Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014878.1 Kokia drynarioides strain JFW-HI SEQ_129921, 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: 372812
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 957 characters in sequence are not A, C, G, or T
Found at i:11289 original size:33 final size:33
Alignment explanation
Indices: 11252--11317 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
11242 AAAAATATAA
* *
11252 TTTAATGTGATAAAGAAGCCGCCGTTGATTATT
1 TTTAATGTGATAAAGAAGCCGCCATTGACTATT
* *
11285 TTTAATGTGATGAAGGAGCCGCCATTGACTATT
1 TTTAATGTGATAAAGAAGCCGCCATTGACTATT
11318 ATTCTATGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (33 bp):
TTTAATGTGATAAAGAAGCCGCCATTGACTATT
Found at i:13249 original size:13 final size:13
Alignment explanation
Indices: 13212--13250 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
13202 TAACATTATT
13212 TATTTATAAAAT-
1 TATTTATAAAATA
13224 TATATTA-AAAATA
1 TAT-TTATAAAATA
13237 TATTTATAAAATA
1 TATTTATAAAATA
13250 T
1 T
13251 TTATTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATTTATAAAATA
Found at i:13251 original size:11 final size:11
Alignment explanation
Indices: 13212--13254 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
13202 TAACATTATT
13212 TATTTATAAAA
1 TATTTATAAAA
*
13223 TTATATTAAAAATA
1 -TAT-TTATAAA-A
13237 TATTTATAAAA
1 TATTTATAAAA
13248 TATTTAT
1 TATTTAT
13255 TCATTTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.30
12 9 0.33
13 9 0.33
14 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
TATTTATAAAA
Found at i:28908 original size:21 final size:20
Alignment explanation
Indices: 28883--28931 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
28873 ATAAATTCAT
28883 AAATATTTTCAAAAAATATAA
1 AAATATTTT-AAAAAATATAA
* * *
28904 TAATAAATTTAAAACATATAA
1 AAAT-ATTTTAAAAAATATAA
28925 AAATATT
1 AAATATT
28932 GTTGACAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.09
21 16 0.73
22 4 0.18
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTTTAAAAAATATAA
Found at i:28978 original size:22 final size:22
Alignment explanation
Indices: 28893--29009 Score: 76
Period size: 23 Copynumber: 5.1 Consensus size: 22
28883 AAATATTTTC
28893 AAAAAATATAATAAT-AAATTT
1 AAAAAATATAATAATAAAATTT
* * *** *
28914 AAAACATATAAAAATATTGTTG
1 AAAAAATATAATAATAAAATTT
*
28936 ACAATAAATAATAGTATATAAAATTT
1 A-AA-AAAT-ATAATA-ATAAAATTT
28962 AAAAAGATATAA-AATAAATATTT
1 AAAAA-ATATAATAATAAA-ATTT
* *
28985 TAAAAATATAATAATTTAAATTT
1 AAAAAATATAATAA-TAAAATTT
29008 AA
1 AA
29010 TATTACTATT
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
21 13 0.19
22 14 0.20
23 18 0.26
24 11 0.16
25 8 0.11
26 6 0.09
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (22 bp):
AAAAAATATAATAATAAAATTT
Found at i:28990 original size:15 final size:16
Alignment explanation
Indices: 28972--29004 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28962 AAAAAGATAT
*
28972 AAAATA-AATATTTTA
1 AAAATATAATAATTTA
28987 AAAATATAATAATTTA
1 AAAATATAATAATTTA
29003 AA
1 AA
29005 TTTAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATAATAATTTA
Found at i:29037 original size:6 final size:6
Alignment explanation
Indices: 29023--29089 Score: 73
Period size: 6 Copynumber: 10.5 Consensus size: 6
29013 TACTATTATT
29023 AATATTA AATATA AATAATA TAAGTATA AATA-A AATATA AATATA AATATA
1 AATA-TA AATATA AAT-ATA -AA-TATA AATATA AATATA AATATA AATATA
*
29074 AACATA AATATTA AAT
1 AATATA AATA-TA AAT
29090 TGATAAAATT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
5 5 0.09
6 28 0.53
7 14 0.26
8 5 0.09
9 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:29061 original size:17 final size:17
Alignment explanation
Indices: 29023--29089 Score: 75
Period size: 17 Copynumber: 3.9 Consensus size: 17
29013 TACTATTATT
29023 AATATTAAATATAAAT--
1 AATA-TAAATATAAATAA
*
29039 AATATAAGTATAAATAA
1 AATATAAATATAAATAA
29056 AATATAAATATAAATATA
1 AATATAAATATAAATA-A
*
29074 AACATAAATATTAAAT
1 AATATAAATA-TAAAT
29090 TGATAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
15 10 0.23
16 4 0.09
17 15 0.34
18 10 0.23
19 5 0.11
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
AATATAAATATAAATAA
Found at i:42630 original size:3 final size:3
Alignment explanation
Indices: 42552--42618 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
42542 ATTATATTAT
* *
42552 TAA TAA TAT TTA T-A TAA TAA TAA TTAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
* * *
42597 TAA TGA CAC TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
42619 TTTTAATAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 48 0.91
4 3 0.06
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:42974 original size:22 final size:22
Alignment explanation
Indices: 42936--42978 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42926 AGGGAAAACC
*
42936 GTTTAGATCTAGGCTAGATCTA
1 GTTTAGATCTAGCCTAGATCTA
42958 GTTT-GATCTAGACCTAGATCT
1 GTTTAGATCTAG-CCTAGATCT
42979 GTTCTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (22 bp):
GTTTAGATCTAGCCTAGATCTA
Found at i:43814 original size:30 final size:30
Alignment explanation
Indices: 43780--44097 Score: 249
Period size: 30 Copynumber: 10.7 Consensus size: 30
43770 TAAATTGTTA
* *
43780 AAAAATCCCATTTTTAAGCTCGAAACTTCC
1 AAAAATCCCATTTTTAACCCCGAAACTTCC
* * *
43810 AAAAAAATCCTATTTTTACCCCCG-AACTTCT
1 --AAAAATCCCATTTTTAACCCCGAAACTTCC
* * *
43841 AAATAT--CATATTTTAACCCCAAAACTTTC
1 AAAAATCCCAT-TTTTAACCCCGAAACTTCC
* * *
43870 GAAAATCCAATTTTT-ACCCTCG-AACTTCT
1 AAAAATCCCATTTTTAACCC-CGAAACTTCC
* * *
43899 AAAAATCCAATTTTTAACCCCAAAACTTCT
1 AAAAATCCCATTTTTAACCCCGAAACTTCC
* * **
43929 AAAAATCCAAATTTTAACCCC-AAAGCTTTT
1 AAAAATCCCATTTTTAACCCCGAAA-CTTCC
* *
43959 TAAAATCCCAATTTTAACCCCGAAACTTCC
1 AAAAATCCCATTTTTAACCCCGAAACTTCC
* * *
43989 AAAAATTCCATTTTTACCCCCG-AACCTCC
1 AAAAATCCCATTTTTAACCCCGAAACTTCC
* *
44018 AAAAATCCCATTTTTAACCCCAAAACTTTC
1 AAAAATCCCATTTTTAACCCCGAAACTTCC
* * *
44048 AAAAGGT-CCATTTTTATCCCC-AAACTTCT
1 AAAA-ATCCCATTTTTAACCCCGAAACTTCC
* *
44077 AAAAATCACATTTTTGACCCC
1 AAAAATCCCATTTTTAACCCC
44098 AAATTTTTCC
Statistics
Matches: 231, Mismatches: 43, Indels: 27
0.77 0.14 0.09
Matches are distributed among these distances:
27 2 0.01
28 10 0.04
29 87 0.38
30 102 0.44
31 12 0.05
32 18 0.08
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (30 bp):
AAAAATCCCATTTTTAACCCCGAAACTTCC
Found at i:43944 original size:59 final size:57
Alignment explanation
Indices: 43780--44100 Score: 267
Period size: 59 Copynumber: 5.4 Consensus size: 57
43770 TAAATTGTTA
* * * * *
43780 AAAAATCCCATTTTTAAGCTCGAAACTTCCAAAAAAATCCTATTTTTACCCCCGAACTTCT
1 AAAAATCCAATTTTTAACCCCAAAACTT-C-TAAAAATCC-ATTTTTA-CCCCGAACTTCT
* *
43841 AAATAT-C-ATATTTTAACCCCAAAACTT-TCGAAAATCCAATTTTTACCCTCGAACTTCT
1 AAAAATCCAAT-TTTTAACCCCAAAACTTCT-AAAAATCC-ATTTTTACCC-CGAACTTCT
* * *
43899 AAAAATCCAATTTTTAACCCCAAAACTTCTAAAAATCCAAATTTTAACCCCAAAGCTTTT
1 AAAAATCCAATTTTTAACCCCAAAACTTCTAAAAATCC--ATTTTTACCCCGAA-CTTCT
* * * * *
43959 TAAAATCCCAA-TTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACCTCC
1 AAAAAT-CCAATTTTTAACCCCAAAACTTCTAAAAA-TCCATTTTTA-CCCCGAACTTCT
* * *
44018 AAAAATCCCATTTTTAACCCCAAAACTT-TCAAAAGGTCCATTTTTATCCCCAAACTTCT
1 AAAAATCCAATTTTTAACCCCAAAACTTCT-AAAA-ATCCATTTTTA-CCCCGAACTTCT
*
44077 AAAAAT-CACATTTTTGACCCCAAA
1 AAAAATCCA-ATTTTTAACCCCAAA
44101 TTTTTCCAAA
Statistics
Matches: 214, Mismatches: 31, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
57 3 0.01
58 32 0.15
59 102 0.48
60 65 0.30
61 12 0.06
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (57 bp):
AAAAATCCAATTTTTAACCCCAAAACTTCTAAAAATCCATTTTTACCCCGAACTTCT
Found at i:44129 original size:119 final size:116
Alignment explanation
Indices: 43780--44113 Score: 332
Period size: 119 Copynumber: 2.8 Consensus size: 116
43770 TAAATTGTTA
* * * * * * * *
43780 AAAAATCCCATTTTTAAGCTCGAAACTTCCAAAAAAATCCTATTTTTACCCCCGAACTTCTAAAT
1 AAAAATCCCATTTTTAACCCCAAAACTTTC-AAAAAATCCAATTTTTAACCCCAAACTTCTAAAA
* * * * *
43845 ATCATATTTTAACCCCAAAACTTTCGAAAA-TCCAATTTTTACCCTCGAACTTCT
65 ATCACATTTTAACCCC-AAA-TTTCCAAAATTCC-ATTTTTACCCCCGAACCTCC
* * * * *
43899 AAAAATCCAATTTTTAACCCCAAAAC-TTCTAAAAATCCAAATTTTAACCCCAAAGCTTTTTAAA
1 AAAAATCCCATTTTTAACCCCAAAACTTTCAAAAAATCCAATTTTTAACCCCAAA-CTTCTAAAA
* *
43963 ATCCCAATTTTAACCCCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACCTCC
65 ATCAC-ATTTTAACCCC-AAATTTCC-AAAATTCCATTTTTACCCCCGAACCTCC
** *
44018 AAAAATCCCATTTTTAACCCCAAAACTTTCAAAAGGTCC-ATTTTTATCCCCAAACTTCTAAAAA
1 AAAAATCCCATTTTTAACCCCAAAACTTTCAAAAAATCCAATTTTTAACCCCAAACTTCTAAAAA
*
44082 TCACATTTTTGACCCCAAATTTTTCCAAAATT
66 TCACA-TTTTAACCCCAAA--TTTCCAAAATT
44114 ATCACTTTTG
Statistics
Matches: 175, Mismatches: 32, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
117 24 0.14
118 40 0.23
119 99 0.57
120 12 0.07
ACGTcount: A:0.37, C:0.28, G:0.03, T:0.31
Consensus pattern (116 bp):
AAAAATCCCATTTTTAACCCCAAAACTTTCAAAAAATCCAATTTTTAACCCCAAACTTCTAAAAA
TCACATTTTAACCCCAAATTTCCAAAATTCCATTTTTACCCCCGAACCTCC
Found at i:55620 original size:5 final size:6
Alignment explanation
Indices: 55604--55629 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
55594 CTTCATCACT
55604 TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TA
55630 GAATGATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:68273 original size:18 final size:20
Alignment explanation
Indices: 68238--68278 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
68228 GTGGTGGTGT
* *
68238 TTTTTTTCATGGTGTTTG-G
1 TTTTGTTCATGGTCTTTGAG
68257 TTTTGTTCAT-GTCTTTGAG
1 TTTTGTTCATGGTCTTTGAG
68276 TTT
1 TTT
68279 GTAAAACCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.07, C:0.07, G:0.22, T:0.63
Consensus pattern (20 bp):
TTTTGTTCATGGTCTTTGAG
Found at i:70631 original size:2 final size:2
Alignment explanation
Indices: 70624--70660 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
70614 GCCTAAAACC
70624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
70661 GCAAATGCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:80285 original size:2 final size:2
Alignment explanation
Indices: 80278--80307 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80268 GATTAGTGGA
80278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
80308 CATTTGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82835 original size:86 final size:85
Alignment explanation
Indices: 82670--82836 Score: 203
Period size: 86 Copynumber: 2.0 Consensus size: 85
82660 GAAGACCTCC
* * * *
82670 ATTTATAATTGAACTCTCCTAGAATTAACGACACTATTGAGTTACATTGATAGTCAAAATTAGAG
1 ATTTATAATTGAACTCTCCTAGAATCAACGACACTATTCAGTTACATTGAGAGTCAAAATTAGAA
82735 TCTATCTACTATTGAGCTTT
66 TCTATCTACTATTGAGCTTT
* * ** *
82755 ATTTATAGTTGAGCTCTCCTAGAATCAACGATGCTGATTCAGTTGCATTGACGA-TCAAAATTAG
1 ATTTATAATTGAACTCTCCTAGAATCAACGACACT-ATTCAGTTACATTGA-GAGTCAAAATTAG
*
82819 AATTTATCTA-TAATTGAG
64 AATCTATCTACT-ATTGAG
82837 AGTCCTAAGA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
85 31 0.45
86 37 0.54
87 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (85 bp):
ATTTATAATTGAACTCTCCTAGAATCAACGACACTATTCAGTTACATTGAGAGTCAAAATTAGAA
TCTATCTACTATTGAGCTTT
Found at i:85775 original size:22 final size:22
Alignment explanation
Indices: 85750--85795 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
85740 GGTTTCAATA
* *
85750 TTCAACTTGATATTTGAGTTTT
1 TTCAACTTGATACTTAAGTTTT
85772 TTCAACTTGATACTTAAGTTTT
1 TTCAACTTGATACTTAAGTTTT
85794 TT
1 TT
85796 TTTTTTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (22 bp):
TTCAACTTGATACTTAAGTTTT
Found at i:90462 original size:43 final size:45
Alignment explanation
Indices: 90414--90529 Score: 128
Period size: 43 Copynumber: 2.6 Consensus size: 45
90404 CCCATTCCAA
* * * *
90414 ACTTATCATATTGAAATAGTTTTTTTACG-G-GTTAGAAATGTAT
1 ACTTATCATATCGAAATAATTTTTTTACGTGTGTAAGAAAGGTAT
* **
90457 ACTTATCAAATCGAAATAATTTTTTTGTGTGTGTAAGAAAGGTAT
1 ACTTATCATATCGAAATAATTTTTTTACGTGTGTAAGAAAGGTAT
*
90502 ACTTATCATATCTACATATAATTTTTTT
1 ACTTATCATATCGA-A-ATAATTTTTTT
90530 GTATGTGTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
43 24 0.40
44 1 0.02
45 23 0.38
46 1 0.02
47 11 0.18
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.45
Consensus pattern (45 bp):
ACTTATCATATCGAAATAATTTTTTTACGTGTGTAAGAAAGGTAT
Found at i:90502 original size:45 final size:48
Alignment explanation
Indices: 90447--90545 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 48
90437 TTTACGGGTT
* *
90447 AGAAATGTATACTTATCAAATCGA-A-ATAATTTTTTTGTGTGTGT-A
1 AGAAAGGTATACTTATCAAATCGACATATAATTTTTTTGTATGTGTCA
* *
90492 AGAAAGGTATACTTATCATATCTACATATAATTTTTTTGTATGTGTCA
1 AGAAAGGTATACTTATCAAATCGACATATAATTTTTTTGTATGTGTCA
90540 A-AAAGG
1 AGAAAGG
90546 CGTTTTTGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 21 0.45
46 1 0.02
47 23 0.49
48 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (48 bp):
AGAAAGGTATACTTATCAAATCGACATATAATTTTTTTGTATGTGTCA
Found at i:109552 original size:15 final size:14
Alignment explanation
Indices: 109524--109550 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
109514 TATCATGTAT
109524 TTTTTTAATATTTA
1 TTTTTTAATATTTA
109538 TTTTTTAATATTT
1 TTTTTTAATATTT
109551 TACGTTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTAATATTTA
Found at i:110280 original size:2 final size:2
Alignment explanation
Indices: 110273--110300 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
110263 TATTCTTGTA
110273 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
110301 GGTAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113538 original size:54 final size:54
Alignment explanation
Indices: 113456--113561 Score: 212
Period size: 54 Copynumber: 2.0 Consensus size: 54
113446 GCTAAACAAT
113456 AATGGGGTTGCTTCATTAGATGGTATTAGTTCAAGACGTCATACATATTTTTAA
1 AATGGGGTTGCTTCATTAGATGGTATTAGTTCAAGACGTCATACATATTTTTAA
113510 AATGGGGTTGCTTCATTAGATGGTATTAGTTCAAGACGTCATACATATTTTT
1 AATGGGGTTGCTTCATTAGATGGTATTAGTTCAAGACGTCATACATATTTTT
113562 TGGAGTTGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.40
Consensus pattern (54 bp):
AATGGGGTTGCTTCATTAGATGGTATTAGTTCAAGACGTCATACATATTTTTAA
Found at i:117751 original size:8 final size:8
Alignment explanation
Indices: 117737--117780 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
117727 ATACATACAC
117737 ATATGTAT
1 ATATGTAT
*
117745 GTATGTAT
1 ATATGTAT
**
117753 GCATGTAT
1 ATATGTAT
*
117761 ACATGTAT
1 ATATGTAT
117769 ATATGTAT
1 ATATGTAT
117777 ATAT
1 ATAT
117781 ACGTGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (8 bp):
ATATGTAT
Found at i:117781 original size:20 final size:20
Alignment explanation
Indices: 117743--117782 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
117733 ACACATATGT
* *
117743 ATGTATGTATGCATGTATAC
1 ATGTATATATGCATATATAC
*
117763 ATGTATATATGTATATATAC
1 ATGTATATATGCATATATAC
117783 GTGTTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (20 bp):
ATGTATATATGCATATATAC
Found at i:117803 original size:162 final size:159
Alignment explanation
Indices: 117499--117891 Score: 455
Period size: 162 Copynumber: 2.5 Consensus size: 159
117489 ATAAAAGCTG
* * *
117499 TTGCATTAACAAGAAGACTACAACAGCAAGCTTCAAAGTTACAGTAATAAAGAAGCCATAGCAAA
1 TTGCACTAACAAGAAGACTACAACAACAAACTTCAAAGTTACAGTAATAAAGAAGCCATAGCAAA
* ** * * *
117564 CCTAGTAAACAAATGATACATATGTATGTTTGTATGCATGTATGTATGTATATATATGTCTTTAT
66 CATAGTAAACAAATGATACATATGTATGCATGTATACATGTATATATGTATATATACGTCTTTAT
117629 AAGACAGCAAAATCCAAATATATGTATCA
131 AAGACAGCAAAATCCAAATATATGTATCA
*
117658 TTGCACTAACAAGAAGACTACAACAACAAACTTCAAAGTTACAGTAAT-AAGGAGCCATGATG-A
1 TTGCACTAACAAGAAGACTACAACAACAAACTTCAAAGTTACAGTAATAAAGAAGCCAT-A-GCA
**
117721 AACAT-GATACATACACATATG-TATGTATGTATGCATGTATACATGTATATATGTATATATACG
64 AACATAG-TA-A-ACA-A-ATGATACATATGTATGCATGTATACATGTATATATGTATATATACG
* * **
117784 TGTTTATAAGATAGCAAAATCCATCTATATGTATCA
124 TCTTTATAAGACAGCAAAATCCAAATATATGTATCA
* * *
117820 TTGAACTAACAAGAAGACT---ACAAC-AACTTCAAAGTTATAGT-ATAAAGAAGTCATGATG-A
1 TTGCACTAACAAGAAGACTACAACAACAAACTTCAAAGTTACAGTAATAAAGAAGCCAT-A-GCA
*
117879 AACCTAGTAAACA
64 AACATAGTAAACA
117892 CATCCATCCA
Statistics
Matches: 204, Mismatches: 21, Indels: 21
0.83 0.09 0.09
Matches are distributed among these distances:
156 3 0.01
157 3 0.01
158 45 0.22
159 59 0.29
160 2 0.01
161 3 0.01
162 86 0.42
163 3 0.01
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (159 bp):
TTGCACTAACAAGAAGACTACAACAACAAACTTCAAAGTTACAGTAATAAAGAAGCCATAGCAAA
CATAGTAAACAAATGATACATATGTATGCATGTATACATGTATATATGTATATATACGTCTTTAT
AAGACAGCAAAATCCAAATATATGTATCA
Found at i:117938 original size:162 final size:160
Alignment explanation
Indices: 117600--117939 Score: 379
Period size: 162 Copynumber: 2.1 Consensus size: 160
117590 TGTTTGTATG
* *
117600 CATGTATGTATGTATATATATGTCTTTATAAGACAGCAAAATCCAAATATATGTATCATTGCACT
1 CATGTATGTATGTATATATACGTCTTTATAAGACAGCAAAATCCAAATATATGTATCATTGAACT
*
117665 AACAAGAAGACTACAACAACAAACTTCAAAGTTACAGTAATAAGGAGCCATGATGAAACATGATA
66 AACAAGAAGACT--AACAACAAACTTCAAAGTTACAGTAATAAGAAGCCATGATGAAACATGATA
** ** * **
117730 CATACACATATGTATGTATGTATGCATGTATA
129 CATACACATATCCATCCATGTATACATACATA
* * * **
117762 CATGTATATATGTATATATACGTGTTTATAAGATAGCAAAATCCATCTATATGTATCATTGAACT
1 CATGTATGTATGTATATATACGTCTTTATAAGACAGCAAAATCCAAATATATGTATCATTGAACT
* * *
117827 AACAAGAAGACT-ACAAC-AACTTCAAAGTTATAGT-ATAAAGAAGTCATGATGAAACCT-AGTA
66 AACAAGAAGACTAACAACAAACTTCAAAGTTACAGTAAT-AAGAAGCCATGATGAAACATGA-TA
*
117888 -A-ACACATCCATCCATCCATTTATACATACATA
129 CATACACAT--ATCCATCCATGTATACATACATA
* *
117920 CAT-AATGTTATGTATGTATA
1 CATGTATG-TATGTATATATA
117940 AGAATTTAAG
Statistics
Matches: 151, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
156 6 0.04
157 6 0.04
158 64 0.42
159 5 0.03
162 70 0.46
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (160 bp):
CATGTATGTATGTATATATACGTCTTTATAAGACAGCAAAATCCAAATATATGTATCATTGAACT
AACAAGAAGACTAACAACAAACTTCAAAGTTACAGTAATAAGAAGCCATGATGAAACATGATACA
TACACATATCCATCCATGTATACATACATA
Found at i:120176 original size:31 final size:31
Alignment explanation
Indices: 120138--120197 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
120128 TATATACATA
120138 AAATTTTAATTGTAATTTAAATT-TATATACG
1 AAATTTTAATTGTAATTT-AATTATATATACG
*
120169 AAATTTTAATTTTAATTTAATTATATATA
1 AAATTTTAATTGTAATTTAATTATATATA
120198 TATTTAAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (31 bp):
AAATTTTAATTGTAATTTAATTATATATACG
Found at i:120220 original size:29 final size:30
Alignment explanation
Indices: 120186--120251 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
120176 AATTTTAATT
120186 TAATTATATATATATTTA-AGTAAATAAATA
1 TAATTATAT-TATATTTATAGTAAATAAATA
* * *
120216 T-ATTAAATTATTTTTATATTAAATAAATA
1 TAATTATATTATATTTATAGTAAATAAATA
120245 TAATTAT
1 TAATTAT
120252 TAACGTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.23
29 18 0.60
30 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TAATTATATTATATTTATAGTAAATAAATA
Found at i:121661 original size:10 final size:10
Alignment explanation
Indices: 121644--121717 Score: 50
Period size: 10 Copynumber: 7.8 Consensus size: 10
121634 TTCTTATTTA
121644 AATT-TAATT
1 AATTATAATT
121653 AATTATAATT
1 AATTATAATT
121663 -ATTATTAATT
1 AATTA-TAATT
121673 -ATTAT--TT
1 AATTATAATT
*
121680 AATTATATTT
1 AATTATAATT
* *
121690 AAATAAAATT
1 AATTATAATT
* *
121700 ATTTATATTT
1 AATTATAATT
*
121710 ATTTATAA
1 AATTATAA
121718 GTCTTCTACT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 9 0.17
10 36 0.69
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
AATTATAATT
Found at i:130623 original size:20 final size:20
Alignment explanation
Indices: 130598--130635 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
130588 TCATACATAT
130598 ACATATCTATAGACTTACAC
1 ACATATCTATAGACTTACAC
*
130618 ACATATCTATGGACTTAC
1 ACATATCTATAGACTTAC
130636 TTCTCCTCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (20 bp):
ACATATCTATAGACTTACAC
Found at i:146151 original size:11 final size:11
Alignment explanation
Indices: 146135--146160 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
146125 GATGGAAAGC
146135 AAAAAAAGGAA
1 AAAAAAAGGAA
146146 AAAAAAAGGAA
1 AAAAAAAGGAA
146157 AAAA
1 AAAA
146161 GTGTATGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAAAAGGAA
Found at i:148032 original size:33 final size:32
Alignment explanation
Indices: 147976--148042 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
147966 CTTAAAAAAC
147976 TTTTAAAAATTTCAATTAGACTCTTCAAAATTT
1 TTTTAAAAATTTCAATTAGACTCTT-AAAATTT
* *
148009 TTTTTAAAATATTC-ATTATACTCTTAAAATTT
1 TTTTAAAAAT-TTCAATTAGACTCTTAAAATTT
148041 TT
1 TT
148043 GAAAATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 9 0.29
33 19 0.61
34 3 0.10
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.51
Consensus pattern (32 bp):
TTTTAAAAATTTCAATTAGACTCTTAAAATTT
Found at i:150479 original size:21 final size:22
Alignment explanation
Indices: 150448--150504 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
150438 ATATAAATTT
*
150448 TAAAT-ATAAACTTTAAA-TCC
1 TAAATAATAAACTATAAACTCC
150468 TAAATAATAAACTATAAACTCC
1 TAAATAATAAACTATAAACTCC
*
150490 -AAATAA-AAAATATAA
1 TAAATAATAAACTATAA
150505 TAATTACGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.39
21 17 0.52
22 3 0.09
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAATAATAAACTATAAACTCC
Found at i:154563 original size:2 final size:2
Alignment explanation
Indices: 154556--154586 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
154546 AAAGGTCAAA
*
154556 AC AC AC AC AG AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
154587 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.45, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:155569 original size:15 final size:17
Alignment explanation
Indices: 155539--155571 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
155529 TCATGACATA
155539 ATATCATTGAGGAATGC
1 ATATCATTGAGGAATGC
155556 ATATCA-TG-GGAATGC
1 ATATCATTGAGGAATGC
155571 A
1 A
155572 GAAGGGACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (17 bp):
ATATCATTGAGGAATGC
Found at i:155658 original size:5 final size:5
Alignment explanation
Indices: 155642--155674 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
155632 ATGCTGCAGC
*
155642 TTTCT TTCCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
155675 TTCCTTGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:177223 original size:30 final size:30
Alignment explanation
Indices: 177187--177247 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
177177 AAAGTTTCAT
177187 AGAAATTTACGGATACTGCCAATTATTGTA
1 AGAAATTTACGGATACTGCCAATTATTGTA
177217 AGAAATTTACGGATACTGCCAATTATTGTA
1 AGAAATTTACGGATACTGCCAATTATTGTA
177247 A
1 A
177248 CTATGCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (30 bp):
AGAAATTTACGGATACTGCCAATTATTGTA
Found at i:178132 original size:14 final size:13
Alignment explanation
Indices: 178113--178155 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
178103 TATGCTAAAA
178113 ATAAAAAATATTAT
1 ATAAAAAAT-TTAT
*
178127 ATAAAAAATCTAT
1 ATAAAAAATTTAT
178140 -TAAACAAATTTAT
1 ATAAA-AAATTTAT
178153 ATA
1 ATA
178156 GAAATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 4 0.16
13 10 0.40
14 11 0.44
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAAAAATTTAT
Found at i:188829 original size:2 final size:2
Alignment explanation
Indices: 188822--188849 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
188812 TAATTAACCC
188822 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
188850 TATATACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:191241 original size:60 final size:59
Alignment explanation
Indices: 191129--191245 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 59
191119 AAGTAGTCAC
*
191129 CCAACTATTAGAAAATTTCACTTTTGGTCATTAAACCATGAAAAGTTACAAAATGGTTA
1 CCAACTATTAGAAAATTTCACTTTTGGTCATTAAACCAGGAAAAGTTACAAAATGGTTA
* ** * * *
191188 CCAACTATTAGTAAATTTCTTTTTTTGGTC-TCTCAACGAGGAAAAGTTGCAAAATGGT
1 CCAACTATTAGAAAATTTC-ACTTTTGGTCAT-TAAACCAGGAAAAGTTACAAAATGGT
191246 CACTTAATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 19 0.39
60 30 0.61
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (59 bp):
CCAACTATTAGAAAATTTCACTTTTGGTCATTAAACCAGGAAAAGTTACAAAATGGTTA
Found at i:192495 original size:7 final size:7
Alignment explanation
Indices: 192483--192507 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
192473 TTTTCATATT
192483 ATTTGAA
1 ATTTGAA
192490 ATTTGAA
1 ATTTGAA
192497 ATTTGAA
1 ATTTGAA
192504 ATTT
1 ATTT
192508 TAATCCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (7 bp):
ATTTGAA
Found at i:206901 original size:20 final size:22
Alignment explanation
Indices: 206866--206934 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 22
206856 ATATCAACAT
* * *
206866 ATATGGTAAGACATTAAT-TTA
1 ATATGGTAAAATATTAATATAA
206887 A-ATGGTAAAATATTATATATAA
1 ATATGGTAAAATATTA-ATATAA
* *
206909 ATATGGTAACATATTAATATAT
1 ATATGGTAAAATATTAATATAA
206931 ATAT
1 ATAT
206935 ATATATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
20 12 0.30
21 3 0.08
22 12 0.30
23 13 0.32
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (22 bp):
ATATGGTAAAATATTAATATAA
Found at i:206915 original size:23 final size:24
Alignment explanation
Indices: 206888--206936 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
206878 ATTAATTTAA
206888 ATGGTAAAATATT-ATATATAAAT
1 ATGGTAAAATATTAATATATAAAT
* *
206911 ATGGTAACATATTAATATATATAT
1 ATGGTAAAATATTAATATATAAAT
206935 AT
1 AT
206937 ATATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (24 bp):
ATGGTAAAATATTAATATATAAAT
Found at i:207205 original size:17 final size:17
Alignment explanation
Indices: 207183--207215 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
207173 ATCTTACAAA
207183 CTTTTTTGTTTTTTTTC
1 CTTTTTTGTTTTTTTTC
207200 CTTTTTTGTTTTTTTT
1 CTTTTTTGTTTTTTTT
207216 ATCAATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (17 bp):
CTTTTTTGTTTTTTTTC
Found at i:209727 original size:29 final size:28
Alignment explanation
Indices: 209669--209727 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 28
209659 TCCTGCATTT
* * *
209669 AATTATAAAAGTTATAAAATTATCACTC
1 AATTATAAAAATTATAAAATAATCAATC
*
209697 AATTATGAAAAATTATAAAATAATTAATC
1 AATTAT-AAAAATTATAAAATAATCAATC
209726 AA
1 AA
209728 CTATTCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (28 bp):
AATTATAAAAATTATAAAATAATCAATC
Found at i:219423 original size:41 final size:43
Alignment explanation
Indices: 219364--219451 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 43
219354 AAAGGGTTCT
*
219364 TATTGTATTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAA
1 TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAA
* *
219407 TATTGT-TTTT-AATTTGTTTGTTGTTTTAATATTTGTTTTAA
1 TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAA
219448 TATT
1 TATT
219452 TTTAAATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
41 32 0.76
42 4 0.10
43 6 0.14
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.65
Consensus pattern (43 bp):
TATTGTATTTTCAATTTGTTTGTTGTTTTAAGAATTGTTTTAA
Found at i:219442 original size:19 final size:18
Alignment explanation
Indices: 219371--219444 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
219361 TCTTATTGTA
*
219371 TTTTCAATTTGTTTGTTG
1 TTTTAAATTTGTTTGTTG
* *
219389 TTTTACGAATTGTTTTAATATTG
1 TTTTA--AATT-TGTT--TGTTG
*
219412 TTTTTAATTTGTTTGTTG
1 TTTTAAATTTGTTTGTTG
219430 TTTTAATATTTGTTT
1 TTTTAA-ATTTGTTT
219445 TAATATTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
18 13 0.30
19 8 0.19
20 7 0.16
21 7 0.16
23 8 0.19
ACGTcount: A:0.18, C:0.03, G:0.14, T:0.66
Consensus pattern (18 bp):
TTTTAAATTTGTTTGTTG
Found at i:219444 original size:12 final size:12
Alignment explanation
Indices: 219427--219452 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
219417 AATTTGTTTG
219427 TTGTTTTAATAT
1 TTGTTTTAATAT
219439 TTGTTTTAATAT
1 TTGTTTTAATAT
219451 TT
1 TT
219453 TTAAATATAT
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:219479 original size:26 final size:24
Alignment explanation
Indices: 219447--219494 Score: 78
Period size: 26 Copynumber: 1.9 Consensus size: 24
219437 ATTTGTTTTA
219447 ATATTTTTAAATATATTTGATATATC
1 ATATTTTTAAAT-TATTT-ATATATC
219473 ATATTTTTAAATTATTTATATA
1 ATATTTTTAAATTATTTATATA
219495 ATAAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.23
25 5 0.23
26 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (24 bp):
ATATTTTTAAATTATTTATATATC
Found at i:233184 original size:2 final size:2
Alignment explanation
Indices: 233177--233202 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
233167 ACAACTGCCA
233177 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
233203 TTCCATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:255743 original size:31 final size:31
Alignment explanation
Indices: 255694--255758 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
255684 TACAATATGG
* *
255694 TCATTAAACTATTTGAAAGTTTTTATTTAAA
1 TCATTAAACTATTCGAAAGTTTTCATTTAAA
* *
255725 TCATTGAATTATTCGAAAGTTTTCATTTAAA
1 TCATTAAACTATTCGAAAGTTTTCATTTAAA
255756 TCA
1 TCA
255759 CTAGATTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (31 bp):
TCATTAAACTATTCGAAAGTTTTCATTTAAA
Found at i:265707 original size:12 final size:12
Alignment explanation
Indices: 265662--265714 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
265652 ATTCCAAAAA
265662 TAATA-TTATTT
1 TAATATTTATTT
*
265673 TAATAGTTTAATAT
1 TAATA-TTT-ATTT
265687 TAA-ATTTATTT
1 TAATATTTATTT
*
265698 TAATACTTATTT
1 TAATATTTATTT
265710 TAATA
1 TAATA
265715 ATATTTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 11 0.31
12 15 0.43
13 3 0.09
14 6 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (12 bp):
TAATATTTATTT
Found at i:265725 original size:37 final size:35
Alignment explanation
Indices: 265662--265730 Score: 86
Period size: 37 Copynumber: 1.9 Consensus size: 35
265652 ATTCCAAAAA
*
265662 TAATATTATTTTAATAGTTTAATATTAAATTTATTT
1 TAATATTATTTTAATAATTTAATATT-AATTTATTT
*
265698 TAATACTTATTTTAATAATATT-TTATTAATTTA
1 TAATA-TTATTTTAATAAT-TTAATATTAATTTA
265731 ATATTAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 11 0.38
37 16 0.55
38 2 0.07
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (35 bp):
TAATATTATTTTAATAATTTAATATTAATTTATTT
Found at i:265745 original size:20 final size:18
Alignment explanation
Indices: 265663--265769 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
265653 TTCCAAAAAT
* *
265663 AATATTATTTTAATAGTTT
1 AATATTAATTTAATA-TTA
*
265682 AATATTAAATTT-AT-TTT
1 AATATT-AATTTAATATTA
* *
265699 AATACTTATTTTAATAATA
1 AATA-TTAATTTAATATTA
**
265718 TTTTATTAATTTAATATTA
1 -AATATTAATTTAATATTA
265737 AAGTGATT-ATCTTAATATTA
1 AA-T-ATTAAT-TTAATATTA
265757 AAT-TTAATTTAAT
1 AATATTAATTTAAT
265770 GTTTATCTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
17 18 0.26
18 6 0.09
19 25 0.36
20 20 0.29
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
AATATTAATTTAATATTA
Found at i:265763 original size:51 final size:48
Alignment explanation
Indices: 265662--265764 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 48
265652 ATTCCAAAAA
* * * *
265662 TAATATTATTTTAATAGTTTAATATTAAATTTATTTTAATACTTATTT
1 TAATAATATTTTAATAATTTAATATTAAATTTATCTTAATACTTAATT
*
265710 TAATAATATTTTATTAATTTAATATTAAAGTGATTATCTTAATA-TTAAATT
1 TAATAATATTTTAATAATTTAATATTAAA-T--TTATCTTAATACTT-AATT
265761 TAAT
1 TAAT
265765 TTAATGTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 26 0.57
49 1 0.02
50 2 0.04
51 17 0.37
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (48 bp):
TAATAATATTTTAATAATTTAATATTAAATTTATCTTAATACTTAATT
Found at i:266429 original size:2 final size:2
Alignment explanation
Indices: 266422--266468 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
266412 ATCCTTTAAT
* *
266422 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
266464 TA TA T
1 TA TA T
266469 CTTTGATCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:272718 original size:56 final size:55
Alignment explanation
Indices: 272651--272761 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 55
272641 CAACAACAAT
272651 TAACATTTTAATCAATTTAAATAAACTAATAATATTATAAAAATAAAATAAAATCA
1 TAACATTTTAATCAATTTAAATAAACTAATAA-ATTATAAAAATAAAATAAAATCA
*
272707 TAACATTTTAATCAATTTAAATAAACTAATAAATTATAAAAATGAAATAAAATCA
1 TAACATTTTAATCAATTTAAATAAACTAATAAATTATAAAAATAAAATAAAATCA
272762 CATAATTTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 22 0.41
56 32 0.59
ACGTcount: A:0.59, C:0.07, G:0.01, T:0.33
Consensus pattern (55 bp):
TAACATTTTAATCAATTTAAATAAACTAATAAATTATAAAAATAAAATAAAATCA
Found at i:272729 original size:29 final size:29
Alignment explanation
Indices: 272651--272738 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
272641 CAACAACAAT
*
272651 TAACATTTTAATCAATTTAAATAAACTAA
1 TAACATTTTAATCAATTTAAATAAAATAA
* * * * *
272680 TAATATTATAA--AAATAAAATAAAATCA
1 TAACATTTTAATCAATTTAAATAAAATAA
*
272707 TAACATTTTAATCAATTTAAATAAACTAA
1 TAACATTTTAATCAATTTAAATAAAATAA
272736 TAA
1 TAA
272739 ATTATAAAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
27 21 0.47
29 24 0.53
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (29 bp):
TAACATTTTAATCAATTTAAATAAAATAA
Found at i:276623 original size:2 final size:2
Alignment explanation
Indices: 276618--276654 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
276608 AATTACACAT
276618 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
276655 TGGACATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:280536 original size:26 final size:26
Alignment explanation
Indices: 280503--280554 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
280493 ATCAATATTT
** *
280503 TAATTAAAATATTTAATGATATTATA
1 TAATTAAAATAACTAATGAAATTATA
*
280529 TAATTAAATTAACTAATGAAATTATA
1 TAATTAAAATAACTAATGAAATTATA
280555 AAGTAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
TAATTAAAATAACTAATGAAATTATA
Found at i:284322 original size:20 final size:20
Alignment explanation
Indices: 284297--284337 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
284287 TTATAATTTA
284297 AAATTATATCTAAAAACTAT
1 AAATTATATCTAAAAACTAT
284317 AAATTATATCTAAAAACTAT
1 AAATTATATCTAAAAACTAT
284337 A
1 A
284338 GTTTTTAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTATATCTAAAAACTAT
Found at i:285648 original size:21 final size:20
Alignment explanation
Indices: 285623--285727 Score: 99
Period size: 20 Copynumber: 5.2 Consensus size: 20
285613 ATTATATTGT
*
285623 TGTTTTGGTGCTTTTTTTTAT
1 TGTTTTGGTG-TTTTTTTTAC
*
285644 TGTTTTGGTTGATTTTTTTTGC
1 TGTTTTGG-TG-TTTTTTTTAC
* *
285666 TGTTTT--TGTGTTTTTTAT
1 TGTTTTGGTGTTTTTTTTAC
285684 TGTTTTGGT-TGTTTTTTTAC
1 TGTTTTGGTGT-TTTTTTTAC
* *
285704 TGTTTTGATGTTGTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
285724 TGTT
1 TGTT
285728 ATTTTTGCTG
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
18 13 0.19
19 3 0.04
20 28 0.41
21 9 0.13
22 16 0.23
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.70
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:285721 original size:40 final size:40
Alignment explanation
Indices: 285623--285727 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
285613 ATTATATTGT
* *
285623 TGTTTTGGTGCTTTTTTTTATTGTTTTGGTTGATTTTTTTTGC
1 TGTTTT-GTG-TTGTTTTTATTGTTTTGGTTGA-TTTTTTTAC
285666 TGTTTT-TG-TGTTTTTTATTGTTTTGGTTG-TTTTTTTAC
1 TGTTTTGTGTTG-TTTTTATTGTTTTGGTTGATTTTTTTAC
*
285704 TGTTTTGATGTTGTTTTTACTGTT
1 TGTTTTG-TGTTGTTTTTATTGTT
285728 ATTTTTGCTG
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
38 14 0.25
39 1 0.02
40 30 0.55
41 4 0.07
43 6 0.11
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.70
Consensus pattern (40 bp):
TGTTTTGTGTTGTTTTTATTGTTTTGGTTGATTTTTTTAC
Found at i:285746 original size:13 final size:12
Alignment explanation
Indices: 285717--285793 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 12
285707 TTTGATGTTG
* *
285717 TTTTTACTGTTA
1 TTTTTGCTGCTA
285729 TTTTTGCTGCTA
1 TTTTTGCTGCTA
*
285741 TCTTTTGTTGCTA
1 T-TTTTGCTGCTA
* *
285754 TTTTTACTGTTA
1 TTTTTGCTGCTA
* * *
285766 TTTTT-TTGTTG
1 TTTTTGCTGCTA
*
285777 TTTTTGTTGCTA
1 TTTTTGCTGCTA
285789 TTTTT
1 TTTTT
285794 TTATTTTGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.17
12 33 0.62
13 11 0.21
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (12 bp):
TTTTTGCTGCTA
Found at i:285796 original size:37 final size:37
Alignment explanation
Indices: 285717--285793 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
285707 TTTGATGTTG
285717 TTTTTACTGTTATTTTTGCTGCTATCTTTTGTTGCTA
1 TTTTTACTGTTATTTTTGCTGCTATCTTTTGTTGCTA
* * *
285754 TTTTTACTGTTATTTTT-TTGTTGT-TTTTGTTGCTA
1 TTTTTACTGTTATTTTTGCTGCTATCTTTTGTTGCTA
285789 TTTTT
1 TTTTT
285794 TTATTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 16 0.43
36 4 0.11
37 17 0.46
ACGTcount: A:0.09, C:0.09, G:0.13, T:0.69
Consensus pattern (37 bp):
TTTTTACTGTTATTTTTGCTGCTATCTTTTGTTGCTA
Found at i:285806 original size:31 final size:34
Alignment explanation
Indices: 285743--285831 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 34
285733 TGCTGCTATC
*
285743 TTTTGTTGCTATTTTTACTGTTATTTTTTTGTTGT
1 TTTTGTTGCTATTTTTA-TGTTATTTTGTTGTTGT
285778 TTTTGTTGCTA-TTTT-T-TTATTTTGTTGTTGT
1 TTTTGTTGCTATTTTTATGTTATTTTGTTGTTGT
* *
285809 TTTGGTTG---TTTTAATGTTATTTT
1 TTTTGTTGCTATTTTTATGTTATTTT
285832 TATGTTTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
29 3 0.06
30 1 0.02
31 28 0.58
32 1 0.02
34 4 0.08
35 11 0.23
ACGTcount: A:0.09, C:0.03, G:0.16, T:0.72
Consensus pattern (34 bp):
TTTTGTTGCTATTTTTATGTTATTTTGTTGTTGT
Found at i:305074 original size:26 final size:26
Alignment explanation
Indices: 305038--305089 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
305028 CCAAAAAGCT
305038 GCCAAAGTTGAATAAGATTGGACAGG
1 GCCAAAGTTGAATAAGATTGGACAGG
305064 GCCAAAGTTGAATAAGATTGGACAGG
1 GCCAAAGTTGAATAAGATTGGACAGG
305090 ATAAGCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.31, T:0.19
Consensus pattern (26 bp):
GCCAAAGTTGAATAAGATTGGACAGG
Found at i:306787 original size:31 final size:34
Alignment explanation
Indices: 306736--306801 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 34
306726 AACAAAAAAC
*
306736 AAAAATTAAATGAGGATTAAAATGATTTTT-TTTA
1 AAAAATTAAATGAGGATT-AAATAATTTTTATTTA
306770 AAAAATTAAA-G-GG-TTAAATAATTTTTATTTA
1 AAAAATTAAATGAGGATTAAATAATTTTTATTTA
306801 A
1 A
306802 TAATAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 10 0.33
31 7 0.23
32 2 0.07
33 1 0.03
34 10 0.33
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (34 bp):
AAAAATTAAATGAGGATTAAATAATTTTTATTTA
Found at i:320124 original size:210 final size:209
Alignment explanation
Indices: 319848--321032 Score: 1424
Period size: 210 Copynumber: 5.6 Consensus size: 209
319838 CACAATGGGA
* * * ** * *
319848 TAGCTTTAACTCTTTCAGACAAGTGGCA-ATAGACGGCCAATCTTCTATCTTGCTTAATTTTTGA
1 TAGCTTTAATTCTTTAAGACAAGTGG-AGGTAGACAACCCATCTCCTATCTTGCTTAATTTTTGA
* *
319912 CACCGGAAAATGTGAAGCTTTTCAAGAGATGAACAT-TGTCTTCTTATTGGAACAATTTCCAGTT
65 CACCGG-AAATGAGAAGCTTTTCAAGAGATGAACATCT-TCCTCTTATTGGAACAATTTCCAGTT
* * * * *
319976 CG-TCGCAGTTTGATATTTCTAAAATTT-GAAGAGAGGAAAACCCTTCCA-AATCTGGAATGGAA
128 CGCT-GCACTTTGATATTTCT-AGATTTCGAAGAAAGGAAAATCCATCCATAA-CTGGAATGGAA
*
320038 CTTAAATTAGGACAATAGCT
190 CTTAAATTAGGACAATTGCT
* * * *
320058 TAACTTTAATTCTTCAAGATAAGTGGAGGTAGACAATCCATCTCCTATCTTGCTTAATTTTTGAC
1 TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCATCTCCTATCTTGCTTAATTTTTGAC
* * * * *
320123 ACAAGGAAATGTGAAGCTTTTCAAGAGATTAACA-CTGTCCTCCTATCGGAACAATTTCCAGATT
66 AC-CGGAAATGAGAAGCTTTTCAAGAGATGAACATCT-TCCTCTTATTGGAACAATTTCCAG-TT
** * * * * * *
320187 -G-TGACAGATTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCCA-AATCAGGAATGGAAC
128 CGCTG-CACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAA-CTGGAATGGAAC
320249 TTAAATTAGGACAATTGCT
191 TTAAATTAGGACAATTGCT
* * * * *
320268 TAACTTTAATTCTTTAAGATAAGTGGAGGTAGACAACCCGTCTCCTATCTTGCTTAAGTTTTCAC
1 TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCATCTCCTATCTTGCTTAATTTTTGAC
* *
320333 ACGAGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTTG
66 AC-CGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTCG
320398 CTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAA
130 CTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAA
320463 ATTAGGACAATTGCT
195 ATTAGGACAATTGCT
* ** ** * * **
320478 CAGCACTAATTCTTTAAGACAAGTGGAGGTAGACCGCCAATCTTCTATCTTGCTTAATTTAGGAC
1 TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCATCTCCTATCTTGCTTAATTTTTGAC
* *
320543 ACCAGGAAATGAAAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTTG
66 ACC-GGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTCG
320608 CTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAA
130 CTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAA
*
320673 ATTAGGACAATTGCA
195 ATTAGGACAATTGCT
* ** * * * * *
320688 CAGCACTAATTCTTTAAGACAAGTGGAAGTAGACAAACCGTCTCCTATCTTGCTTAAGTTTTCAC
1 TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCATCTCCTATCTTGCTTAATTTTTGAC
** *
320753 ATGAGGAAATGAAAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTCG
66 A-CCGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTCG
*
320818 CTGCACTTTTATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAA
130 CTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAA
* ***
320883 ATTAGCACAACCACT
195 ATTAGGACAATTGCT
* * *
320898 TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCGTCTCCAATCTTGCTTAATTCCTT-A
1 TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCATCTCCTATCTTGCTTAATT-TTTGA
* * * * *
320962 CACTCAGAAATGCA-AA-ATTCTTCAAGAGATGAACATATTCCTGC-TATTGGAACAATATCCAA
65 CAC-CGGAAATG-AGAAGCTT-TTCAAGAGATGAACATCTTCCT-CTTATTGGAACAATTTCCAG
*
321024 TTTGCTGCA
126 TTCGCTGCA
321033 ATCATAAACA
Statistics
Matches: 865, Mismatches: 93, Indels: 34
0.87 0.09 0.03
Matches are distributed among these distances:
209 11 0.01
210 840 0.97
211 14 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (209 bp):
TAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCATCTCCTATCTTGCTTAATTTTTGAC
ACCGGAAATGAGAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAATTTCCAGTTCGC
TGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGAATGGAACTTAAA
TTAGGACAATTGCT
Found at i:320678 original size:630 final size:629
Alignment explanation
Indices: 319858--321032 Score: 1597
Period size: 630 Copynumber: 1.9 Consensus size: 629
319848 TAGCTTTAAC
* * **
319858 TCTTTCAGACAAGTGGCAATAGACGGCCAATCTTCTATCTTGCTTAATTTTTGACACCGGAAAAT
1 TCTTTAAGACAAGTGGCAATAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACCGGAAAAT
** * *
319923 GTGAAGCTTTTCAAGAGATGAACATTGTCTTCTTATTGGAACAATTTCCAGTTCGTCGCAGTTTG
66 GAAAAGCTTTTCAAGAGATGAACATTGTCCTCTTATTGGAACAATTTCCAGTTCGTCGCACTTTG
* *
319988 ATATTTCTAAAATTTGAAGAGAGGAAAACCCTTCCAAATCTGGAATGGAACTTAAATTAGGACAA
131 ATATTTCTAAAATTTGAAGAAAGGAAAACCCATCCAAATCTGGAATGGAACTTAAATTAGGACAA
** ** * * * *
320053 TAGCTTAACTTTAATTCTTCAAGATAAGTGGAGGTAGACAATCCATCTCCTATCTTGCTTAATTT
196 TAGCACAACACTAATTCTTCAAGACAAGTGGAAGTAGACAAACCATCTCCTATCTTGCTTAAGTT
* ** *
320118 TTGACACAAGGAAATGTGAAGCTTTTCAAGAGATTAACA-CTGTCCTCCTATCGGAACAATTTCC
261 TTCACACAAGGAAATGAAAAGCTTTTCAAGAGATGAACATCT-TCCTCCTATCGGAACAATTTCC
* * *
320182 AGATT-G-TGACAGATTGATATATCTAAAATTCGAAGAGAGGAAAATCCTTCCA-AATCAGGAAT
325 AG-TTCGCTG-CACATTGATATATCTAAAATTCGAAGAAAGGAAAATCCATCCATAA-CAGGAAT
* *** *
320244 GGAACTTAAATTAGGACAATTGCTTAACTTTAATTCTTTAAGATAAGTGGAGGTAGACAACCCGT
387 GGAACTTAAATTAGCACAACCACTTAACTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCGT
* * * *
320309 CTCCTATCTTGCTTAAGTT-TTCACAC-GAGGAAATG-AGAAGCTT-TTCAAGAGATGAACATCT
452 CTCCAATCTTGCTTAA-TTCTT-ACACTCA-GAAATGCA-AA-ATTCTTCAAGAGATGAACATAT
* *
320370 TCCT-CTTATTGGAACAATTTCCAGTTTGCTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAA
512 TCCTGC-TATTGGAACAATATCCAATTTGCTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAA
320434 AATCCATCCATAACTGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAAT
576 AATCCATCCATAACTGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAAT
*
320488 TCTTTAAGACAAGTGG-AGGTAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACCAGG-AA
1 TCTTTAAGACAAGTGGCA-ATAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACC-GGAAA
*
320551 ATGAAAAGCTTTTCAAGAGATGAACATCT-TCCTCTTATTGGAACAATTTCCAGTTTG-CTGCAC
64 ATGAAAAGCTTTTCAAGAGATGAACAT-TGTCCTCTTATTGGAACAATTTCCAGTTCGTC-GCAC
* *
320614 TTTGATATTTCT-AGATTTCGAAGAAAGGAAAATCCATCCATAA-CTGGAATGGAACTTAAATTA
127 TTTGATATTTCTAAAATTT-GAAGAAAGGAAAACCCATCCA-AATCTGGAATGGAACTTAAATTA
* * * *
320677 GGACAATTGCACAGCACTAATTCTTTAAGACAAGTGGAAGTAGACAAACCGTCTCCTATCTTGCT
190 GGACAATAGCACAACACTAATTCTTCAAGACAAGTGGAAGTAGACAAACCATCTCCTATCTTGCT
** * *
320742 TAAGTTTTCACATGAGGAAATGAAAAGCTTTTCAAGAGATGAACATCTTCCTCTTATTGGAACAA
255 TAAGTTTTCACACAAGGAAATGAAAAGCTTTTCAAGAGATGAACATCTTCCTCCTATCGGAACAA
* * * * * *
320807 TTTCCAGTTCGCTGCACTTTTATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCATAACTGGA
320 TTTCCAGTTCGCTGCACATTGATATATCTAAAATTCGAAGAAAGGAAAATCCATCCATAACAGGA
*
320872 ATGGAACTTAAATTAGCACAACCACTTAGCTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCC
385 ATGGAACTTAAATTAGCACAACCACTTAACTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCC
320937 GTCTCCAATCTTGCTTAATTCCTTACACTCAGAAATGCAAAATTCTTCAAGAGATGAACATATTC
450 GTCTCCAATCTTGCTTAATT-CTTACACTCAGAAATGCAAAATTCTTCAAGAGATGAACATATTC
321002 CTGCTATTGGAACAATATCCAATTTGCTGCA
514 CTGCTATTGGAACAATATCCAATTTGCTGCA
321033 ATCATAAACA
Statistics
Matches: 474, Mismatches: 55, Indels: 32
0.84 0.10 0.06
Matches are distributed among these distances:
629 13 0.03
630 445 0.94
631 16 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (629 bp):
TCTTTAAGACAAGTGGCAATAGACCGCCAATCTTCTATCTTGCTTAATTTAGGACACCGGAAAAT
GAAAAGCTTTTCAAGAGATGAACATTGTCCTCTTATTGGAACAATTTCCAGTTCGTCGCACTTTG
ATATTTCTAAAATTTGAAGAAAGGAAAACCCATCCAAATCTGGAATGGAACTTAAATTAGGACAA
TAGCACAACACTAATTCTTCAAGACAAGTGGAAGTAGACAAACCATCTCCTATCTTGCTTAAGTT
TTCACACAAGGAAATGAAAAGCTTTTCAAGAGATGAACATCTTCCTCCTATCGGAACAATTTCCA
GTTCGCTGCACATTGATATATCTAAAATTCGAAGAAAGGAAAATCCATCCATAACAGGAATGGAA
CTTAAATTAGCACAACCACTTAACTTTAATTCTTTAAGACAAGTGGAGGTAGACAACCCGTCTCC
AATCTTGCTTAATTCTTACACTCAGAAATGCAAAATTCTTCAAGAGATGAACATATTCCTGCTAT
TGGAACAATATCCAATTTGCTGCACTTTGATATTTCTAGATTTCGAAGAAAGGAAAATCCATCCA
TAACTGGAATGGAACTTAAATTAGGACAATTGCTCAGCACTAAT
Found at i:332061 original size:21 final size:23
Alignment explanation
Indices: 332018--332062 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
332008 CGCGCTTTTC
*
332018 ATTTATCACTTTGTGTGCTCTCT
1 ATTTAGCACTTTGTGTGCTCTCT
*
332041 ATTTAGCACTTTGTGTCCTCTC
1 ATTTAGCACTTTGTGTGCTCTC
332063 CGTTTAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.13, T:0.49
Consensus pattern (23 bp):
ATTTAGCACTTTGTGTGCTCTCT
Found at i:332068 original size:23 final size:23
Alignment explanation
Indices: 332017--332068 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
332007 GCGCGCTTTT
* *
332017 CATTTATCACTTTGTGTGCTCTC
1 CATTTAGCACTTTGTGTCCTCTC
*
332040 TATTTAGCACTTTGTGTCCTCTC
1 CATTTAGCACTTTGTGTCCTCTC
*
332063 CGTTTA
1 CATTTA
332069 ACACGTCTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.13, T:0.48
Consensus pattern (23 bp):
CATTTAGCACTTTGTGTCCTCTC
Found at i:333028 original size:20 final size:20
Alignment explanation
Indices: 332999--333054 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
332989 TCGATTTAAA
332999 GAAAA-GTATCGATATTTTT
1 GAAAATGTATCGATATTTTT
**
333018 GAGAAAT-TATCGATACATTT
1 GA-AAATGTATCGATATTTTT
333038 GAAAATGTATCGATATT
1 GAAAATGTATCGATATT
333055 AGAGTTTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (20 bp):
GAAAATGTATCGATATTTTT
Found at i:333805 original size:21 final size:22
Alignment explanation
Indices: 333780--333823 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
333770 TAAGCAAAAA
* *
333780 ATAAAAGGTTAATTTA-TTTTT
1 ATAAAACGTCAATTTACTTTTT
*
333801 ATAAATCGTCAATTTACTTTTT
1 ATAAAACGTCAATTTACTTTTT
333823 A
1 A
333824 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (22 bp):
ATAAAACGTCAATTTACTTTTT
Found at i:354571 original size:27 final size:26
Alignment explanation
Indices: 354541--354596 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
354531 GTCTGAAGAA
*
354541 ATTTATAATTTATAATTTAATGAATTT
1 ATTTATAATTTAT-ATTTAATCAATTT
**
354568 ATTTATTCTTTATATTTAATCAATTT
1 ATTTATAATTTATATTTAATCAATTT
354594 ATT
1 ATT
354597 GATCGTTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTATAATTTATATTTAATCAATTT
Found at i:355807 original size:39 final size:39
Alignment explanation
Indices: 355764--355842 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
355754 ATAAAAAGTT
*
355764 TCAAATTGGCTACAGATAAATTCTAACCATATGATAAAA
1 TCAAATTGGCTACAGATAAATTCTAACCATAAGATAAAA
* *
355803 TCAAATTGGGTACCGATAAATTCTAACCATAAGATAAAA
1 TCAAATTGGCTACAGATAAATTCTAACCATAAGATAAAA
355842 T
1 T
355843 AGTACCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (39 bp):
TCAAATTGGCTACAGATAAATTCTAACCATAAGATAAAA
Found at i:357717 original size:21 final size:21
Alignment explanation
Indices: 357693--357734 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
357683 GTTTGACTCA
357693 AACAAATAAACAGAGTTTAAT
1 AACAAATAAACAGAGTTTAAT
*
357714 AACAAATAAATAGAGTTTAAT
1 AACAAATAAACAGAGTTTAAT
357735 TGAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.10, T:0.26
Consensus pattern (21 bp):
AACAAATAAACAGAGTTTAAT
Found at i:371548 original size:39 final size:41
Alignment explanation
Indices: 371469--371550 Score: 141
Period size: 39 Copynumber: 2.0 Consensus size: 41
371459 ACGTGTCAAC
371469 TATGGTGGTAGGGTAGCTGACATTGATTGTAATTGGCTTTA
1 TATGGTGGTAGGGTAGCTGACATTGATTGTAATTGGCTTTA
*
371510 TATGGTGGTAGGGTAGCT-ATATT-ATTGTAATTGGCTTTA
1 TATGGTGGTAGGGTAGCTGACATTGATTGTAATTGGCTTTA
371549 TA
1 TA
371551 CGTTGTCGGT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
39 18 0.45
40 4 0.10
41 18 0.45
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.41
Consensus pattern (41 bp):
TATGGTGGTAGGGTAGCTGACATTGATTGTAATTGGCTTTA
Found at i:372157 original size:37 final size:37
Alignment explanation
Indices: 372115--372225 Score: 222
Period size: 37 Copynumber: 3.0 Consensus size: 37
372105 GGAGGCATGG
372115 ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
1 ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
372152 ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
1 ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
372189 ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
1 ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
372226 TGCGTATGTC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (37 bp):
ACAATCATACCAAATCAACTTAAAAGAAATGATTTTA
Done.