360291--360343 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
360281 CATTATTTAA
*
360291 AAAAATATATTTAATTTTTAGAGAAT
1 AAAAATATATCTAATTTTTAGAGAAT
* * *
360317 AAAAATTTCTCTATTTTTTAGAGAAT
1 AAAAATATATCTAATTTTTAGAGAAT
360343 A
1 A
360344 GCGATATCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (26 bp):
AAAAATATATCTAATTTTTAGAGAAT
Found at i:367486 original size:27 final size:27
Alignment explanation
Indices: 367361--367571 Score: 160
Period size: 27 Copynumber: 7.7 Consensus size: 27
367351 TGACAATTTT
**
367361 TGTAAAGGAATGAATTTGTGGCAAAT-T-
1 TGTAAAGGAA-GCCTTTGTGG-AAATCTC
* *
367388 TGTAAATGAAGCCTTTGTGGAAATATC
1 TGTAAAGGAAGCCTTTGTGGAAATCTC
* *
367415 TGTAAAGGAATGCCCTTAT-GATAATCTC
1 TGTAAAGGAA-GCCTTTGTGGA-AATCTC
* * * *
367443 TGTAAAAGAAACATTTGTGGTAATCTC
1 TGTAAAGGAAGCCTTTGTGGAAATCTC
* * * *
367470 TGT-AATGAATGCCTTTGTGGCAATTTT
1 TGTAAAGGAA-GCCTTTGTGGAAATCTC
* *
367497 TGTAAAGGGATGACTTTGTGGAAATCTC
1 TGTAAA-GGAAGCCTTTGTGGAAATCTC
* *
367525 TGTAAAGGAAGCCTTTGTGGCAATCTT
1 TGTAAAGGAAGCCTTTGTGGAAATCTC
* *
367552 TGTAATGAAAGCCTTTGTGG
1 TGTAAAGGAAGCCTTTGTGG
367572 CGAATGTGGG
Statistics
Matches: 145, Mismatches: 31, Indels: 16
0.76 0.16 0.08
Matches are distributed among these distances:
25 4 0.03
26 14 0.10
27 83 0.57
28 42 0.29
29 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (27 bp):
TGTAAAGGAAGCCTTTGTGGAAATCTC
Found at i:367501 original size:82 final size:81
Alignment explanation
Indices: 367374--367572 Score: 224
Period size: 82 Copynumber: 2.4 Consensus size: 81
367364 AAAGGAATGA
* *
367374 ATTTGTGGCAAAT-T-TGTAAATGAAGCCTTTGTGGAAATATCTGTAAAGGAATGCCCTTAT-GA
1 ATTTGTGGC-AATCTCTGT-AATGAAGCCTTTGTGGCAATATCTGTAAAGGAATGACCTTATGGA
367436 TAATCTCTGTAAAAGAAAC
64 -AATCTCTGTAAAAGAAAC
* * * * * *
367455 ATTTGTGGTAATCTCTGTAATGAATGCCTTTGTGGCAATTTTTGTAAAGGGATGACTTTGTGGAA
1 ATTTGTGGCAATCTCTGTAATGAA-GCCTTTGTGGCAATATCTGTAAAGGAATGACCTTATGGAA
* *
367520 ATCTCTGTAAAGGAAGC
65 ATCTCTGTAAAAGAAAC
* *
367537 CTTTGTGGCAATCTTTGTAATGAAAGCCTTTGTGGC
1 ATTTGTGGCAATCTCTGTAATG-AAGCCTTTGTGGC
367573 GAATGTGGGA
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
80 3 0.03
81 15 0.15
82 78 0.78
83 4 0.04
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (81 bp):
ATTTGTGGCAATCTCTGTAATGAAGCCTTTGTGGCAATATCTGTAAAGGAATGACCTTATGGAAA
TCTCTGTAAAAGAAAC
Found at i:370320 original size:22 final size:22
Alignment explanation
Indices: 370271--370314 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
370261 AAGGTGGGCT
370271 GAAA-GGCTCAAACGATCCAAA
1 GAAATGGCTCAAACGATCCAAA
370292 GAAATGGCTCAAACGATCCAAA
1 GAAATGGCTCAAACGATCCAAA
370314 G
1 G
370315 TTATGGTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.45, C:0.23, G:0.20, T:0.11
Consensus pattern (22 bp):
GAAATGGCTCAAACGATCCAAA
Found at i:375649 original size:21 final size:21
Alignment explanation
Indices: 375623--375662 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
375613 AATAAAATTT
*
375623 AAAAAAAAGGAAAAAATAATA
1 AAAAAAAAGAAAAAAATAATA
*
375644 AAAAAAAATAAAAAAATAA
1 AAAAAAAAGAAAAAAATAA
375663 AGAATAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (21 bp):
AAAAAAAAGAAAAAAATAATA
Found at i:375651 original size:13 final size:13
Alignment explanation
Indices: 375633--375670 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
375623 AAAAAAAAGG
375633 AAAAAATAATAAA
1 AAAAAATAATAAA
375646 AAAAAATAA-AAA
1 AAAAAATAATAAA
* *
375658 AATAAAGAATAAA
1 AAAAAATAATAAA
375671 GAATTAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAAATAATAAA
Done.