Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014851.1 Kokia drynarioides strain JFW-HI SEQ_129894, 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: 317943
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 641 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2409 original size:36 final size:36
Alignment explanation
Indices: 2352--2482 Score: 199
Period size: 36 Copynumber: 3.6 Consensus size: 36
2342 TTTTAAAAAC
* * *
2352 CCTCAAAACGACGACGCTTTGAGGGCTGAGCTTCAG
1 CCTCAAAACGGCGTCGTTTTGAGGGCTGAGCTTCAG
2388 CCTCAAAACGGCGTCGTTTTGAGGGCTGAGCTTCAG
1 CCTCAAAACGGCGTCGTTTTGAGGGCTGAGCTTCAG
** *
2424 CCTCAAAATAGCGTCGTTTTGAGGGCTGAGTTTCAG
1 CCTCAAAACGGCGTCGTTTTGAGGGCTGAGCTTCAG
*
2460 CCTCAAAACGGCGCCGTTTTGAG
1 CCTCAAAACGGCGTCGTTTTGAG
2483 CTCTTACCCA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 86 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.24
Consensus pattern (36 bp):
CCTCAAAACGGCGTCGTTTTGAGGGCTGAGCTTCAG
Found at i:2766 original size:29 final size:30
Alignment explanation
Indices: 2703--2767 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 30
2693 GCCACGTATT
2703 ATTATTTTGGCTTATTTATGCAAATAGTCTCTC
1 ATTATTTTGGCTTATTTATGCAAATAG---CTC
*
2736 ATTATTTTGGTTTATTTATGCAAATAG-TC
1 ATTATTTTGGCTTATTTATGCAAATAGCTC
2765 ATT
1 ATT
2768 TGACTTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.16
33 26 0.84
ACGTcount: A:0.26, C:0.11, G:0.12, T:0.51
Consensus pattern (30 bp):
ATTATTTTGGCTTATTTATGCAAATAGCTC
Found at i:2899 original size:29 final size:29
Alignment explanation
Indices: 2867--3183 Score: 250
Period size: 29 Copynumber: 10.8 Consensus size: 29
2857 TATTACCCCT
2867 AAACTTTCC-AAAATTCCATTTTTAACCTC
1 AAAC-TTCCAAAAATTCCATTTTTAACCTC
** * *
2896 AAACTTTTAAAAAATTACATTTGT-ACCTCC
1 AAAC-TTCCAAAAATTCCATTTTTAACCT-C
* * *
2926 GAACTTCCAAAAATTTCATTTTTAACCCTA
1 AAACTTCCAAAAATTCCATTTTTAA-CCTC
* *
2956 AAACTTCCAAAAATTCCATTTTGATCC-C
1 AAACTTCCAAAAATTCCATTTTTAACCTC
* *
2984 AAAACTTCCAAAAATTACATTTTTACCCTC
1 -AAACTTCCAAAAATTCCATTTTTAACCTC
* *
3014 AAACTCCCAAAAATTCTATTTTTAACCTC
1 AAACTTCCAAAAATTCCATTTTTAACCTC
*** * *
3043 GAAACTTTTGAAAATTACATTTTT-ACCCC
1 -AAACTTCCAAAAATTCCATTTTTAACCTC
* * *
3072 AAACTTCCAAAAATTTCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTT-AACCTC
* *
3102 AAACATCCAAAAATTACATTTTT-ACCTC
1 AAACTTCCAAAAATTCCATTTTTAACCTC
* * *
3130 GAACCTCCATAAAATTCCATTTTTGA-CTCC
1 AAACTTCCA-AAAATTCCATTTTTAACCT-C
*
3160 AAAACTTTCAAAAATTACCATTTT
1 -AAACTTCCAAAAATT-CCATTTT
3184 ACCCCTGAAT
Statistics
Matches: 228, Mismatches: 46, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
28 29 0.13
29 96 0.42
30 87 0.38
31 16 0.07
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTAACCTC
Found at i:2968 original size:59 final size:57
Alignment explanation
Indices: 2872--3187 Score: 218
Period size: 59 Copynumber: 5.4 Consensus size: 57
2862 CCCCTAAACT
* * **
2872 TTCC-AAAATTCCATTTTTAACCTCAAACTTTTAAAAAATTACATTTGT-ACCTCCGAAC
1 TTCCAAAAATTACATTTTTACCCTCAAAC-TTCCAAAAATT-CATTT-TAACCTCCGAAC
* * * **
2930 TTCCAAAAATTTCATTTTTAACCCTAAAACTTCCAAAAATTCCATTTTGATCC-CAAAAC
1 TTCCAAAAATTACATTTTT-ACCCTCAAACTTCCAAAAATT-CATTTT-AACCTCCGAAC
*
2989 TTCCAAAAATTACATTTTTACCCTCAAACTCCCAAAAATTCTATTTTTAACCT-CGAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTC-A-TTTTAACCTCCG-AAC
*** * **
3048 TTTTGAAAATTACATTTTTACCC-CAAACTTCCAAAAATTTCATTTTTGACC-CTAAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAA-TTCA-TTTTAACCTC-CGAAC
* * * * *
3106 ATCCAAAAATTACATTTTTA-CCTCGAACCTCCATAAAATTCCATTTTTGA-CTCCAAAAC
1 TTCCAAAAATTACATTTTTACCCTCAAACTTCCA-AAAATT-CA-TTTTAACCTCC-GAAC
*
3165 TTTCAAAAATTACCA-TTTTACCC
1 TTCCAAAAATTA-CATTTTTACCC
3188 CTGAATGTCC
Statistics
Matches: 209, Mismatches: 31, Indels: 34
0.76 0.11 0.12
Matches are distributed among these distances:
57 3 0.01
58 80 0.38
59 112 0.54
60 14 0.07
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (57 bp):
TTCCAAAAATTACATTTTTACCCTCAAACTTCCAAAAATTCATTTTAACCTCCGAAC
Found at i:3003 original size:88 final size:85
Alignment explanation
Indices: 2864--3187 Score: 282
Period size: 88 Copynumber: 3.7 Consensus size: 85
2854 TATTATTACC
* ** *
2864 CCTAAACTTTCC-AAAATTCCATTTTTAACCTC-AAACTTTTAAAAAATTACATTTGTA-CCTCC
1 CCTAAAC-TTCCAAAAATTCCA-TTTTGACC-CAAAAC-TTCCAAAAATTACATTTTTACCCT-C
*
2926 GAACTTCCAAAAATTTCATTTTTAA
61 AAACTTCCAAAAATTTCATTTTTAA
2951 CCCTAAAACTTCCAAAAATTCCATTTTGATCCCAAAACTTCCAAAAATTACATTTTTACCCTCAA
1 -CCT-AAACTTCCAAAAATTCCATTTTGA-CCCAAAACTTCCAAAAATTACATTTTTACCCTCAA
*
3016 ACTCCCAAAAA-TTCTATTTTTAA
63 ACTTCCAAAAATTTC-ATTTTTAA
*** * * * * *
3039 CCTCGAAACTTTTGAAAATTACATTTTTACCCCAAACTTCCAAAAATTTCATTTTTGACCCTAAA
1 CCT--AAACTTCCAAAAATTCCATTTTGACCCAAAACTTCCAAAAATTACATTTTT-ACCCTCAA
* *
3104 ACATCCAAAAATTACATTTTT-A
63 ACTTCCAAAAATTTCATTTTTAA
* * *
3126 CCTCGAACCTCCATAAAATTCCATTTTTGACTCCAAAACTTTCAAAAATTACCA-TTTTACCC
1 CCT-AAACTTCCA-AAAATTCCA-TTTTGAC-CCAAAACTTCCAAAAATTA-CATTTTTACCC
3188 CTGAATGTCC
Statistics
Matches: 194, Mismatches: 29, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
86 4 0.02
87 43 0.22
88 101 0.52
89 44 0.23
90 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.02, T:0.35
Consensus pattern (85 bp):
CCTAAACTTCCAAAAATTCCATTTTGACCCAAAACTTCCAAAAATTACATTTTTACCCTCAAACT
TCCAAAAATTTCATTTTTAA
Found at i:3203 original size:59 final size:59
Alignment explanation
Indices: 2927--3214 Score: 243
Period size: 59 Copynumber: 4.9 Consensus size: 59
2917 TGTACCTCCG
* * * * *
2927 AACTTCCAAAAATTTCATTTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTGA-TCCCAA
1 AACTTTCAAAAATTACATTTTTACCCCTGAATC-TCCAAAAATTCCATTTTTGACT-CCAA
* * * * * *
2986 AACTTCCAAAAATTACATTTTTA-CCCTCAAACTCCCAAAAATTCTATTTTTAAC-CTCGA
1 AACTTTCAAAAATTACATTTTTACCCCTGAATCT-CCAAAAATTCCATTTTTGACTC-CAA
** * *
3045 AACTTTTGAAAATTACATTTTTACCCC--AAACTTCCAAAAATTTCATTTTTGAC-CCTAA
1 AACTTTCAAAAATTACATTTTTACCCCTGAATC-TCCAAAAATTCCATTTTTGACTCC-AA
* * * *
3103 AACATCCAAAAATTACATTTTTACCTC-GAACCTCCATAAAATTCCATTTTTGACTCCAA
1 AACTTTCAAAAATTACATTTTTACCCCTGAATCTCCA-AAAATTCCATTTTTGACTCCAA
* **
3162 AACTTTCAAAAATTACCA-TTTTACCCCTGAATGTCCAAAAATTCTTTTTTTGA
1 AACTTTCAAAAATTA-CATTTTTACCCCTGAATCTCCAAAAATTCCATTTTTGA
3215 TCCCGATTTT
Statistics
Matches: 191, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
57 2 0.01
58 69 0.36
59 106 0.55
60 14 0.07
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (59 bp):
AACTTTCAAAAATTACATTTTTACCCCTGAATCTCCAAAAATTCCATTTTTGACTCCAA
Found at i:3211 original size:117 final size:116
Alignment explanation
Indices: 2876--3218 Score: 324
Period size: 117 Copynumber: 2.9 Consensus size: 116
2866 TAAACTTTCC
* * *** * * ** *
2876 AAAATTCCATTTTTAACCTCAAACTTTTAAAAAATTACATTTGT-ACCTCCGAACTTCCAAAAAT
1 AAAATTACATTTTTACCCTCAAAC-TCCCAAAAATTCCATTTTTAACCTCAAAACTTTCAAAAAT
* * *
2940 TTCATTTTTAACCCTAAAACTTCCAAAAATTCCA-TTTTGATCCCAAAACTTCCA
65 TACATTTTT-ACCC-CAAACTTCCAAAAATT-CATTTTTGATCCCAAAACATCCA
* * **
2994 AAAATTACATTTTTACCCTCAAACTCCCAAAAATTCTATTTTTAACCTCGAAACTTTTGAAAATT
1 AAAATTACATTTTTACCCTCAAACTCCCAAAAATTCCATTTTTAACCTCAAAACTTTCAAAAATT
3059 ACATTTTTACCCCAAACTTCCAAAAATTTCATTTTTGA-CCCTAAAACATCCA
66 ACATTTTTACCCCAAACTTCCAAAAA-TTCATTTTTGATCCC-AAAACATCCA
* *
3111 AAAATTACATTTTTA-CCTCGAAC-CTCCATAAAATTCCATTTTTGA-CTCCAAAACTTTCAAAA
1 AAAATTACATTTTTACCCTCAAACTC-CCA-AAAATTCCATTTTTAACCT-CAAAACTTTCAAAA
* *
3173 ATTACCA-TTTTACCCCTGAA-TGTCCAAAAATTCTTTTTTTGATCCC
63 ATTA-CATTTTTACCCC-AAACT-TCCAAAAATTC-ATTTTTGATCCC
3219 GATTTTTCTA
Statistics
Matches: 189, Mismatches: 24, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
115 1 0.01
116 30 0.16
117 91 0.48
118 64 0.34
119 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (116 bp):
AAAATTACATTTTTACCCTCAAACTCCCAAAAATTCCATTTTTAACCTCAAAACTTTCAAAAATT
ACATTTTTACCCCAAACTTCCAAAAATTCATTTTTGATCCCAAAACATCCA
Found at i:3302 original size:59 final size:59
Alignment explanation
Indices: 2961--3307 Score: 168
Period size: 59 Copynumber: 5.9 Consensus size: 59
2951 CCCTAAAACT
* * ** ** * **
2961 TCCAAAAATTCCA-TTTTGATCCCAAAACTTCCAAAAATTA-CATTTTTACCCTCAAAC
1 TCCAAAAATTCTATTTTTGAACCCAAATTTTCCAAAAATTACCATTTTCCCCCTGAATG
* * *
3018 TCCCAAAAATTCTATTTTT-AACCTCGAAACTTTT--GAAAATTA-CATTTTTACCCC-AAACT-
1 T-CCAAAAATTCTATTTTTGAACC-C-AAA-TTTTCCAAAAATTACCA-TTTTCCCCCTGAA-TG
*** ** **
3077 TCCAAAAATT-TCATTTTTG-ACCCTAAAACATCCAAAAATTA-CATTTT-TACCTCGAACC
1 TCCAAAAATTCT-ATTTTTGAACCC-AAATTTTCCAAAAATTACCATTTTCCCCCT-GAATG
* * *
3135 TCCATAAAATTCCATTTTTG-ACTCCAAAACTTT-CAAAAATTACCATTTTACCCCTGAATG
1 TCCA-AAAATTCTATTTTTGAAC-CC-AAATTTTCCAAAAATTACCATTTTCCCCCTGAATG
* * * * * * *
3195 TCCAAAAATTCTTTTTTTGATCCCGATTTTTCTAAAAATTATCGTTTTCCCCCTGAATG
1 TCCAAAAATTCTATTTTTGAACCCAAATTTTCCAAAAATTACCATTTTCCCCCTGAATG
* * *
3254 -CCTAAAATTCTATTTTT-AACAGCAAATTTTCCCAAAATTACCATTTTTCCCCCT
1 TCCAAAAATTCTATTTTTGAAC-CCAAATTTTCCAAAAATTACCA-TTTTCCCCCT
3308 CGAGAGTCTA
Statistics
Matches: 220, Mismatches: 47, Indels: 44
0.71 0.15 0.14
Matches are distributed among these distances:
56 3 0.01
57 12 0.05
58 81 0.37
59 89 0.40
60 30 0.14
61 5 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
TCCAAAAATTCTATTTTTGAACCCAAATTTTCCAAAAATTACCATTTTCCCCCTGAATG
Found at i:7824 original size:14 final size:14
Alignment explanation
Indices: 7807--7840 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7797 AGCATTTATA
*
7807 CCAATTCAACCATT
1 CCAAATCAACCATT
7821 CCAAATCAACCATT
1 CCAAATCAACCATT
*
7835 CAAAAT
1 CCAAAT
7841 GAATTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (14 bp):
CCAAATCAACCATT
Found at i:8676 original size:32 final size:31
Alignment explanation
Indices: 8640--8745 Score: 126
Period size: 31 Copynumber: 3.4 Consensus size: 31
8630 TTTAATGAAT
*
8640 TTAATTTAATATTTTATCTAGATAGTATTTTA
1 TTAATTTAATA-TTTATCTAGATAATATTTTA
* * **
8672 TTAATTTAATATTAATAT-GA-AATATTAAA
1 TTAATTTAATATTTATCTAGATAATATTTTA
*
8701 TTTAATTTAATATTTATCTAAATAATATTTTA
1 -TTAATTTAATATTTATCTAGATAATATTTTA
8733 TTAATTTAATATT
1 TTAATTTAATATT
8746 ATTGTGATTA
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
29 6 0.10
30 18 0.30
31 19 0.31
32 18 0.30
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (31 bp):
TTAATTTAATATTTATCTAGATAATATTTTA
Found at i:8748 original size:19 final size:21
Alignment explanation
Indices: 8721--8763 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
8711 TATTTATCTA
*
8721 AATAATATT-TTATTAATT-T
1 AATAATATTGTGATTAATTCT
*
8740 AATATTATTGTGATTAATTCT
1 AATAATATTGTGATTAATTCT
8761 AAT
1 AAT
8764 CCTAGTTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 8 0.40
21 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (21 bp):
AATAATATTGTGATTAATTCT
Found at i:9794 original size:5 final size:5
Alignment explanation
Indices: 9761--9787 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
9751 ATGTAGCCGT
9761 TTTTA TTTTA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT
9788 ATTTTATGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:10864 original size:25 final size:25
Alignment explanation
Indices: 10836--10901 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
10826 TAGTTTAGTG
10836 TATATTATAAATTATTAATTTATAT
1 TATATTATAAATTATTAATTTATAT
* * * *
10861 TATATGA-AAATTAAATATTTTGTAT
1 TATATTATAAATT-ATTAATTTATAT
*
10886 TATAATAT-AATTATTA
1 TATATTATAAATTATTA
10902 GAAAAATATC
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
24 8 0.25
25 24 0.75
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
TATATTATAAATTATTAATTTATAT
Found at i:14899 original size:2 final size:2
Alignment explanation
Indices: 14892--14917 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14882 CACACTTAAA
14892 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
14918 TTTTTTTTTT
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:14958 original size:16 final size:16
Alignment explanation
Indices: 14925--14975 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
14915 TATTTTTTTT
**
14925 TTTTTCATCT-TTTTA
1 TTTTTCATCTATTCAA
14940 TTTTTCTATC-ATTCAA
1 TTTTTC-ATCTATTCAA
*
14956 TTTTTCATCTTTTCAA
1 TTTTTCATCTATTCAA
14972 TTTT
1 TTTT
14976 CTTTTCCCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTCATCTATTCAA
Found at i:19149 original size:12 final size:12
Alignment explanation
Indices: 19115--19208 Score: 88
Period size: 12 Copynumber: 8.2 Consensus size: 12
19105 TTATCATCCA
19115 AACAACAAAAAC
1 AACAACAAAAAC
* *
19127 AATAACCAAAAC
1 AACAACAAAAAC
* *
19139 AACAGCAAAAAT
1 AACAACAAAAAC
*
19151 AACAGC-AAAAC
1 AACAACAAAAAC
19162 AACAAC--AAA-
1 AACAACAAAAAC
*
19171 AACAACAAAAAT
1 AACAACAAAAAC
* *
19183 AGCAACAAAAAT
1 AACAACAAAAAC
19195 AACAACAAAAAC
1 AACAACAAAAAC
19207 AA
1 AA
19209 TACCAAAACA
Statistics
Matches: 68, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
9 6 0.09
10 3 0.04
11 12 0.18
12 47 0.69
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.04
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:19159 original size:23 final size:22
Alignment explanation
Indices: 19114--19204 Score: 98
Period size: 21 Copynumber: 4.1 Consensus size: 22
19104 ATTATCATCC
19114 AAACAACAA-AAACAATAAC-CA
1 AAACAACAACAAA-AATAACACA
*
19135 AAACAACAGCAAAAATAACAGCA
1 AAACAACAACAAAAATAACA-CA
*
19158 AAACAACAACAAAAACAACA-A
1 AAACAACAACAAAAATAACACA
* *
19179 AAATAGCAACAAAAATAACAACA
1 AAACAACAACAAAAATAAC-ACA
19202 AAA
1 AAA
19205 ACAATACCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
21 31 0.53
22 4 0.07
23 24 0.41
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.04
Consensus pattern (22 bp):
AAACAACAACAAAAATAACACA
Found at i:19162 original size:44 final size:44
Alignment explanation
Indices: 19114--19204 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
19104 ATTATCATCC
* * * *
19114 AAACAACAA-AAACAATAACCAAAACAACAGCAAAAATAACAGCA
1 AAACAACAACAAA-AACAACAAAAACAACAACAAAAATAACAACA
* *
19158 AAACAACAACAAAAACAACAAAAATAGCAACAAAAATAACAACA
1 AAACAACAACAAAAACAACAAAAACAACAACAAAAATAACAACA
19202 AAA
1 AAA
19205 ACAATACCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.93
45 3 0.08
ACGTcount: A:0.71, C:0.21, G:0.03, T:0.04
Consensus pattern (44 bp):
AAACAACAACAAAAACAACAAAAACAACAACAAAAATAACAACA
Found at i:19243 original size:12 final size:12
Alignment explanation
Indices: 19226--19251 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19216 ACAGTAAAAA
19226 AACCAAAATAGT
1 AACCAAAATAGT
19238 AACCAAAATAGT
1 AACCAAAATAGT
19250 AA
1 AA
19252 AATAACATTA
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:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (12 bp):
AACCAAAATAGT
Found at i:21689 original size:16 final size:15
Alignment explanation
Indices: 21668--21711 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
21658 GAAAATTTTT
21668 ATGTTAAAGGACTAAA
1 ATGTTAAAGGACT-AA
*
21684 ATGTTAAAGGAATAA
1 ATGTTAAAGGACTAA
21699 AT-TTGAAAGGACT
1 ATGTT-AAAGGACT
21712 TGGGGAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (15 bp):
ATGTTAAAGGACTAA
Found at i:22590 original size:120 final size:119
Alignment explanation
Indices: 22356--22594 Score: 320
Period size: 120 Copynumber: 2.0 Consensus size: 119
22346 ATATGTACAG
* * * * **
22356 ATACCGTATCGATGGCTGGGTACTACATATGTTGTGAGTCCTCGACAGCTTGTGTGAACAACATC
1 ATACAGTATCAATGGCTGGGTACCACATATGTTGCGAGTCCTCGACAGCTCATGTGAACAACATC
* *
22421 GTATACTGGTACTAGAGTTGATATAGACATGAGAATGAAATTTGAGATTATAAC
66 ATATACTGGTACTAGAGTTGATACAGACATGAGAATGAAATTTGAGATTATAAC
* **
22475 ATACAGTATCAATGGCTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGTAACAT
1 ATACAGTATCAATGGCT-GGGTACCACATATGTTGCGAGTCCTCGACAGCTCATGTGAACAACAT
* *
22540 CATATACTGGTAAC-AGAGTTGATACAGATATGAGGATGAAATTTTG-GATTATAAC
65 CATATACTGGT-ACTAGAGTTGATACAGACATGAGAATGAAA-TTTGAGATTATAAC
22595 TTGTGGAAGC
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
119 15 0.14
120 83 0.80
121 6 0.06
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.29
Consensus pattern (119 bp):
ATACAGTATCAATGGCTGGGTACCACATATGTTGCGAGTCCTCGACAGCTCATGTGAACAACATC
ATATACTGGTACTAGAGTTGATACAGACATGAGAATGAAATTTGAGATTATAAC
Found at i:25806 original size:16 final size:14
Alignment explanation
Indices: 25785--25819 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
25775 ATAGATCATA
25785 TATTTACTTTATATTT
1 TATTTA-TTT-TATTT
25801 TATTTATTTTATTT
1 TATTTATTTTATTT
25815 TATTT
1 TATTT
25820 TAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 3 0.16
16 6 0.32
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTATTTTATTT
Found at i:28777 original size:30 final size:32
Alignment explanation
Indices: 28741--28807 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 32
28731 TGGACCTTAT
* *
28741 AACTAGGTC-TTTAAT-TAAAATAAACTTCAA
1 AACTAGGTCATTGAATCTAAAATAAACCTCAA
*
28771 AACTAGGTCATTGAATCTAAAATAGACCTCAA
1 AACTAGGTCATTGAATCTAAAATAAACCTCAA
28803 AACTA
1 AACTA
28808 AGACACTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 9 0.28
31 5 0.16
32 18 0.56
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.28
Consensus pattern (32 bp):
AACTAGGTCATTGAATCTAAAATAAACCTCAA
Found at i:29074 original size:33 final size:33
Alignment explanation
Indices: 29004--29075 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
28994 TCCCAATATT
* *
29004 TTCTATCCTAAAGACAACTTCTTACCTCAGTTA
1 TTCTATCCTAAAGACAACTTCTTACCTCAATGA
* * * *
29037 TTCTATCCTAGAGATAATTTCTTACCTCAATGG
1 TTCTATCCTAAAGACAACTTCTTACCTCAATGA
29070 TTCTAT
1 TTCTAT
29076 AAATTTCTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (33 bp):
TTCTATCCTAAAGACAACTTCTTACCTCAATGA
Found at i:35690 original size:17 final size:17
Alignment explanation
Indices: 35668--35706 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
35658 AGGTGGAGAA
* *
35668 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
35685 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
35702 CTTGT
1 CTTGT
35707 CAAGGTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:36181 original size:7 final size:7
Alignment explanation
Indices: 36169--36200 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
36159 TTTCTCTTCC
36169 TTTTCAT
1 TTTTCAT
36176 TTTTCAT
1 TTTTCAT
36183 TTTTCAT
1 TTTTCAT
36190 TTTTCAT
1 TTTTCAT
36197 TTTT
1 TTTT
36201 TCTCAAGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTCAT
Found at i:51072 original size:4 final size:4
Alignment explanation
Indices: 51063--51098 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
51053 ACATCACAAC
51063 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
51099 TACCATATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:52136 original size:20 final size:20
Alignment explanation
Indices: 52113--52154 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
52103 ATGTGCATAT
*
52113 AGGGGCACCGAAGTGAAAAC
1 AGGGGCAACGAAGTGAAAAC
* *
52133 AGGGGCAATGAAGTGCAAAC
1 AGGGGCAACGAAGTGAAAAC
52153 AG
1 AG
52155 TAAAAGCATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.17, G:0.36, T:0.07
Consensus pattern (20 bp):
AGGGGCAACGAAGTGAAAAC
Found at i:64938 original size:47 final size:47
Alignment explanation
Indices: 64867--64956 Score: 130
Period size: 47 Copynumber: 1.9 Consensus size: 47
64857 AGCCACACCA
64867 TTTTCTTCGACTTTCCTCCCATCCAAACT-CCCACCACTTCATTATCG
1 TTTTCTTCGACTTTCCTCCCATCCAAA-TACCCACCACTTCATTATCG
* *
64914 TTTTCTTTC-ACTTTCCTCCTATCCAAATACCCACGACTTCATT
1 TTTTC-TTCGACTTTCCTCCCATCCAAATACCCACCACTTCATT
64957 CCCAGCAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 1 0.03
47 35 0.90
48 3 0.08
ACGTcount: A:0.20, C:0.38, G:0.03, T:0.39
Consensus pattern (47 bp):
TTTTCTTCGACTTTCCTCCCATCCAAATACCCACCACTTCATTATCG
Found at i:67000 original size:29 final size:29
Alignment explanation
Indices: 66948--67003 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
66938 TGTCCACTTC
*
66948 TCCTAGATTGGTACCTAAAGTTTTTTTTG
1 TCCTAGATTGGTACCTAAACTTTTTTTTG
* *
66977 TCCTAGATTGGTACTTGAACTTTTTTT
1 TCCTAGATTGGTACCTAAACTTTTTTT
67004 CCGTTCACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (29 bp):
TCCTAGATTGGTACCTAAACTTTTTTTTG
Found at i:68644 original size:26 final size:26
Alignment explanation
Indices: 68601--68742 Score: 87
Period size: 26 Copynumber: 6.0 Consensus size: 26
68591 AGATTCATTT
* *
68601 TTACAAGCCAGTATAGTATATCGCTC
1 TTACGAGCCAGTACAGTATATCGCTC
* * *
68627 TTACGAGCCAGTTCAGTATTTCACTC
1 TTACGAGCCAGTACAGTATATCGCTC
68653 ---C-A---AGTACAGTATATCGCTC
1 TTACGAGCCAGTACAGTATATCGCTC
* *
68672 TTACGAGCCAGTACAATATATTG--C
1 TTACGAGCCAGTACAGTATATCGCTC
* * *
68696 -T-C---CCAATATAGTATACCGCTC
1 TTACGAGCCAGTACAGTATATCGCTC
*
68717 TTATGAGCCAGTACAGTATATCGCTC
1 TTACGAGCCAGTACAGTATATCGCTC
68743 CCAGTATAGT
Statistics
Matches: 83, Mismatches: 19, Indels: 28
0.64 0.15 0.22
Matches are distributed among these distances:
19 25 0.30
21 1 0.01
22 4 0.05
23 3 0.04
24 1 0.01
26 49 0.59
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (26 bp):
TTACGAGCCAGTACAGTATATCGCTC
Found at i:68679 original size:45 final size:45
Alignment explanation
Indices: 68610--68799 Score: 211
Period size: 45 Copynumber: 4.2 Consensus size: 45
68600 TTTACAAGCC
* * * *
68610 AGTATAGTATATCGCTCTTACGAGCCAGTTCAGTATTTCACTCCA
1 AGTATAGTATACCGCTCTTACGAGCCAGTACAGTATATCGCTCCA
* * * *
68655 AGTACAGTATATCGCTCTTACGAGCCAGTACAATATATTGCTCCCA
1 AGTATAGTATACCGCTCTTACGAGCCAGTACAGTATATCGCT-CCA
* *
68701 A-TATAGTATACCGCTCTTATGAGCCAGTACAGTATATCGCTCCC
1 AGTATAGTATACCGCTCTTACGAGCCAGTACAGTATATCGCTCCA
* * * * * *
68745 AGTATAGTATACCACTCTTATGAGTCAATTCAGTATATCGCTCCC
1 AGTATAGTATACCGCTCTTACGAGCCAGTACAGTATATCGCTCCA
*
68790 AGTACAGTAT
1 AGTATAGTAT
68800 TTCCTTCAGT
Statistics
Matches: 126, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
44 3 0.02
45 119 0.94
46 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (45 bp):
AGTATAGTATACCGCTCTTACGAGCCAGTACAGTATATCGCTCCA
Found at i:71351 original size:30 final size:30
Alignment explanation
Indices: 71317--71379 Score: 119
Period size: 29 Copynumber: 2.1 Consensus size: 30
71307 CTTTTTTAGA
71317 TTTAAAAAAATTTACCTAATATTTAATTTT
1 TTTAAAAAAATTTACCTAATATTTAATTTT
71347 TTT-AAAAAATTTACCTAATATTTAATTTT
1 TTTAAAAAAATTTACCTAATATTTAATTTT
71376 TTTA
1 TTTA
71380 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (30 bp):
TTTAAAAAAATTTACCTAATATTTAATTTT
Found at i:82808 original size:91 final size:91
Alignment explanation
Indices: 82642--82865 Score: 255
Period size: 88 Copynumber: 2.5 Consensus size: 91
82632 ATTAGGGGCG
*
82642 GTTCAAGTACCCAATTGAGTGCAAAA-ATAA-TAAGGGGCTTAATTGCTTTTTTTAGAAAAAAGT
1 GTTCAAGTACCCAATTGAGTGCAAAATAAAAGTAA-GGGCTTAATTGCTTTTTTTAGAAAAAAGT
* * * ** *
82705 TTGAGGGTTTTTTTTATATTTTTTGAAA
65 TTAAAGG-TTTTTTGATACATTTTAAAA
* *
82733 GTTCAAGTACCCAATTAAGTGCAAAATAAAAGTAAGGGCTTAATTGCTTTTTTT-G-AAAAATTT
1 GTTCAAGTACCCAATTGAGTGCAAAATAAAAGTAAGGGCTTAATTGCTTTTTTTAGAAAAAAGTT
82796 TAAAGGTATTTTTGATACATTTTAAAA
66 TAAAGGT-TTTTTGATACATTTTAAAA
* * *
82823 GTT--AGTATCCAAGTGAGTGCAAAATAAAAG-CAGAGGCTTAATT
1 GTTCAAGTACCCAATTGAGTGCAAAATAAAAGTAAG-GGCTTAATT
82866 ATTTTTTAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
87 2 0.02
88 33 0.28
89 1 0.01
90 29 0.25
91 26 0.22
92 22 0.19
93 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.37
Consensus pattern (91 bp):
GTTCAAGTACCCAATTGAGTGCAAAATAAAAGTAAGGGCTTAATTGCTTTTTTTAGAAAAAAGTT
TAAAGGTTTTTTGATACATTTTAAAA
Found at i:83760 original size:57 final size:58
Alignment explanation
Indices: 83651--83761 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
83641 CGAGAATTTA
*
83651 AAAAAAAAAATTGGTGTTGGCCATGCAATAGTCGACACCCCCTTTTTTATCTGACAGG
1 AAAAAAAAAATTGGTGTTGGCCATGCAATAGTCGACACCCCCTTTTTAATCTGACAGG
** * *
83709 AAAAAAAATTTTGGTGTTGGCTATTGC-ATGGTCGACA-CCCCTTTTTAATCTGA
1 AAAAAAAAAATTGGTGTTGGCCA-TGCAATAGTCGACACCCCCTTTTTAATCTGA
83762 TAAAAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
57 15 0.32
58 29 0.62
59 3 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Consensus pattern (58 bp):
AAAAAAAAAATTGGTGTTGGCCATGCAATAGTCGACACCCCCTTTTTAATCTGACAGG
Found at i:83829 original size:16 final size:16
Alignment explanation
Indices: 83798--83831 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
83788 TGACCAACAC
* *
83798 CAAATTTTTTTTTTTT
1 CAAATTTTTGTATTTT
83814 CAAATTTTTGTATTTT
1 CAAATTTTTGTATTTT
83830 CA
1 CA
83832 TATATCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.65
Consensus pattern (16 bp):
CAAATTTTTGTATTTT
Found at i:84399 original size:22 final size:22
Alignment explanation
Indices: 84374--84428 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
84364 AGGTCTGTCC
84374 ATATTATTTT-TTTAAAATATTT
1 ATATTATTTTATTT-AAATATTT
* *
84396 ATATTGTTTTATTTTAATATTT
1 ATATTATTTTATTTAAATATTT
*
84418 A-ATAATTTTAT
1 ATATTATTTTAT
84429 ACATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 8 0.29
22 17 0.61
23 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
ATATTATTTTATTTAAATATTT
Found at i:86499 original size:28 final size:27
Alignment explanation
Indices: 86464--86518 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
86454 CTGAATTCCT
86464 TTTTAAATTT-ATTATAAGATTAAATTTG
1 TTTTAAATTTAATT-TAA-ATTAAATTTG
86492 TTTTAAATTTAAATTTAAATTAAATTT
1 TTTTAAATTT-AATTTAAATTAAATTT
86519 AAATTTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 19 0.76
29 3 0.12
30 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (27 bp):
TTTTAAATTTAATTTAAATTAAATTTG
Found at i:86504 original size:6 final size:6
Alignment explanation
Indices: 86493--86539 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
86483 TTAAATTTGT
** *
86493 TTTAAA TTTAAA TTTAAA -TTAAA TTTAAA TTTACC TTTAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
86540 ATTATTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:86514 original size:11 final size:11
Alignment explanation
Indices: 86493--86523 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
86483 TTAAATTTGT
86493 TTTAAATTTAAA
1 TTTAAA-TTAAA
86505 TTTAAATTAAA
1 TTTAAATTAAA
86516 TTTAAATT
1 TTTAAATT
86524 TACCTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.68
12 6 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:86550 original size:17 final size:17
Alignment explanation
Indices: 86466--86550 Score: 80
Period size: 17 Copynumber: 4.9 Consensus size: 17
86456 GAATTCCTTT
* *
86466 TTAAATTTATTATAAGA
1 TTAAATTTATTTTAAAA
* *
86483 TTAAATTTGTTTTAAAT
1 TTAAATTTATTTTAAAA
** *
86500 TTAAATTTAAATTAAAT
1 TTAAATTTATTTTAAAA
*
86517 TTAAATTTACCTTTAAAA
1 TTAAATTTA-TTTTAAAA
*
86535 TTAAAATTATTTTAAA
1 TTAAATTTATTTTAAA
86551 CTAAAAAAAC
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 42 0.76
18 13 0.24
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:87198 original size:16 final size:16
Alignment explanation
Indices: 87162--87221 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
87152 TTGTTTATTT
87162 TAAA-AACAATTAATAA
1 TAAATAACAA-TAATAA
87178 T-AATAACAATAATAA
1 TAAATAACAATAATAA
*
87193 TAAAT---AATAGTAA
1 TAAATAACAATAATAA
*
87206 TAAATAACATTAATAA
1 TAAATAACAATAATAA
87222 ATATTAATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
13 12 0.33
15 9 0.25
16 15 0.42
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (16 bp):
TAAATAACAATAATAA
Found at i:87206 original size:13 final size:13
Alignment explanation
Indices: 87172--87242 Score: 67
Period size: 13 Copynumber: 5.7 Consensus size: 13
87162 TAAAAACAAT
87172 TAATAATAAT-AA
1 TAATAATAATAAA
*
87184 CAATAATAATAAA
1 TAATAATAATAAA
*
87197 TAATAGTAATAAA
1 TAATAATAATAAA
* *
87210 TAACATTAATAAA
1 TAATAATAATAAA
* *
87223 TATTAATTA-AAA
1 TAATAATAATAAA
87235 TAA-AATAA
1 TAATAATAA
87243 AGAAAGTGAG
Statistics
Matches: 47, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
11 4 0.09
12 14 0.30
13 29 0.62
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:93993 original size:17 final size:16
Alignment explanation
Indices: 93955--94063 Score: 94
Period size: 17 Copynumber: 6.4 Consensus size: 16
93945 TAAATTCCTT
93955 TTTAAATTTATTATAAGA
1 TTTAAATTTATT-TAA-A
93973 -TTAAATTTATTTGAAA
1 TTTAAATTTATTT-AAA
*
93989 TTTAAATTTGTTTTAAA
1 TTTAAATTT-ATTTAAA
* *
94006 TTTAAATTTAAATTAAG
1 TTTAAATTT-ATTTAAA
94023 TTTAAATTTACCTTTAAA
1 TTTAAATTTA--TTTAAA
* *
94041 ATTAAAATTATTTTAAA
1 TTTAAATTTA-TTTAAA
94058 TTTAAA
1 TTTAAA
94064 CAAAAGTCTC
Statistics
Matches: 75, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
16 3 0.04
17 57 0.76
18 15 0.20
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:93997 original size:6 final size:6
Alignment explanation
Indices: 93973--94063 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
93963 TATTATAAGA
**
93973 TTAAAT TT--AT TTGAAAT TTAAAT TT-GTT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* ** * * *
94018 TTAAGT TTAAAT TTACCT TTAAAA TTAAAA TT-ATT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
94064 CAAAAGTCTC
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
4 4 0.06
5 10 0.15
6 47 0.72
7 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (6 bp):
TTAAAT
Found at i:94012 original size:23 final size:23
Alignment explanation
Indices: 93981--94063 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
93971 GATTAAATTT
*
93981 ATTTGAAATTTAAATT-TGTTTTAA
1 ATTT-AAATTTAAATTAAG-TTTAA
94005 ATTTAAATTTAAATTAAGTTTAA
1 ATTTAAATTTAAATTAAGTTTAA
** **
94028 ATTTACCTTTAAAATTAAAATT-A
1 ATTTAAATTT-AAATTAAGTTTAA
*
94051 TTTTAAATTTAAA
1 ATTTAAATTTAAA
94064 CAAAAGTCTC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
22 3 0.06
23 32 0.65
24 14 0.29
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTAAATTTAAATTAAGTTTAA
Found at i:94032 original size:29 final size:29
Alignment explanation
Indices: 94000--94063 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
93990 TTAAATTTGT
*
94000 TTTAAATTT-AAATTTAAATTAAGTTTAAA
1 TTTAAATTTAAAATTAAAATT-AGTTTAAA
** *
94029 TTTACCTTTAAAATTAAAATTATTTTAAA
1 TTTAAATTTAAAATTAAAATTAGTTTAAA
94058 TTTAAA
1 TTTAAA
94064 CAAAAGTCTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
29 18 0.64
30 10 0.36
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTAAATTTAAAATTAAAATTAGTTTAAA
Found at i:94726 original size:16 final size:16
Alignment explanation
Indices: 94690--94737 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
94680 TTGTTTATTT
94690 TAAA-AACAATTAATAA
1 TAAATAACAA-TAATAA
94706 T-AATAACAATAATAA
1 TAAATAACAATAATAA
* *
94721 TAAATAATAGTAATAA
1 TAAATAACAATAATAA
94737 T
1 T
94738 TAACATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 9 0.32
16 19 0.68
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (16 bp):
TAAATAACAATAATAA
Found at i:95914 original size:30 final size:30
Alignment explanation
Indices: 95880--96275 Score: 137
Period size: 29 Copynumber: 13.5 Consensus size: 30
95870 TTGAAGTTTT
*
95880 TAAAAATTAAATTTTTACCCTCAAACTTCA
1 TAAAAATTACATTTTTACCCTCAAACTTCA
* **
95910 TAAAAATTACATTTTT-CCTTTGAACTTCCA
1 TAAAAATTACATTTTTACCCTCAAACTT-CA
* *
95940 -AAAAATTACATTTTTTTACCAT-GAACTTTC-
1 TAAAAATTACA--TTTTTACCCTCAAAC-TTCA
*
95970 TAAAAATTACATTTTTACCCCCTAAACTT-A
1 TAAAAATTACATTTTTACCCTC-AAACTTCA
* *
96000 TAAAAATTTCA-TTTTACCCTTAAACTT--
1 TAAAAATTACATTTTTACCCTCAAACTTCA
* * *
96027 TCCAAAATTACATTTTAACCCT-AAATTTTC-
1 T-AAAAATTACATTTTTACCCTCAAA-CTTCA
* * * *
96057 CAAAAATCACATTTTTTACCCACGAACTT--
1 TAAAAATTACA-TTTTTACCCTCAAACTTCA
* * *
96086 TCAAAAATTACATTTTTGACCAT-AAAATT-T
1 T-AAAAATTACATTTTT-ACCCTCAAACTTCA
* * *
96116 TCAAAAATCACA-TTTTACCCCCGAACCTTC-
1 T-AAAAATTACATTTTTACCCTC-AAACTTCA
* * *
96146 -AATAATTACATTTTTAACCCT-AAAATT-T
1 TAAAAATTACATTTTT-ACCCTCAAACTTCA
** * *
96174 TCAAAAATCCCAATTTTACTCC-CGAA-TATC-
1 T-AAAAATTACATTTTTAC-CCTCAAACT-TCA
* *
96204 CAAAAATTACATTTTT-CCCCCAAA-TGTC-
1 TAAAAATTACATTTTTACCCTCAAACT-TCA
*
96232 TAAAAATTACATTTTT-CCCCCAAA-TGTC-
1 TAAAAATTACATTTTTACCCTCAAACT-TCA
96260 TAAAAATTACCATTTT
1 TAAAAATTA-CATTTT
96276 GCCCCTGAAG
Statistics
Matches: 284, Mismatches: 50, Indels: 65
0.71 0.13 0.16
Matches are distributed among these distances:
27 3 0.01
28 75 0.26
29 90 0.32
30 86 0.30
31 25 0.09
32 5 0.02
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.37
Consensus pattern (30 bp):
TAAAAATTACATTTTTACCCTCAAACTTCA
Found at i:95935 original size:29 final size:29
Alignment explanation
Indices: 95880--96014 Score: 107
Period size: 30 Copynumber: 4.5 Consensus size: 29
95870 TTGAAGTTTT
* **
95880 TAAAAATTAAATTTTTACCCTCAAACTTCA
1 TAAAAATTACATTTTTA-CCTTGAACTTCA
95910 TAAAAATTACATTTTT-CCTTTGAACTTCCA
1 TAAAAATTACATTTTTACC-TTGAACTT-CA
*
95940 -AAAAATTACATTTTTTTACCATGAACTTTC-
1 TAAAAATTACA--TTTTTACCTTGAAC-TTCA
* *
95970 TAAAAATTACATTTTTACCCCCTAAACTT-A
1 TAAAAATTACATTTTTA--CCTTGAACTTCA
*
96000 TAAAAATTTCATTTT
1 TAAAAATTACATTTT
96015 ACCCTTAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.02
29 22 0.25
30 33 0.38
31 27 0.31
32 4 0.05
ACGTcount: A:0.39, C:0.19, G:0.01, T:0.41
Consensus pattern (29 bp):
TAAAAATTACATTTTTACCTTGAACTTCA
Found at i:96015 original size:29 final size:27
Alignment explanation
Indices: 95970--96281 Score: 121
Period size: 28 Copynumber: 10.8 Consensus size: 27
95960 ATGAACTTTC
95970 TAAAAATTACATTTTTACCCCCTAAACTT
1 TAAAAATTACA-TTTTA-CCCCTAAACTT
* *
95999 ATAAAAATTTCATTTTACCCTTAAACTT
1 -TAAAAATTACATTTTACCCCTAAACTT
* * *
96027 TCCAAAATTACATTTTAACCCTAAATTT
1 T-AAAAATTACATTTTACCCCTAAACTT
* *
96055 TCCAAAAATCACATTTTTTACCCAC-GAACTT
1 T--AAAAATTACA--TTTTACCC-CTAAACTT
* *
96086 TCAAAAATTACATTTTTGA-CCATAAAATTT
1 T-AAAAATTACA-TTTT-ACCCCT-AAACTT
* * *
96116 TCAAAAATCACATTTTACCCCCGAACCTT
1 T-AAAAATTACATTTTA-CCCCTAAACTT
* * * *
96145 CAATAATTACATTTTTAACCCTAAAATTT
1 TAAAAATTACA-TTTTACCCCT-AAACTT
** * *
96174 TCAAAAATCCCAATTTTACTCCCGAATA-TC
1 T-AAAAATTAC-ATTTTAC-CCCTAA-ACTT
* * *
96204 CAAAAATTACATTTTTCCCCCAAA-TGT
1 TAAAAATTACATTTTACCCCTAAACT-T
* *
96231 CTAAAAATTACATTTTTCCCCCAAA-TGT
1 -TAAAAATTACATTTTACCCCTAAACT-T
*
96259 CTAAAAATTACCATTTTGCCCCT
1 -TAAAAATTA-CATTTTACCCCT
96282 GAAGTATCCA
Statistics
Matches: 219, Mismatches: 44, Indels: 39
0.73 0.15 0.13
Matches are distributed among these distances:
26 2 0.01
27 6 0.03
28 86 0.39
29 55 0.25
30 52 0.24
31 17 0.08
32 1 0.00
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (27 bp):
TAAAAATTACATTTTACCCCTAAACTT
Found at i:96033 original size:28 final size:28
Alignment explanation
Indices: 95963--96179 Score: 118
Period size: 30 Copynumber: 7.4 Consensus size: 28
95953 TTTTACCATG
* *
95963 AACTTTCTAAAAATTACATTTTTACCCCCTA
1 AACTTTC-CAAAATTACA-TTTTA-ACCCTA
* *
95994 AACTTAT-AAAAATTTCATTTT-ACCCTTA
1 AACTT-TCCAAAATTACATTTTAACCC-TA
96022 AACTTTCCAAAATTACATTTTAACCCTA
1 AACTTTCCAAAATTACATTTTAACCCTA
* * *
96050 AATTTTCCAAAAATCACATTTTTTACCC-A
1 AACTTTCC-AAAATTACA-TTTTAACCCTA
* * *
96079 CGAACTTTCAAAAATTACATTTTTGACCATAA
1 --AACTTTCCAAAATTACA-TTTTAACCCT-A
* * * * **
96111 AATTTTCAAAAATCACATTTTACCCCCG
1 AACTTTCCAAAATTACATTTTAACCCTA
*
96139 AACCTT-CAATAATTACATTTTTAACCCTA
1 AACTTTCCAA-AATTACA-TTTTAACCCTA
* *
96168 AAATTTTCAAAA
1 AACTTTCCAAAA
96180 ATCCCAATTT
Statistics
Matches: 145, Mismatches: 28, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
27 6 0.04
28 38 0.26
29 37 0.26
30 51 0.35
31 11 0.08
32 2 0.01
ACGTcount: A:0.39, C:0.23, G:0.01, T:0.37
Consensus pattern (28 bp):
AACTTTCCAAAATTACATTTTAACCCTA
Found at i:96085 original size:59 final size:57
Alignment explanation
Indices: 95953--96219 Score: 247
Period size: 58 Copynumber: 4.6 Consensus size: 57
95943 AATTACATTT
** * * * * **
95953 TTTTACCATGAACTTTCTAAAAATTACATTTTTACCCCCTAAACTTAT-AAAAATTTCA
1 TTTTACCCCGAACTTTC-CAAAATTACATTTTTA-ACCCTAAAATTTTCAAAAATCACA
**
96011 TTTTACCCTTAAACTTTCCAAAATTACA-TTTTAACCCT-AAATTTTCCAAAAATCACA
1 TTTTACCC-CGAACTTTCCAAAATTACATTTTTAACCCTAAAATTTT-CAAAAATCACA
* * *
96068 TTTTTTACCCACGAACTTTCAAAAATTACATTTTTGACCATAAAATTTTCAAAAATCACA
1 --TTTTACCC-CGAACTTTCCAAAATTACATTTTTAACCCTAAAATTTTCAAAAATCACA
* *
96128 TTTTACCCCCGAACCTT-CAATAATTACATTTTTAACCCTAAAATTTTCAAAAATCCCAA
1 TTTTA-CCCCGAACTTTCCAA-AATTACATTTTTAACCCTAAAATTTTCAAAAATCAC-A
*
96187 TTTTACTCCCGAA-TATCCAAAAATTACATTTTT
1 TTTTAC-CCCGAACTTTCC-AAAATTACATTTTT
96220 CCCCCAAATG
Statistics
Matches: 175, Mismatches: 21, Indels: 25
0.79 0.10 0.11
Matches are distributed among these distances:
55 5 0.03
56 4 0.02
57 15 0.09
58 63 0.36
59 60 0.34
60 21 0.12
61 7 0.04
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (57 bp):
TTTTACCCCGAACTTTCCAAAATTACATTTTTAACCCTAAAATTTTCAAAAATCACA
Found at i:96131 original size:117 final size:118
Alignment explanation
Indices: 95935--96255 Score: 304
Period size: 117 Copynumber: 2.7 Consensus size: 118
95925 TCCTTTGAAC
* * * *
95935 TTCCAAAAAATTACATTTTTTTA-CCATGAACTTTCTAAAAATTACATTTTTACCCCCTAAACTT
1 TTCC-AAAAATCACA-TTTTTTACCCACGAACTTTC-AAAAATTACATTTTTA-CCCATAAAATT
** ** *
95999 ATAAAAATTTCATTTTACCCTTAAACTTTCCAA-AATTACA-TTTTAACCCT-AAATT
62 ATAAAAATCACATTTTACCCCCAAACCTT-CAATAATTACATTTTTAACCCTAAAATT
*
96054 TTCCAAAAATCACATTTTTTACCCACGAACTTTCAAAAATTACATTTTTGA-CCATAAAATTTTC
1 TTCCAAAAATCACATTTTTTACCCACGAACTTTCAAAAATTACATTTTT-ACCCATAAAATTAT-
*
96118 AAAAATCACATTTTACCCCCGAACCTTCAATAATTACATTTTTAACCCTAAAATT
64 AAAAATCACATTTTACCCCCAAACCTTCAATAATTACATTTTTAACCCTAAAATT
* * * ** *
96173 TT-CAAAAATCCCA-ATTTTACTCC-CGAA-TATCCAAAAATTACATTTTT-CCC-CCAAATGTC
1 TTCCAAAAATCACATTTTTTAC-CCACGAACT-TTCAAAAATTACATTTTTACCCATAAAAT-TA
* *
96232 TAAAAATTACATTTTTCCCCCAAA
63 TAAAAATCACATTTTACCCCCAAA
96256 TGTCTAAAAA
Statistics
Matches: 172, Mismatches: 20, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
115 24 0.14
116 17 0.10
117 77 0.45
118 43 0.25
119 11 0.06
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.36
Consensus pattern (118 bp):
TTCCAAAAATCACATTTTTTACCCACGAACTTTCAAAAATTACATTTTTACCCATAAAATTATAA
AAATCACATTTTACCCCCAAACCTTCAATAATTACATTTTTAACCCTAAAATT
Found at i:96217 original size:28 final size:29
Alignment explanation
Indices: 96186--96311 Score: 105
Period size: 28 Copynumber: 4.4 Consensus size: 29
96176 AAAAATCCCA
*
96186 ATTTTACTCCCGAATATCCAAAAATTA-C
1 ATTTTACCCCCGAATATCCAAAAATTACC
* * * *
96214 ATTTTTCCCCCAAATGTCTAAAAATTA-C
1 ATTTTACCCCCGAATATCCAAAAATTACC
* * * *
96242 ATTTTTCCCCCAAATGTCTAAAAATTACC
1 ATTTTACCCCCGAATATCCAAAAATTACC
* *
96271 ATTTTGCCCCTGAAGTATCC-AAAATTACC
1 ATTTTACCCCCGAA-TATCCAAAAATTACC
* *
96300 GTTTTACTCCCG
1 ATTTTACCCCCG
96312 GGCATCCAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
28 50 0.61
29 29 0.35
30 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (29 bp):
ATTTTACCCCCGAATATCCAAAAATTACC
Found at i:96622 original size:30 final size:29
Alignment explanation
Indices: 96571--96974 Score: 194
Period size: 30 Copynumber: 13.8 Consensus size: 29
96561 AAGGTTCCTA
* * *
96571 AACTGTCCACAAATTATATTTTGACCCTCG
1 AACTTTCCAAAAATTACATTTT-ACCCTCG
** * *
96601 AACTTTTTAAAAATTACATTTTGATCACT-A
1 AACTTTCCAAAAATTACATTTT-A-CCCTCG
*
96631 AACTTTCC-AAAATTACCATTTTACCC-CT
1 AACTTTCCAAAAATTA-CATTTTACCCTCG
* ** *
96659 AAATTTCACAAAAATTATGTTTTTACCC-CTA
1 AACTTTC-CAAAAATTA-CATTTTACCCTC-G
* *
96690 AAC-TTCCAAAAATTATATTTTTGACCCT-A
1 AACTTTCCAAAAATTACA-TTTT-ACCCTCG
* *
96719 AACTTCCCAAAAAATTACCATTTTACCCTTG
1 AACTTTCC-AAAAATTA-CATTTTACCCTCG
* * *
96750 AA-TTTCCAAAAATTCCATTTTGATCC-CA
1 AACTTTCCAAAAATTACATTTT-ACCCTCG
96778 AACTTTCCAAAAATTACCA-TTTACCCTC-
1 AACTTTCCAAAAATTA-CATTTTACCCTCG
*
96806 AAATTTCACAAAAATTACATTTTTACCCTCG
1 AACTTTC-CAAAAATTACA-TTTTACCCTCG
* *
96837 AA-TTTCCAAAAATTCCATTTTTGACGCT-G
1 AACTTTCCAAAAATTACA-TTTT-ACCCTCG
* *
96866 AAC-TTCTAGAAAATTACCATTTTACCCCCG
1 AACTTTCCA-AAAATTA-CATTTTACCCTCG
* * * * * *
96896 AA-TTTCTAAAATTTTCTTTTTTAACCTTG
1 AACTTTCCAAAAATTAC-ATTTTACCCTCG
96925 AAC-TTCTCAAAAATTATCATTTTA-CCTCG
1 AACTTTC-CAAAAATTA-CATTTTACCCTCG
** *
96954 AA-TTTTTAAAAATTCCATTTT
1 AACTTTCCAAAAATTACATTTT
96975 TGCCTCTGAG
Statistics
Matches: 292, Mismatches: 50, Indels: 67
0.71 0.12 0.16
Matches are distributed among these distances:
27 6 0.02
28 35 0.12
29 112 0.38
30 114 0.39
31 24 0.08
32 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (29 bp):
AACTTTCCAAAAATTACATTTTACCCTCG
Found at i:96660 original size:29 final size:29
Alignment explanation
Indices: 96567--96892 Score: 214
Period size: 30 Copynumber: 11.1 Consensus size: 29
96557 CCAGAAGGTT
* * *
96567 CCTAAACTGTCCACAAATTA-TATTTTGAC
1 CCTAAACTTTCCAAAAATTACCATTTT-AC
* **
96596 CCTCGAACTTTTTAAAAATTA-CATTTTGATC
1 CCT-AAACTTTCCAAAAATTACCATTTT-A-C
*
96627 ACTAAACTTTCC-AAAATTACCATTTTACC
1 CCTAAACTTTCCAAAAATTACCATTTTA-C
***
96656 CCTAAA-TTTCACAAAAATTATGTTTTTACC
1 CCTAAACTTTC-CAAAAATTACCATTTTA-C
*
96686 CCTAAAC-TTCCAAAAATTA-TATTTTTGAC
1 CCTAAACTTTCCAAAAATTACCA-TTTT-AC
*
96715 CCTAAACTTCCCAAAAAATTACCATTTTAC
1 CCTAAACTTTCC-AAAAATTACCATTTTAC
*
96745 CCTTGAA-TTTCCAAAAATT-CCATTTTGATC
1 CC-TAAACTTTCCAAAAATTACCATTTT-A-C
96775 CC-AAACTTTCCAAAAATTACCA-TTTAC
1 CCTAAACTTTCCAAAAATTACCATTTTAC
96802 CCTCAAA-TTTCACAAAAATTA-CATTTTTAC
1 CCT-AAACTTTC-CAAAAATTACCA-TTTTAC
*
96832 CCTCGAA-TTTCCAAAAATT-CCATTTTTGAC
1 CCT-AAACTTTCCAAAAATTACCA-TTTT-AC
* * *
96862 GCTGAAC-TTCTAGAAAATTACCATTTTAC
1 CCTAAACTTTCCA-AAAATTACCATTTTAC
96891 CC
1 CC
96893 CCGAATTTCT
Statistics
Matches: 245, Mismatches: 26, Indels: 52
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.01
28 20 0.08
29 99 0.40
30 101 0.41
31 21 0.09
32 1 0.00
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
CCTAAACTTTCCAAAAATTACCATTTTAC
Found at i:96673 original size:59 final size:56
Alignment explanation
Indices: 96609--96892 Score: 192
Period size: 59 Copynumber: 4.8 Consensus size: 56
96599 CGAACTTTTT
*
96609 AAAAATTACATTTTGATCACTAAACTTTCC-AAAATTACCATTTTACCCCTAAATTTCAC
1 AAAAATTACATTTT-A-CCCTAAACTTTCCAAAAATTACCATTTTA-CCCTAAATTTC-C
** * *
96668 AAAAATTATGTTTTTACCCCTAAAC-TTCCAAAAATTA-TATTTTTGACCCTAAACTTCCC
1 AAAAATTA-CATTTTA-CCCTAAACTTTCCAAAAATTACCA-TTTT-ACCCTAAA-TTTCC
*
96727 AAAAAATTACCATTTTACCCTTGAA-TTTCCAAAAATT-CCATTTTGATCCC-AAACTTTCC
1 -AAAAATTA-CATTTTACCC-TAAACTTTCCAAAAATTACCATTTT-A-CCCTAAA-TTTCC
*
96786 AAAAATTACCA-TTTACCCTCAAA-TTTCACAAAAATTA-CATTTTTACCCTCGAATTTCC
1 AAAAATTA-CATTTTACCCT-AAACTTTC-CAAAAATTACCA-TTTTACCCT-AAATTTCC
* * * *
96844 AAAAATTCCATTTTTGACGCTGAAC-TTCTAGAAAATTACCATTTTACCC
1 AAAAATTACA-TTTT-ACCCTAAACTTTCCA-AAAATTACCATTTTACCC
96893 CCGAATTTCT
Statistics
Matches: 185, Mismatches: 18, Indels: 44
0.75 0.07 0.18
Matches are distributed among these distances:
56 1 0.01
57 18 0.10
58 40 0.22
59 81 0.44
60 45 0.24
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.36
Consensus pattern (56 bp):
AAAAATTACATTTTACCCTAAACTTTCCAAAAATTACCATTTTACCCTAAATTTCC
Found at i:96818 original size:58 final size:56
Alignment explanation
Indices: 96680--96856 Score: 180
Period size: 58 Copynumber: 3.1 Consensus size: 56
96670 AAATTATGTT
* * *
96680 TTTACCC-CTAAACTTCCAAAAATTATATTTTTGACCCTAAACTTCCCAAAAAATTACCA
1 TTTACCCTC-AAATTTCCAAAAATTACA-TTTTGACCC-AAACTTTCC-AAAAATTACCA
** *
96739 TTTTACCCTTGAATTTCCAAAAATTCCATTTTGATCCCAAACTTTCCAAAAATTACCA
1 -TTTACCCTCAAATTTCCAAAAATTACATTTTGA-CCCAAACTTTCCAAAAATTACCA
* *
96797 TTTACCCTCAAATTTCACAAAAATTACATTTTTACCCTCGAA-TTTCCAAAAATT-CCA
1 TTTACCCTCAAATTTC-CAAAAATTACATTTTGA-CC-CAAACTTTCCAAAAATTACCA
96854 TTT
1 TTT
96857 TTGACGCTGA
Statistics
Matches: 101, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
57 20 0.20
58 40 0.40
59 17 0.17
60 24 0.24
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (56 bp):
TTTACCCTCAAATTTCCAAAAATTACATTTTGACCCAAACTTTCCAAAAATTACCA
Found at i:96898 original size:59 final size:57
Alignment explanation
Indices: 96815--97009 Score: 196
Period size: 59 Copynumber: 3.4 Consensus size: 57
96805 CAAATTTCAC
* *
96815 AAAAATTA-CATTTTTACCCTCGAATTTCCAAAAATTCCATTTTTGACGCTGAACTTCT
1 AAAAATTACCA-TTTTACCCCCGAATTTCTAAAAATTCCATTTTTGAC-CTGAACTTCT
* * * *
96873 AGAAAATTACCATTTTACCCCCGAATTTCTAAAATTTTCTTTTTTAACCTTGAACTTCT
1 A-AAAATTACCATTTTACCCCCGAATTTCTAAAAATTCCATTTTTGACC-TGAACTTCT
* * * * **
96932 CAAAAATTATCATTTTA-CCTCGAATTTTTAAAAATTCCATTTTTGCCTCTGAGTTTCT
1 -AAAAATTACCATTTTACCCCCGAATTTCTAAAAATTCCATTTTTGAC-CTGAACTTCT
* *
96990 AAATATTACCGTTTTACCCC
1 AAAAATTACCATTTTACCCC
97010 TGATCCTCCA
Statistics
Matches: 111, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
57 13 0.12
58 34 0.31
59 61 0.55
60 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (57 bp):
AAAAATTACCATTTTACCCCCGAATTTCTAAAAATTCCATTTTTGACCTGAACTTCT
Found at i:96951 original size:29 final size:30
Alignment explanation
Indices: 96629--96950 Score: 163
Period size: 29 Copynumber: 10.9 Consensus size: 30
96619 TTTTGATCAC
* *
96629 TAAACTT-TCCAAAATTACCATTTTACCCC
1 TAAACTTCTCAAAAATTACCATTTTACCCT
* * *** *
96658 TAAATTTCACAAAAATTATGTTTTTACCCC
1 TAAACTTCTCAAAAATTACCATTTTACCCT
*
96688 TAAACTTC-CAAAAATTA-TATTTTTGACCC-
1 TAAACTTCTCAAAAATTACCA-TTTT-ACCCT
*
96717 TAAACTTCCCAAAAAATTACCATTTTACCCT
1 TAAACTTCTC-AAAAATTACCATTTTACCCT
* *
96748 TGAATTTC-CAAAAATT-CCATTTTGATCCC-
1 TAAACTTCTCAAAAATTACCATTTT-A-CCCT
96777 -AAACTT-TCCAAAAATTACCA-TTTACCCT
1 TAAACTTCT-CAAAAATTACCATTTTACCCT
* * *
96805 CAAATTTCACAAAAATTA-CATTTTTACCCT
1 TAAACTTCTCAAAAATTACCA-TTTTACCCT
** * *
96835 CGAATTTC-CAAAAATT-CCATTTTTGACGC-
1 TAAACTTCTCAAAAATTACCA-TTTT-ACCCT
* *
96864 TGAACTTCT-AGAAAATTACCATTTTACCCC
1 TAAACTTCTCA-AAAATTACCATTTTACCCT
** * * * ** *
96894 CGAATTTCT-AAAATTTTCTTTTTTAACCT
1 TAAACTTCTCAAAAATTACCATTTTACCCT
* *
96923 TGAACTTCTCAAAAATTATCATTTTACC
1 TAAACTTCTCAAAAATTACCATTTTACC
96951 TCGAATTTTT
Statistics
Matches: 232, Mismatches: 37, Indels: 47
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.01
28 14 0.06
29 105 0.45
30 88 0.38
31 21 0.09
32 1 0.00
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (30 bp):
TAAACTTCTCAAAAATTACCATTTTACCCT
Found at i:96958 original size:147 final size:146
Alignment explanation
Indices: 96609--96975 Score: 373
Period size: 147 Copynumber: 2.5 Consensus size: 146
96599 CGAACTTTTT
* * * * *
96609 AAAAATTACATTTTGATCACTAAACTTTCCAAAATTACCATTTTACCCCTAAATTTCACAAAAAT
1 AAAAATTCCATTTTGAAC-CCAAACTTTCAAAAATTACCATTTTACCTC-AAATTTCACAAAAAT
** *
96674 TATGTTTTTACCCCTAAACTTCCAAAAATTATATTTTTGACCCTAAACTTCCCAAAAAATTACCA
64 TACATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGACCCTAAACTTCCCAAAAAATTACCA
**
96739 TTTTACCCTTGAATTTCC
129 TTTTACCCCCGAATTTCC
*
96757 AAAAATTCCATTTTGATCCCAAACTTTCCAAAAATTACCA-TTTACCCTCAAATTTCACAAAAAT
1 AAAAATTCCATTTTGAACCCAAACTTT-CAAAAATTACCATTTTA-CCTCAAATTTCACAAAAAT
* * * * * * *
96821 TACATTTTTA-CCCTCGAATTTCCAAAAATTCCATTTTTGACGCTGAACTT-CTAGAAAATTACC
64 TACATTTTTACCCCT-AAACTTCCAAAAATTACATTTTTGACCCTAAACTTCCCAAAAAATTACC
*
96884 ATTTTACCCCCGAATTTCT
128 ATTTTACCCCCGAATTTCC
* * * * ** * * **
96903 AAAATTTTCTTTTTTAACCTTGAACTTCTCAAAAATTATCATTTTACCTCGAATTT-TTAAAAAT
1 AAAAATTCCATTTTGAACC-CAAACTT-TCAAAAATTACCATTTTACCTCAAATTTCACAAAAAT
*
96967 TCCATTTTT
64 TACATTTTT
96976 GCCTCTGAGT
Statistics
Matches: 184, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
146 59 0.32
147 89 0.48
148 36 0.20
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (146 bp):
AAAAATTCCATTTTGAACCCAAACTTTCAAAAATTACCATTTTACCTCAAATTTCACAAAAATTA
CATTTTTACCCCTAAACTTCCAAAAATTACATTTTTGACCCTAAACTTCCCAAAAAATTACCATT
TTACCCCCGAATTTCC
Found at i:104235 original size:18 final size:20
Alignment explanation
Indices: 104196--104239 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
104186 ATAGAGGTAA
104196 TAAAATGTATATAATAAAAT
1 TAAAATGTATATAATAAAAT
*
104216 TAAAATGTATA-AA-AATAT
1 TAAAATGTATATAATAAAAT
104234 TAAAAT
1 TAAAAT
104240 AAAATTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.43
19 2 0.09
20 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAATGTATATAATAAAAT
Found at i:104698 original size:19 final size:20
Alignment explanation
Indices: 104657--104702 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
104647 ATGGAAATAA
104657 TAAAATATACAAAATAAAAT
1 TAAAATATACAAAATAAAAT
*
104677 TAAAATGTA-AAAA-AAAATT
1 TAAAATATACAAAATAAAA-T
104696 TAAAATA
1 TAAAATA
104703 AAATTTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 4 0.17
19 11 0.48
20 8 0.35
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (20 bp):
TAAAATATACAAAATAAAAT
Found at i:117400 original size:16 final size:16
Alignment explanation
Indices: 117370--117404 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
117360 TTATCAATCC
117370 GAAAACTTGATTAAAG
1 GAAAACTTGATTAAAG
117386 GAAAA-TTGATATAAAG
1 GAAAACTTGAT-TAAAG
117402 GAA
1 GAA
117405 TTCGTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.20, T:0.23
Consensus pattern (16 bp):
GAAAACTTGATTAAAG
Found at i:121988 original size:20 final size:18
Alignment explanation
Indices: 121941--122019 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 18
121931 CAAGATAAAC
121941 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
121958 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
121978 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
121997 ATTAAATTAA-GTTTAAT
1 ATTAAATTAATATTTAAT
122014 ATTAAA
1 ATTAAA
122020 CTATTAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 17 0.35
18 1 0.02
19 15 0.31
20 16 0.33
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:125581 original size:9 final size:10
Alignment explanation
Indices: 125567--125599 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
125557 AGTTTTGAAG
125567 TTTATT-CAA
1 TTTATTACAA
*
125576 TTTATTCCAA
1 TTTATTACAA
125586 TTTATTACAA
1 TTTATTACAA
125596 TTTA
1 TTTA
125600 GTCTTTAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (10 bp):
TTTATTACAA
Found at i:139178 original size:18 final size:18
Alignment explanation
Indices: 139155--139200 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
139145 AATTAAATAT
* *
139155 TTAAATTTATTGGAATGA
1 TTAAATTGATGGGAATGA
139173 TTAAATTGATGGGAATGA
1 TTAAATTGATGGGAATGA
139191 TTAAATTGAT
1 TTAAATTGAT
139201 CAATAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (18 bp):
TTAAATTGATGGGAATGA
Found at i:140311 original size:17 final size:18
Alignment explanation
Indices: 140289--140323 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
140279 GTCCTACTGA
140289 TGGATGAGG-TTCTGCAT
1 TGGATGAGGATTCTGCAT
*
140306 TGGATGCGGATTCTGCAT
1 TGGATGAGGATTCTGCAT
140324 AGCTCGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.14, G:0.34, T:0.34
Consensus pattern (18 bp):
TGGATGAGGATTCTGCAT
Found at i:140587 original size:38 final size:38
Alignment explanation
Indices: 140535--140625 Score: 164
Period size: 38 Copynumber: 2.4 Consensus size: 38
140525 CAGACCCATT
140535 TCACAGCTTGTGTGAGCATATATGGTTACATGTTATAG
1 TCACAGCTTGTGTGAGCATATATGGTTACATGTTATAG
*
140573 TCACAGCTTTTGTGAGCATATATGGTTACATGTTATAG
1 TCACAGCTTGTGTGAGCATATATGGTTACATGTTATAG
*
140611 TCACAACTTGTGTGA
1 TCACAGCTTGTGTGA
140626 ATAGTTTTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.37
Consensus pattern (38 bp):
TCACAGCTTGTGTGAGCATATATGGTTACATGTTATAG
Found at i:143714 original size:26 final size:26
Alignment explanation
Indices: 143639--143716 Score: 102
Period size: 26 Copynumber: 3.0 Consensus size: 26
143629 AGACTTGAAG
* * **
143639 ATATTGTACTAGCTCGTAAGAGTAAT
1 ATATTGAACTGGCTCGTAAGAGCGAT
*
143665 TTATTGAACTGGCTCGTAAGAGCGAT
1 ATATTGAACTGGCTCGTAAGAGCGAT
*
143691 ATATTGAACTGGCTCGAAAGAGCGAT
1 ATATTGAACTGGCTCGTAAGAGCGAT
143717 GCACTACTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (26 bp):
ATATTGAACTGGCTCGTAAGAGCGAT
Found at i:164355 original size:21 final size:21
Alignment explanation
Indices: 164317--164356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
164307 TGAAGCAGAC
**
164317 TTCTACCGATACTTATGACAA
1 TTCTACCGATACAAATGACAA
*
164338 TTCTATCGATACAAATGAC
1 TTCTACCGATACAAATGAC
164357 TCTACTACCG
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:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAATGACAA
Found at i:165160 original size:52 final size:54
Alignment explanation
Indices: 165031--165289 Score: 287
Period size: 52 Copynumber: 4.7 Consensus size: 54
165021 ATTAATTTTC
* *
165031 ATTTA-ATACTCACGATGACACATAGTCATCGAACCTC-TTATCCACAGAGGTTAAAGG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAAT-C-CA-A-G-TAAAGG
* *
165088 ATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCC-A-TAAAGG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCAAGTAAAGG
*
165140 ATTTATATACTCACGATGACACATAATCATCGGACCTCATAATCCGTATAATCCGTAAAGG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCC----AA---GTAAAGG
* * *
165201 ATTTATATACTCATGATGACACATAATTATCGGACCTCATAATCC--GTAAAGG
1 ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCAAGTAAAGG
165253 ATTTATATACTCACGATGACACCATAGTCATCGGACC
1 ATTTATATACTCACGATGACA-CATAGTCATCGGACC
165290 CTTTTCGTTT
Statistics
Matches: 178, Mismatches: 12, Indels: 28
0.82 0.06 0.13
Matches are distributed among these distances:
52 75 0.42
53 13 0.07
55 1 0.01
57 6 0.03
58 31 0.17
59 3 0.02
61 49 0.28
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.28
Consensus pattern (54 bp):
ATTTATATACTCACGATGACACATAGTCATCGGACCTCATAATCCAAGTAAAGG
Found at i:165221 original size:61 final size:61
Alignment explanation
Indices: 165126--165289 Score: 220
Period size: 61 Copynumber: 2.8 Consensus size: 61
165116 ATCGGACCTC
165126 ATAATCCATAAAGGATTTATATACTCACGATGACACATAATCATCGGACCTCATAATCCGT
1 ATAATCCATAAAGGATTTATATACTCACGATGACACATAATCATCGGACCTCATAATCCGT
* * *
165187 ATAATCCGTAAAGGATTTATATACTCATGATGACACATAATTATCGGACCTCATAATCCG-
1 ATAATCCATAAAGGATTTATATACTCACGATGACACATAATCATCGGACCTCATAATCCGT
*
165247 --------TAAAGGATTTATATACTCACGATGACACCATAGTCATCGGACC
1 ATAATCCATAAAGGATTTATATACTCACGATGACA-CATAATCATCGGACC
165290 CTTTTCGTTT
Statistics
Matches: 96, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
52 26 0.27
53 13 0.14
61 57 0.59
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (61 bp):
ATAATCCATAAAGGATTTATATACTCACGATGACACATAATCATCGGACCTCATAATCCGT
Found at i:165225 original size:113 final size:114
Alignment explanation
Indices: 165082--165289 Score: 364
Period size: 113 Copynumber: 1.8 Consensus size: 114
165072 CCACAGAGGT
*
165082 TAAAGGATTCATATACTCATGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTTATA
1 TAAAGGATTCATATACTCATGATGACACATAATCATCGGACCTCATAATCCATAAAGGATTTATA
165147 TACTCACGATGACA-CATAATCATCGGACCTCATAATCCGTATAATCCG
66 TACTCACGATGACACCATAATCATCGGACCTCATAATCCGTATAATCCG
* * *
165195 TAAAGGATTTATATACTCATGATGACACATAATTATCGGACCTCATAATCCGTAAAGGATTTATA
1 TAAAGGATTCATATACTCATGATGACACATAATCATCGGACCTCATAATCCATAAAGGATTTATA
*
165260 TACTCACGATGACACCATAGTCATCGGACC
66 TACTCACGATGACACCATAATCATCGGACC
165290 CTTTTCGTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 75 0.84
114 14 0.16
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (114 bp):
TAAAGGATTCATATACTCATGATGACACATAATCATCGGACCTCATAATCCATAAAGGATTTATA
TACTCACGATGACACCATAATCATCGGACCTCATAATCCGTATAATCCG
Found at i:172296 original size:13 final size:12
Alignment explanation
Indices: 172280--172336 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
172270 TAAAAATAAT
172280 ATTTTAATTGATCA
1 ATTTTAATT-AT-A
* *
172294 TTTTTAAAATTATT
1 ATTTT-AA-TTATA
172308 ATTTTAATTTATA
1 ATTTTAA-TTATA
172321 ATTTTAATTATA
1 ATTTTAATTATA
172333 ATTT
1 ATTT
172337 AACTATTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 9 0.25
13 13 0.36
14 8 0.22
15 4 0.11
16 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
ATTTTAATTATA
Found at i:172310 original size:28 final size:28
Alignment explanation
Indices: 172268--172325 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
172258 GAATTAAATA
*
172268 TTTAAAAATAATATTTTAATTGATCATT
1 TTTAAAAATAATATTTTAATTGATAATT
* * *
172296 TTTAAAATTATTATTTTAATTTATAATT
1 TTTAAAAATAATATTTTAATTGATAATT
172324 TT
1 TT
172326 AATTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTAAAAATAATATTTTAATTGATAATT
Found at i:172323 original size:19 final size:19
Alignment explanation
Indices: 172296--172338 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
172286 ATTGATCATT
*
172296 TTTAAAATTATT-ATTTTAA
1 TTTAAAATT-TTAATTATAA
*
172315 TTTATAATTTTAATTATAA
1 TTTAAAATTTTAATTATAA
172334 TTTAA
1 TTTAA
172339 CTATTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAAATTTTAATTATAA
Found at i:172331 original size:12 final size:12
Alignment explanation
Indices: 172301--172336 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
172291 TCATTTTTAA
*
172301 AATTATTATTTT
1 AATTATAATTTT
172313 AATTTATAATTTT
1 AA-TTATAATTTT
172326 AATTATAATTT
1 AATTATAATTT
172337 AACTATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
AATTATAATTTT
Found at i:175421 original size:275 final size:275
Alignment explanation
Indices: 174924--175475 Score: 1005
Period size: 275 Copynumber: 2.0 Consensus size: 275
174914 TCAGTATAAA
* *
174924 CATCATCACTTAGTCTGATTCATCTCAAGCAGTCAAACTCAATTACAACATAAACAAATATGTTT
1 CATCACCACTTAGTCTAATTCATCTCAAGCAGTCAAACTCAATTACAACATAAACAAATATGTTT
* *
174989 TAAGTCACGAAGATAACATATAATTAATTTCATAAATTTACGAACTTACTTTGACAACATTTGAA
66 TAAGTCACAAAGATAACATATAATTAATTTCATAAATTTACGAACTTACTTTGACAAAATTTGAA
175054 ACACACTTTTACTCAATTTAAATTCGATTAATACATATTTAAGTCAATTTCATATAACTACTTCA
131 ACACACTTTTACTCAATTTAAATTCGATTAATACATATTTAAGTCAATTTCATATAACTACTTCA
* * *
175119 AGATAAATCATTTCTTTCTTAGCATTGGACTGTAGCGATAAGGATATAAAATATCATAATATATA
196 AGATAAATCAATTCTTTCTTAGCATTGGACTGTAGCAATAAAGATATAAAATATCATAATATATA
175184 GAATTTAATAAACAT
261 GAATTTAATAAACAT
175199 CATCACCACTTAGTCTAATTCATCTCAAGCAGTCAAACTCAATTACAACATAAACAAATATGTTT
1 CATCACCACTTAGTCTAATTCATCTCAAGCAGTCAAACTCAATTACAACATAAACAAATATGTTT
* *
175264 TAAGTCACAAAGATAACATATAATTAATTTCATAAATTTACGAATTTACTTTGACAAAATTTGTA
66 TAAGTCACAAAGATAACATATAATTAATTTCATAAATTTACGAACTTACTTTGACAAAATTTGAA
* *
175329 ACATACTTTTACTCAATTTCAATTCGATTAATACATATTTAAGTCAATTTCATATAACTACTTCA
131 ACACACTTTTACTCAATTTAAATTCGATTAATACATATTTAAGTCAATTTCATATAACTACTTCA
175394 AGATAAATCAATTCTTTCTTAGCATTGGACTGTAGCAATAAAGATATAAAATATCATAATATATA
196 AGATAAATCAATTCTTTCTTAGCATTGGACTGTAGCAATAAAGATATAAAATATCATAATATATA
175459 GAATTTAATAAACAT
261 GAATTTAATAAACAT
175474 CA
1 CA
175476 AACTAAAAAT
Statistics
Matches: 266, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
275 266 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (275 bp):
CATCACCACTTAGTCTAATTCATCTCAAGCAGTCAAACTCAATTACAACATAAACAAATATGTTT
TAAGTCACAAAGATAACATATAATTAATTTCATAAATTTACGAACTTACTTTGACAAAATTTGAA
ACACACTTTTACTCAATTTAAATTCGATTAATACATATTTAAGTCAATTTCATATAACTACTTCA
AGATAAATCAATTCTTTCTTAGCATTGGACTGTAGCAATAAAGATATAAAATATCATAATATATA
GAATTTAATAAACAT
Found at i:176950 original size:58 final size:58
Alignment explanation
Indices: 176882--177010 Score: 168
Period size: 58 Copynumber: 2.2 Consensus size: 58
176872 ACATTAACCG
*
176882 CATTAATCACATGAGTACTTAAGCATTTAACACAAAACATATTAATCACATTTAATCA
1 CATTAATCACATGAATACTTAAGCATTTAACACAAAACATATTAATCACATTTAATCA
* * * * ** * *
176940 CATTAGTCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAGTCT
1 CATTAATCACATGAATACTTAAGCATTTAACACAAAACATATTAATCACATTTAATCA
176998 CATTTAATCACAT
1 CA-TTAATCACAT
177011 TAGTCACATA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
58 51 0.85
59 9 0.15
ACGTcount: A:0.40, C:0.20, G:0.05, T:0.35
Consensus pattern (58 bp):
CATTAATCACATGAATACTTAAGCATTTAACACAAAACATATTAATCACATTTAATCA
Found at i:177011 original size:10 final size:10
Alignment explanation
Indices: 176973--177011 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
176963 CATTTATCAC
176973 ATCACATATTA
1 ATCACAT-TTA
176984 ATCACATTTA
1 ATCACATTTA
* *
176994 GTCTCATTTA
1 ATCACATTTA
177004 ATCACATT
1 ATCACATT
177012 AGTCACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 17 0.71
11 7 0.29
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.41
Consensus pattern (10 bp):
ATCACATTTA
Found at i:177039 original size:68 final size:68
Alignment explanation
Indices: 176930--177061 Score: 237
Period size: 68 Copynumber: 1.9 Consensus size: 68
176920 ATATTAATCA
* *
176930 CATTTAATCACATTAGTCACATGAATATTTCAGCATTTATCACATCACATATTAATCACATTTAG
1 CATTTAATCACATTAGTCACATAAATATTTCAACATTTATCACATCACATATTAATCACATTTAG
176995 TCT
66 TCT
*
176998 CATTTAATCACATTAGTCACATAAATATTTCAACGTTTATCACATCACATATTAATCACATTTA
1 CATTTAATCACATTAGTCACATAAATATTTCAACATTTATCACATCACATATTAATCACATTTA
177062 ATCATATGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.38
Consensus pattern (68 bp):
CATTTAATCACATTAGTCACATAAATATTTCAACATTTATCACATCACATATTAATCACATTTAG
TCT
Found at i:177086 original size:49 final size:49
Alignment explanation
Indices: 177001--177117 Score: 164
Period size: 49 Copynumber: 2.4 Consensus size: 49
176991 TTAGTCTCAT
* *
177001 TTAATCACA-TTAGTCACATAAATATTTCAACGTTTATCACATCACATA
1 TTAATCACATTTAATCACATAAATATTTCAACATTTATCACATCACATA
* * * *
177049 TTAATCACATTTAATCATATGAATATTTCAGCATTTATCATATCACATA
1 TTAATCACATTTAATCACATAAATATTTCAACATTTATCACATCACATA
*
177098 TTAATCACATTTAGTCACAT
1 TTAATCACATTTAATCACAT
177118 TTAATATTGA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
48 9 0.15
49 51 0.85
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (49 bp):
TTAATCACATTTAATCACATAAATATTTCAACATTTATCACATCACATA
Found at i:177098 original size:24 final size:23
Alignment explanation
Indices: 177022--177110 Score: 81
Period size: 25 Copynumber: 3.6 Consensus size: 23
177012 AGTCACATAA
* *
177022 ATATTTCAACGTTTATCACATCAC
1 ATATTTC-ACATTTATCATATCAC
*
177046 ATATTAATCACATTTAATCATATGA-
1 ATATT--TCACATTT-ATCATATCAC
177071 ATATTTCAGCATTTATCATATCAC
1 ATATTTCA-CATTTATCATATCAC
177095 ATATTAATCACATTTA
1 ATATT--TCACATTTA
177111 GTCACATTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
23 11 0.20
24 15 0.28
25 16 0.30
26 12 0.22
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.40
Consensus pattern (23 bp):
ATATTTCACATTTATCATATCAC
Found at i:177205 original size:23 final size:23
Alignment explanation
Indices: 177112--177224 Score: 129
Period size: 23 Copynumber: 4.9 Consensus size: 23
177102 TCACATTTAG
* *
177112 TCACATTTAATATTGAAGCAAAAA
1 TCACA-TTAATATTTAAGCACAAA
* * * *
177136 TTAAAATAACATTTAAGCACAAA
1 TCACATTAATATTTAAGCACAAA
177159 TCACATTAATATTTAAGCACAAA
1 TCACATTAATATTTAAGCACAAA
* **
177182 TCATATTAATATTTAAGCTTAAA
1 TCACATTAATATTTAAGCACAAA
177205 TCACATTAATATTTAA-CACA
1 TCACATTAATATTTAAGCACA
177225 TATAATCACA
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
22 2 0.03
23 68 0.93
24 3 0.04
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (23 bp):
TCACATTAATATTTAAGCACAAA
Found at i:177246 original size:20 final size:19
Alignment explanation
Indices: 177215--177254 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
177205 TCACATTAAT
*
177215 ATTTAACACATATAATCAC
1 ATTTAACACATATAAACAC
177234 ATTTAATCACATATAAACAC
1 ATTTAA-CACATATAAACAC
177254 A
1 A
177255 ATTCATGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
ATTTAACACATATAAACAC
Found at i:177718 original size:36 final size:36
Alignment explanation
Indices: 177645--177718 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
177635 TAATCAATCT
**
177645 CATGGCATGAAGAACATACCCACATATTTTCTGTCA
1 CATGGCATGAAGAACATACCCACATATTCACTGTCA
* * * *
177681 CATGGCATGAATAACATAGCCTCATATTCACTTTCA
1 CATGGCATGAAGAACATACCCACATATTCACTGTCA
177717 CA
1 CA
177719 ACACTCATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.34, C:0.26, G:0.12, T:0.28
Consensus pattern (36 bp):
CATGGCATGAAGAACATACCCACATATTCACTGTCA
Found at i:180142 original size:31 final size:31
Alignment explanation
Indices: 180107--180199 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
180097 GCCTTTCCGT
*
180107 TTGATATCCATTTTGGATATGACCTTTTCAA
1 TTGATATCCATTTTGGATATAACCTTTTCAA
* *
180138 TTGATATCCATTTTGGATTTAACCATTTCAA
1 TTGATATCCATTTTGGATATAACCTTTTCAA
* ** *
180169 TTAATATCCATTTCAGATAAAACCTTTTCAA
1 TTGATATCCATTTTGGATATAACCTTTTCAA
180200 CCTTTTCAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (31 bp):
TTGATATCCATTTTGGATATAACCTTTTCAA
Found at i:188069 original size:18 final size:18
Alignment explanation
Indices: 188048--188086 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
188038 TTAATTTTTT
188048 AAAATAAAAATATTTTAA
1 AAAATAAAAATATTTTAA
** *
188066 AAAATATTAATTTTTTAA
1 AAAATAAAAATATTTTAA
188084 AAA
1 AAA
188087 TTTGTAAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATAAAAATATTTTAA
Found at i:188291 original size:23 final size:23
Alignment explanation
Indices: 188247--188292 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
188237 ATATAAAGTT
**
188247 AAAAATATTTAAAATTCTTTTTA
1 AAAAATATTTAAAATTAATTTTA
188270 AAAAATATTTAAAATTAATTTTA
1 AAAAATATTTAAAATTAATTTTA
188293 TCTAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AAAAATATTTAAAATTAATTTTA
Found at i:189255 original size:17 final size:17
Alignment explanation
Indices: 189213--189259 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
189203 AATTCAATTT
*
189213 TAATATAAAT-ATTTAA
1 TAATATAAATAATTCAA
189229 T-ATGATTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
189247 TAATATAAATAAT
1 TAATATAAATAAT
189260 ATAAAATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 2 0.08
16 2 0.08
17 13 0.50
18 7 0.27
19 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:190364 original size:17 final size:17
Alignment explanation
Indices: 190311--190363 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
190301 TTATTTTTTT
* *
190311 AAATTTTTAAATTTTAA
1 AAATTTATATATTTTAA
* *
190328 TATTTTATATATTTTAA
1 AAATTTATATATTTTAA
190345 AAATTTATAT-TTTTAA
1 AAATTTATATATTTTAA
190361 AAA
1 AAA
190364 AATATTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 9 0.30
17 21 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATTTATATATTTTAA
Found at i:190393 original size:29 final size:29
Alignment explanation
Indices: 190336--190401 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 29
190326 AATATTTTAT
190336 ATATTTTAAAAATTTATATTTTTAAAAAA
1 ATATTTTAAAAATTTATATTTTTAAAAAA
190365 ATATTTT-AAAATTT-T-TTTTTAAAATAA
1 ATATTTTAAAAATTTATATTTTTAAAA-AA
190392 A-ATTTTAAAA
1 ATATTTTAAAA
190402 CGATCCAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
26 14 0.40
27 7 0.20
28 7 0.20
29 7 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
ATATTTTAAAAATTTATATTTTTAAAAAA
Found at i:195979 original size:62 final size:59
Alignment explanation
Indices: 195902--196032 Score: 181
Period size: 62 Copynumber: 2.2 Consensus size: 59
195892 AAACGTGTTG
* * * * * *
195902 AAAAATATTTAAAAGAGCTTCTATTTCATTAAATGATACAATATGTCAAAATTAATGTGTAC
1 AAAAATATTCAAAAGAACTTCGATTTCATTAAATGATA-AA-ATAT-AAAAATAATGTCTAC
195964 AAAAATATTCAAAAGAACTTCGATTTCATTAAATGATAAAATATAAAAATAATGTCTAC
1 AAAAATATTCAAAAGAACTTCGATTTCATTAAATGATAAAATATAAAAATAATGTCTAC
196023 AAAAATATTC
1 AAAAATATTC
196033 GAAATAAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
59 23 0.37
60 3 0.05
61 2 0.03
62 35 0.56
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (59 bp):
AAAAATATTCAAAAGAACTTCGATTTCATTAAATGATAAAATATAAAAATAATGTCTAC
Found at i:196599 original size:91 final size:91
Alignment explanation
Indices: 196444--196627 Score: 332
Period size: 91 Copynumber: 2.0 Consensus size: 91
196434 ATTTCATTGC
* *
196444 TTACACCGTTTCCTCTATGCAAAACTAGACTCAGGATTTAATTTCATATTTGATTCAACCTCCAA
1 TTACACCATTTCCTCTATGCAAAACTAGACTCAGGATTTAATTCCATATTTGATTCAACCTCCAA
*
196509 TTCAATTTTTACAGTTTTTGGTGAAT
66 TTCAATTTTTACAATTTTTGGTGAAT
196535 TTACACCATTTCCTCTATGCAAAACTAGACTCAGGATTTAATTCCATATTTGATTCAACCTCCAA
1 TTACACCATTTCCTCTATGCAAAACTAGACTCAGGATTTAATTCCATATTTGATTCAACCTCCAA
*
196600 TTCAATTTTTACAATTTTTTGTGAAT
66 TTCAATTTTTACAATTTTTGGTGAAT
196626 TT
1 TT
196628 TCAAAGTTTA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.41
Consensus pattern (91 bp):
TTACACCATTTCCTCTATGCAAAACTAGACTCAGGATTTAATTCCATATTTGATTCAACCTCCAA
TTCAATTTTTACAATTTTTGGTGAAT
Found at i:200169 original size:33 final size:33
Alignment explanation
Indices: 200131--200195 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
200121 AGCTTTATAG
200131 TATCTTGATTCCCTAGTTCTTATAAGCCTATGA
1 TATCTTGATTCCCTAGTTCTTATAAGCCTATGA
200164 TATCTTGATTCCCTAGTTCTTATAAGCCTATG
1 TATCTTGATTCCCTAGTTCTTATAAGCCTATG
200196 GAATTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (33 bp):
TATCTTGATTCCCTAGTTCTTATAAGCCTATGA
Found at i:207881 original size:16 final size:17
Alignment explanation
Indices: 207860--207891 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
207850 AACCCGCAGA
207860 ATTTTTTT-TTATTTTT
1 ATTTTTTTCTTATTTTT
207876 ATTTTTTTCTTATTTT
1 ATTTTTTTCTTATTTT
207892 CTTTTTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (17 bp):
ATTTTTTTCTTATTTTT
Found at i:223930 original size:4 final size:4
Alignment explanation
Indices: 223923--223949 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
223913 AATATATTTA
223923 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
223950 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:225491 original size:12 final size:12
Alignment explanation
Indices: 225476--225525 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
225466 GCTTTTGCTA
225476 TTATTTTTGTTG
1 TTATTTTTGTTG
*
225488 TTATTTTTGCTG
1 TTATTTTTGTTG
* * *
225500 CTGTTTTGGTTG
1 TTATTTTTGTTG
225512 TTATTTTTGTTG
1 TTATTTTTGTTG
225524 TT
1 TT
225526 TGGATGTTAT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.06, C:0.04, G:0.20, T:0.70
Consensus pattern (12 bp):
TTATTTTTGTTG
Found at i:225495 original size:24 final size:24
Alignment explanation
Indices: 225435--225520 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 24
225425 TTTGTTGTTG
*
225435 TTTTGGTTGCTATTTTT--TACTA
1 TTTTGGTTGTTATTTTTGCTACTA
* ** *
225457 -TATGG-TGTTGCTTTTGCTATTA
1 TTTTGGTTGTTATTTTTGCTACTA
* * *
225479 TTTTTGTTGTTATTTTTGCTGCTG
1 TTTTGGTTGTTATTTTTGCTACTA
225503 TTTTGGTTGTTATTTTTG
1 TTTTGGTTGTTATTTTTG
225521 TTGTTTGGAT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
20 7 0.15
21 4 0.09
22 4 0.09
23 3 0.06
24 29 0.62
ACGTcount: A:0.09, C:0.07, G:0.20, T:0.64
Consensus pattern (24 bp):
TTTTGGTTGTTATTTTTGCTACTA
Found at i:225533 original size:20 final size:20
Alignment explanation
Indices: 225504--225543 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
225494 TTGCTGCTGT
*
225504 TTTGGTTGTTATTTTTGTTG
1 TTTGGATGTTATTTTTGTTG
225524 TTTGGATGTTATTTTTGTTG
1 TTTGGATGTTATTTTTGTTG
225544 CATTTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.25, T:0.68
Consensus pattern (20 bp):
TTTGGATGTTATTTTTGTTG
Found at i:236691 original size:20 final size:21
Alignment explanation
Indices: 236638--236691 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
236628 GTTTGTGAAA
*
236638 TTAAAATTTCTTATAATTACATT
1 TTAAAATTT-TT-TAATTACAAT
*
236661 TTAACA-TTTTTAATTA-AAT
1 TTAAAATTTTTTAATTACAAT
236680 TTAAAATTTTTT
1 TTAAAATTTTTT
236692 CAAAAAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.26
20 11 0.41
21 2 0.07
22 2 0.07
23 5 0.19
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATTTTTTAATTACAAT
Found at i:238833 original size:31 final size:31
Alignment explanation
Indices: 238798--238856 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
238788 GCCCAATGAA
238798 TTAAATAAAAACTTT-TGAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCTG-ATAGTTCAGTGAC
*
238829 TTAAATGAAAACTTTCTGATAGTTCAGT
1 TTAAATAAAAACTTTCTGATAGTTCAGT
238857 CATCATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (31 bp):
TTAAATAAAAACTTTCTGATAGTTCAGTGAC
Found at i:248598 original size:6 final size:7
Alignment explanation
Indices: 248577--248627 Score: 57
Period size: 7 Copynumber: 6.6 Consensus size: 7
248567 GAGTGGAAAA
248577 TTAATTT
1 TTAATTT
248584 TTAATTT
1 TTAATTT
248591 TTAATTT
1 TTAATTT
248598 TTAATAATCT
1 TTAAT--T-T
248608 ATTAATTT
1 -TTAATTT
248616 TATAATTT
1 T-TAATTT
248624 TTAA
1 TTAA
248628 AAGATTAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 23 0.59
8 8 0.21
9 2 0.05
10 1 0.03
11 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (7 bp):
TTAATTT
Found at i:249913 original size:30 final size:30
Alignment explanation
Indices: 249879--249941 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
249869 TATAAAATAT
*
249879 AAATTTATAAAAAA-ATTATAAAAGAACTTA
1 AAATTTATAAAAAATA-TATAAAAGAACTAA
* *
249909 AAATTTATAATATATATATAAAAGAACTAA
1 AAATTTATAAAAAATATATAAAAGAACTAA
249939 AAA
1 AAA
249942 GCATGTTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (30 bp):
AAATTTATAAAAAATATATAAAAGAACTAA
Found at i:250255 original size:23 final size:23
Alignment explanation
Indices: 250212--250255 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
250202 AAAATTAAAT
* *
250212 TATAATTTTTATAATAATAAAAA
1 TATAATTTTTAAAAGAATAAAAA
*
250235 TATAATTTTTAAAAGATTAAA
1 TATAATTTTTAAAAGAATAAA
250256 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TATAATTTTTAAAAGAATAAAAA
Found at i:250474 original size:17 final size:15
Alignment explanation
Indices: 250451--250511 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 15
250441 TCGATATGAA
250451 AAATTTATATTTTTT
1 AAATTTATATTTTTT
*
250466 ATTAATTTATATCATTTTA
1 A--AATTTATAT--TTTTT
250485 AAGATTTATTATTTTTT
1 AA-ATTTA-TATTTTTT
250502 AAATTTATAT
1 AAATTTATAT
250512 CTATCACGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
15 4 0.11
16 5 0.13
17 16 0.42
18 5 0.13
19 8 0.21
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (15 bp):
AAATTTATATTTTTT
Found at i:251092 original size:2 final size:2
Alignment explanation
Indices: 251085--251114 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
251075 AGGGTTAATA
*
251085 AT AT AT AT AT GT 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
251115 TAAGGATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252503 original size:17 final size:18
Alignment explanation
Indices: 252468--252507 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
252458 GTCAACAAAT
*
252468 AATTCAAAAATAAATTAA
1 AATTAAAAAATAAATTAA
* *
252486 AATTAAAAAATATATAAA
1 AATTAAAAAATAAATTAA
252504 AATT
1 AATT
252508 CATAAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTAAAAAATAAATTAA
Found at i:263563 original size:14 final size:14
Alignment explanation
Indices: 263534--263587 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 14
263524 CCGAATCTTG
*
263534 AATTTAAAAATCTA
1 AATTTAAATATCTA
263548 AATCTTAAAT-TCTA
1 AAT-TTAAATATCTA
*
263562 AATTATAAATATTTA
1 AATT-TAAATATCTA
263577 AATTTTAAATA
1 AA-TTTAAATA
263588 ATTGATCATG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
13 1 0.03
14 15 0.44
15 16 0.47
16 2 0.06
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTAAATATCTA
Found at i:264808 original size:2 final size:2
Alignment explanation
Indices: 264801--264849 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
264791 ATCTATTTTA
264801 AT AT AT AT AT AT 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 AT AT AT AT AT AT
264843 AT A- AT AT
1 AT AT AT AT
264850 TAATAAAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:276121 original size:4 final size:4
Alignment explanation
Indices: 276114--276144 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
276104 CAACCATTTC
*
276114 AAAT AAAT CAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
276145 GATTCCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:276755 original size:15 final size:15
Alignment explanation
Indices: 276741--276773 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
276731 GAGCAATTTA
276741 ATTTTTTT-TCTTTT
1 ATTTTTTTCTCTTTT
276755 ATTTTTTTCTC-TTT
1 ATTTTTTTCTCTTTT
276769 ATTTT
1 ATTTT
276774 CCGTTCTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (15 bp):
ATTTTTTTCTCTTTT
Found at i:276761 original size:13 final size:14
Alignment explanation
Indices: 276743--276773 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
276733 GCAATTTAAT
276743 TTTTTTTCT-TTTA
1 TTTTTTTCTCTTTA
276756 TTTTTTTCTCTTTA
1 TTTTTTTCTCTTTA
276770 TTTT
1 TTTT
276774 CCGTTCTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTCTTTA
Found at i:277207 original size:29 final size:30
Alignment explanation
Indices: 277174--277240 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 30
277164 GACTCATTGT
*
277174 CTAAAATGTTAACGCTAT-AACGTAAGTAA
1 CTAAAATGTTAACACTATAAACGTAAGTAA
* * * *
277203 CTAAAACG-TAACATTTTAAACGTAAGTGA
1 CTAAAATGTTAACACTATAAACGTAAGTAA
277232 CTAAAATGT
1 CTAAAATGT
277241 AATCTAAGAC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.28
Consensus pattern (30 bp):
CTAAAATGTTAACACTATAAACGTAAGTAA
Found at i:292842 original size:22 final size:22
Alignment explanation
Indices: 292817--292861 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
292807 TGGTCACTAA
292817 AAATCCCTATTAAAATCAAAAT
1 AAATCCCTATTAAAATCAAAAT
292839 AAATCCCTATTAAAATCAAAAT
1 AAATCCCTATTAAAATCAAAAT
292861 A
1 A
292862 TCTATATGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATCCCTATTAAAATCAAAAT
Found at i:297908 original size:6 final size:6
Alignment explanation
Indices: 297897--297928 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
297887 ACTATTATCC
*
297897 CAGCCT CAGCCT CAGCCT CAGTCT CAGCCT CA
1 CAGCCT CAGCCT CAGCCT CAGCCT CAGCCT CA
297929 ACCCCAGGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.47, G:0.16, T:0.19
Consensus pattern (6 bp):
CAGCCT
Found at i:312118 original size:31 final size:31
Alignment explanation
Indices: 312074--312134 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
312064 ATTTAAACCC
*
312074 TTTTAACATTTTTAGCTTT-ATCCTTT-AAAAT
1 TTTTAACAATTTTA--TTTGATCCTTTCAAAAT
*
312105 TTTTAATAATTTTATTTGATCCTTTCAAAA
1 TTTTAACAATTTTATTTGATCCTTTCAAAA
312135 AATTTTGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 3 0.12
30 7 0.27
31 16 0.62
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTTAACAATTTTATTTGATCCTTTCAAAAT
Found at i:312268 original size:22 final size:22
Alignment explanation
Indices: 312225--312268 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
312215 TGATTGGTAC
* *
312225 ATATTTTAAATATTTAATTAAA
1 ATATTTTAAATATTAAAATAAA
312247 ATATTTTAAA-ATTAAGAATAAA
1 ATATTTTAAATATTAA-AATAAA
312269 TTGAACCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATTTTAAATATTAAAATAAA
Done.