Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013811.1 Kokia drynarioides strain JFW-HI SEQ_128839, 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: 211003
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:154850 original size:34 final size:35
Alignment explanation
Indices: 154812--154903 Score: 132
Period size: 34 Copynumber: 2.7 Consensus size: 35
154802 CCAAACTCAT
* *
154812 TTTAAATTTATTTTAAGATTAAATTTGTTTT-AAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTTCAAA
*
154846 TTTAAATTTAATTTAAGTTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAGTTTAAATTTATTTTCAAA
* *
154881 TTTAAAATTATTATAAGTTTAAA
1 TTTAAATTTATTTTAAGTTTAAA
154904 ATAAATAAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 28 0.55
35 23 0.45
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGTTTAAATTTATTTTCAAA
Found at i:154858 original size:11 final size:11
Alignment explanation
Indices: 154830--154885 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
154820 TATTTTAAGA
**
154830 TTAAATTTGTT
1 TTAAATTTAAT
154841 TTAAATTTAAAT
1 TTAAATTT-AAT
154853 TT-AATTTAAGT
1 TTAAATTTAA-T
*
154864 TTAAATTTATT
1 TTAAATTTAAT
154875 TTCAAATTTAA
1 TT-AAATTTAA
154886 AATTATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
10 2 0.05
11 19 0.51
12 16 0.43
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:154905 original size:17 final size:17
Alignment explanation
Indices: 154812--154903 Score: 112
Period size: 17 Copynumber: 5.4 Consensus size: 17
154802 CCAAACTCAT
154812 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAG
* * *
154829 ATTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAG
*
154846 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAG
*
154863 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAG
* *
154881 TTTAAAATTATTATAAG
1 TTTAAATTTATTTTAAG
154898 TTTAAA
1 TTTAAA
154904 ATAAATAAAG
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
17 48 0.77
18 14 0.23
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:156793 original size:30 final size:29
Alignment explanation
Indices: 156726--156858 Score: 89
Period size: 30 Copynumber: 4.6 Consensus size: 29
156716 CCCTAGAGGC
*
156726 CCCTAAACTGTCCAAAAATTATA--TTTGA
1 CCCTAAACT-TTCAAAAATTATATTTTTGA
** *
156754 CCCCCAACTTCTCCAAAATTATATTTTTGA
1 CCCTAAACTT-TCAAAAATTATATTTTTGA
*
156784 CCCTAAACTTTCAAAAAAATT-TGTTTTT-A
1 CCCTAAACTTTC--AAAAATTATATTTTTGA
**
156813 CCCCTAAACTTTCCAAAAATTCCA--TTTGA
1 -CCCTAAACTTT-CAAAAATTATATTTTTGA
*
156842 CCCCAAAACTTTCAAAA
1 -CCCTAAACTTTCAAAA
156859 TTTACCCTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
27 1 0.01
28 25 0.29
29 22 0.26
30 30 0.35
31 7 0.08
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTAAACTTTCAAAAATTATATTTTTGA
Found at i:156832 original size:29 final size:29
Alignment explanation
Indices: 156725--156833 Score: 100
Period size: 30 Copynumber: 3.7 Consensus size: 29
156715 ACCCTAGAGG
* * *
156725 CCCCTAAACTGTCCAAAAATTATATTTGA
1 CCCCTAAACTTTCCAAAAATTATTTTTTA
*
156754 CCCC-CAACTTCTCC-AAAATTATATTTTTGA
1 CCCCTAAACTT-TCCAAAAATTAT-TTTTT-A
*
156784 -CCCTAAACTTTCAAAAAAATT-TGTTTTTA
1 CCCCTAAACTTTC-CAAAAATTAT-TTTTTA
156813 CCCCTAAACTTTCCAAAAATT
1 CCCCTAAACTTTCCAAAAATT
156834 CCATTTGACC
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
28 12 0.18
29 23 0.35
30 24 0.37
31 6 0.09
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.35
Consensus pattern (29 bp):
CCCCTAAACTTTCCAAAAATTATTTTTTA
Found at i:156844 original size:29 final size:29
Alignment explanation
Indices: 156725--156858 Score: 116
Period size: 29 Copynumber: 4.6 Consensus size: 29
156715 ACCCTAGAGG
*
156725 CCCCTAAACTGTCCAAAAATTATATTTGA
1 CCCCTAAACTTTCCAAAAATTATATTTGA
*
156754 CCCC-CAACTTCTCC-AAAATTATATTTTTGA
1 CCCCTAAACTT-TCCAAAAATTATA--TTTGA
* * *
156784 -CCCTAAACTTTCAAAAAAATT-TGTTTTTA
1 CCCCTAAACTTTC-CAAAAATTAT-ATTTGA
**
156813 CCCCTAAACTTTCCAAAAATTCCATTTGA
1 CCCCTAAACTTTCCAAAAATTATATTTGA
*
156842 CCCCAAAACTTT-CAAAA
1 CCCCTAAACTTTCCAAAA
156859 TTTACCCTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
28 18 0.21
29 38 0.45
30 23 0.27
31 6 0.07
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCCTAAACTTTCCAAAAATTATATTTGA
Found at i:156873 original size:29 final size:29
Alignment explanation
Indices: 156808--156873 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
156798 AAAAATTTGT
*
156808 TTTTACCCCTAAACTTTCCAAAAATTCCA
1 TTTTACCCCAAAACTTTCCAAAAATTCCA
* * *
156837 TTTGACCCCAAAACTTT-CAAAATTTACCC
1 TTTTACCCCAAAACTTTCCAAAAATT-CCA
156866 TTTTACCC
1 TTTTACCC
156874 TCGAATGTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.35
Consensus pattern (29 bp):
TTTTACCCCAAAACTTTCCAAAAATTCCA
Found at i:162449 original size:7 final size:7
Alignment explanation
Indices: 162437--162526 Score: 57
Period size: 7 Copynumber: 13.1 Consensus size: 7
162427 TGAATAAAAG
162437 AAAAGAA
1 AAAAGAA
162444 AAAAG-A
1 AAAAGAA
*
162450 AGAAG-A
1 AAAAGAA
162456 AAAAGAA
1 AAAAGAA
162463 AAAAG-A
1 AAAAGAA
162469 AAAAG-A
1 AAAAGAA
162475 AAAAGAA
1 AAAAGAA
162482 ACAAA-AA
1 A-AAAGAA
*
162489 ATAAATAA
1 A-AAAGAA
*
162497 TAAAATAA
1 -AAAAGAA
162505 TAAAA-AA
1 -AAAAGAA
*
162512 AAGAGAA
1 AAAAGAA
*
162519 AAGAGAA
1 AAAAGAA
162526 A
1 A
162527 GAAAAGGATA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
6 25 0.34
7 31 0.42
8 16 0.22
9 1 0.01
ACGTcount: A:0.80, C:0.01, G:0.13, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:162449 original size:12 final size:12
Alignment explanation
Indices: 162432--162531 Score: 71
Period size: 12 Copynumber: 8.2 Consensus size: 12
162422 TTCAATGAAT
162432 AAAAGAAAAGAA
1 AAAAGAAAAGAA
162444 AAAAGAAGAAG-A
1 AAAAGAA-AAGAA
*
162456 AAAAGAAAAAAGA
1 AAAAGAAAAGA-A
162469 AAAAGAAAAAGAA
1 AAAAG-AAAAGAA
* *
162482 ACAA-AAAATAA
1 AAAAGAAAAGAA
* * *
162493 ATAATAAAATAA
1 AAAAGAAAAGAA
*
162505 TAAAA-AAAAGAG
1 -AAAAGAAAAGAA
162517 AAAAGAGAAAGAA
1 AAAAGA-AAAGAA
162530 AA
1 AA
162532 GGATAGGTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
11 15 0.21
12 28 0.39
13 23 0.32
14 5 0.07
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:162461 original size:19 final size:19
Alignment explanation
Indices: 162432--162482 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
162422 TTCAATGAAT
162432 AAAAG-AAAAGAAAAAAGA
1 AAAAGAAAAAGAAAAAAGA
*
162450 AGAAGAAAAAGAAAAAAGA
1 AAAAGAAAAAGAAAAAAGA
162469 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
162483 CAAAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAAGAAAAAAGA
Found at i:162531 original size:19 final size:17
Alignment explanation
Indices: 162432--162531 Score: 67
Period size: 19 Copynumber: 5.5 Consensus size: 17
162422 TTCAATGAAT
*
162432 AAAAGAAAAGAAAAAAGA
1 AAAAGAAAA-AGAAAAGA
*
162450 AGAAGAAAAAGAAAAAAGA
1 AAAAGAAAAAG--AAAAGA
162469 AAAAGAAAAAGAAACA-A
1 AAAAGAAAAAGAAA-AGA
* * *
162486 AAAATAAATAATAAAATA
1 AAAAGAAA-AAGAAAAGA
*
162504 ATAAAAAAAAGAGAAAAGA
1 A-AAAGAAAA-AGAAAAGA
*
162523 GAAAGAAAA
1 AAAAGAAAA
162532 GGATAGGTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
17 13 0.20
18 24 0.37
19 28 0.43
ACGTcount: A:0.80, C:0.01, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAGA
Found at i:165091 original size:29 final size:30
Alignment explanation
Indices: 165006--165177 Score: 121
Period size: 29 Copynumber: 5.9 Consensus size: 30
164996 ACCTTGAAGG
*
165006 CCCCTAAACTGTCCAAAAATTAT-ATTTTGA
1 CCCC-AAACTTTCCAAAAATTATCATTTTGA
*
165036 CCCC-GACTTCTCC-AAAATTAT-ATTTTTGA
1 CCCCAAACTT-TCCAAAAATTATCA-TTTTGA
* *
165065 CCCAAAACTTTCCAAAAATT-TCATTTTTA
1 CCCCAAACTTTCCAAAAATTATCATTTTGA
* * * *
165094 CCCCGAACTTTCTAAAAATT-CCATTTTAA
1 CCCCAAACTTTCCAAAAATTATCATTTTGA
* * *
165123 CCCCGAAACATT-CAAAAATTACCCTTTT-A
1 CCCC-AAACTTTCCAAAAATTATCATTTTGA
* *
165152 CCCCAGA-TGTCCAAAAATT-TCATTTT
1 CCCCAAACTTTCCAAAAATTATCATTTT
165178 TGATCTCGAT
Statistics
Matches: 115, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
27 6 0.05
28 22 0.19
29 61 0.53
30 26 0.23
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (30 bp):
CCCCAAACTTTCCAAAAATTATCATTTTGA
Found at i:172451 original size:36 final size:36
Alignment explanation
Indices: 172403--172502 Score: 173
Period size: 36 Copynumber: 2.8 Consensus size: 36
172393 CGTGCAAGTG
*
172403 AATATGTAGGTATGTTATTCATGCCATGAGACAAAA
1 AATATGTGGGTATGTTATTCATGCCATGAGACAAAA
*
172439 AATATGTGGGTATGTTATTCATGGCATGAGACAAAA
1 AATATGTGGGTATGTTATTCATGCCATGAGACAAAA
*
172475 AATATGTGGGTATGTTATTCATGTCATG
1 AATATGTGGGTATGTTATTCATGCCATG
172503 TGATAGTGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (36 bp):
AATATGTGGGTATGTTATTCATGCCATGAGACAAAA
Found at i:172537 original size:45 final size:45
Alignment explanation
Indices: 172486--172575 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
172476 ATATGTGGGT
172486 ATGTTATTCATGTCATGTGATAGTGAATGTATTGTGCTAATGATA
1 ATGTTATTCATGTCATGTGATAGTGAATGTATTGTGCTAATGATA
172531 ATGTTATTCATGTCATGTGATAGTGAATGTATTGTGCTAATGATA
1 ATGTTATTCATGTCATGTGATAGTGAATGTATTGTGCTAATGATA
172576 TGAATATTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.07, G:0.22, T:0.42
Consensus pattern (45 bp):
ATGTTATTCATGTCATGTGATAGTGAATGTATTGTGCTAATGATA
Found at i:172961 original size:10 final size:10
Alignment explanation
Indices: 172946--172988 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
172936 CCAAACTATC
172946 ATTAAATGTG
1 ATTAAATGTG
172956 ATTAAATGTG
1 ATTAAATGTG
*
172966 ACTAAATGTG
1 ATTAAATGTG
172976 ATTAATATGTG
1 ATTAA-ATGTG
172987 AT
1 AT
172989 GTGATAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.19, T:0.40
Consensus pattern (10 bp):
ATTAAATGTG
Found at i:173023 original size:49 final size:48
Alignment explanation
Indices: 172961--173083 Score: 176
Period size: 49 Copynumber: 2.5 Consensus size: 48
172951 ATGTGATTAA
* *
172961 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTC
1 ATGTGA-TTAATGTGATTAATATGTGATGTGATAAATGTTGAAATAATC
*
173010 ATGTGATTTAATGTGATTAATATTTGATGTGATAAATGTTGAAATAATC
1 ATGTGA-TTAATGTGATTAATATGTGATGTGATAAATGTTGAAATAATC
* *
173059 ATGTGACTAATGTGACTAA-ATGTGA
1 ATGTGATTAATGTGATTAATATGTGA
173084 CTAAATGTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 5 0.07
48 11 0.16
49 51 0.76
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (48 bp):
ATGTGATTAATGTGATTAATATGTGATGTGATAAATGTTGAAATAATC
Found at i:173082 original size:10 final size:10
Alignment explanation
Indices: 173059--173104 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
173049 TGAAATAATC
173059 ATGTGACT-A
1 ATGTGACTAA
173068 ATGTGACTAA
1 ATGTGACTAA
173078 ATGTGACTAA
1 ATGTGACTAA
*
173088 ATGTGATTAA
1 ATGTGACTAA
173098 TATGTGA
1 -ATGTGA
173105 TGTGATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
9 8 0.24
10 20 0.59
11 6 0.18
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.35
Consensus pattern (10 bp):
ATGTGACTAA
Found at i:173083 original size:19 final size:21
Alignment explanation
Indices: 173036--173170 Score: 77
Period size: 19 Copynumber: 6.3 Consensus size: 21
173026 TTAATATTTG
*
173036 ATGTGA-TAAATGTTGAAATAAT
1 ATGTGACTAAATG-TG-ACTAAT
173058 CATGTGACT-AATGTGACTAA-
1 -ATGTGACTAAATGTGACTAAT
*
173078 ATGTGACTAAATGTGATTAAT
1 ATGTGACTAAATGTGACTAAT
* * *
173099 ATGTGATGTGATAAATGTTGAAATATT
1 ATGTGA----CTAAATG-TG-ACTAAT
*
173126 CATGTGACT-AATGTGATTAA-
1 -ATGTGACTAAATGTGACTAAT
173146 ATGTGACTAAATGTG--TAAT
1 ATGTGACTAAATGTGACTAAT
173165 ATGTGA
1 ATGTGA
173171 TGTGATCAGT
Statistics
Matches: 92, Mismatches: 8, Indels: 28
0.72 0.06 0.22
Matches are distributed among these distances:
18 3 0.03
19 22 0.24
20 16 0.17
21 13 0.14
22 4 0.04
23 14 0.15
24 2 0.02
25 6 0.07
26 2 0.02
27 4 0.04
28 6 0.07
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGTGACTAAATGTGACTAAT
Found at i:173091 original size:68 final size:68
Alignment explanation
Indices: 173010--173217 Score: 312
Period size: 68 Copynumber: 3.1 Consensus size: 68
173000 TGAAATATTC
* * * * *
173010 ATGTGATTTAATGTGATTAATATTTGATGTGATAAATGTTGAAATAATCATGTGACTAATGTGAC
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATGTGAT
173075 TAA
66 TAA
173078 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATGTGAT
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATGTGAT
173143 TAA
66 TAA
* * * *
173146 ATGTGACTAAATGTG--TAATATGTGATGTGATCAGTGCTAAAATATTCATGTGACTAATGTGAT
1 ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATGTGAT
173209 TAAA
66 T-AA
173213 ATGTG
1 ATGTG
173218 TTATGTTAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
66 45 0.35
67 7 0.05
68 78 0.60
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (68 bp):
ATGTGACTAAATGTGATTAATATGTGATGTGATAAATGTTGAAATATTCATGTGACTAATGTGAT
TAA
Found at i:173150 original size:10 final size:10
Alignment explanation
Indices: 173127--173160 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
173117 TGAAATATTC
173127 ATGTGACT-A
1 ATGTGACTAA
*
173136 ATGTGATTAA
1 ATGTGACTAA
173146 ATGTGACTAA
1 ATGTGACTAA
173156 ATGTG
1 ATGTG
173161 TAATATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (10 bp):
ATGTGACTAA
Found at i:174923 original size:128 final size:125
Alignment explanation
Indices: 174705--174936 Score: 295
Period size: 128 Copynumber: 1.8 Consensus size: 125
174695 GCTATGTGAG
* * ***
174705 CATACTGTTTGGAAATTAATGCATAGGGCATACACAAGATGGAACCACGACCGTGCTGGACCGTG
1 CATACTGTTTGGAAATTAATGCACAGGGCAAACACAAGATGGAACCACGACCGTGCCAAACCGTG
*
174770 TGTACATATTGTTTCATGACACACGGGCTAGGCACATGGGCGTGTGCCAAGCCGTGTGTA
66 TGTACATACTGTTTCATGACACACGGGCTAGGCACATGGGCGTGTGCCAAGCCGTGTGTA
* * * *
174830 CATAGTGTTTGGAAATTAATGCACAGGG-AAACACAAGGGTGCGACCCACGATCGTGTCCCAAAC
1 CATACTGTTTGGAAATTAATGCACAGGGCAAACACAA-GATG-GAACCACGACCGTG--CCAAAC
* ** *
174894 CGTGTGTGCATACTGTTTGGTGACACACGGGCTGGGCACATGG
62 CGTGTGTACATACTGTTTCATGACACACGGGCTAGGCACATGG
174937 ACATGGGCCT
Statistics
Matches: 89, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
124 7 0.08
125 29 0.33
126 12 0.13
128 41 0.46
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (125 bp):
CATACTGTTTGGAAATTAATGCACAGGGCAAACACAAGATGGAACCACGACCGTGCCAAACCGTG
TGTACATACTGTTTCATGACACACGGGCTAGGCACATGGGCGTGTGCCAAGCCGTGTGTA
Found at i:174967 original size:128 final size:125
Alignment explanation
Indices: 174700--174967 Score: 286
Period size: 128 Copynumber: 2.1 Consensus size: 125
174690 GCTAGGCTAT
* * * ***
174700 GTGAGCATACTGTTTGGAAATTAATGCATAGGGCATACACAAGATGGAACCACGACCGTGCTGGA
1 GTGAACATACTGTTTGGAAATTAATGCACAGGGCAAACACAAGATGGAACCACGACCGTGCCAAA
* * * * *
174765 CCGTGTGTACATATTGTTTCATGACACACGGGCTAGGCACATGGGCGTGTGCCAAGCCGT
66 CCGTGTGTACATACTGTTTCATGACACACGGGCTAGGCACATGGACATGGGCCAAGCCGG
* * * * *
174825 GTGTACATAGTGTTTGGAAATTAATGCACAGGG-AAACACAAGGGTGCGACCCACGATCGTGTCC
1 GTGAACATACTGTTTGGAAATTAATGCACAGGGCAAACACAA-GATG-GAACCACGACCGTG--C
* ** * **
174889 CAAACCGTGTGTGCATACTGTTTGGTGACACACGGGCTGGGCACATGGACATGGGCCTGGCCGG
62 CAAACCGTGTGTACATACTGTTTCATGACACACGGGCTAGGCACATGGACATGGGCCAAGCCGG
*
174953 GTGAATATACTGTTT
1 GTGAACATACTGTTT
174968 TTCAATTACA
Statistics
Matches: 114, Mismatches: 25, Indels: 5
0.79 0.17 0.03
Matches are distributed among these distances:
124 7 0.06
125 32 0.28
126 12 0.11
128 63 0.55
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (125 bp):
GTGAACATACTGTTTGGAAATTAATGCACAGGGCAAACACAAGATGGAACCACGACCGTGCCAAA
CCGTGTGTACATACTGTTTCATGACACACGGGCTAGGCACATGGACATGGGCCAAGCCGG
Found at i:178471 original size:248 final size:248
Alignment explanation
Indices: 178033--178532 Score: 747
Period size: 248 Copynumber: 2.0 Consensus size: 248
178023 TCACTCACTA
*
178033 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAATTCTATCCTTCACCCATTGTTAAAAG
1 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAACTCTATCCTTCACCCATTGTTAAAAG
* *
178098 GGGTTTACAAAGCAATAGCAATAGCAATGGCAGGAGAAAAAGTTAAACTTGCATGGATAGCTAAC
66 GGGTTTACAAAGCAATAGCAATAGCAATGGAAGGAGAAAAAGTTAAACTTGCATGGATAGCGAAC
*** * * **
178163 AATGTTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTTAACTATTCCCTTCTTCTTCAACTT
131 AACACTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAACTACTCCCTTCTTCTTCAACAC
* * * * *
178228 CTCTCTCTCAAGGAGATGTTAATCTTATTGCTGTTGTTGTTATTGTTTTTGTT
196 CTCTCACTCAAGGAGATGTTAATATTATTACTGTTGTCGTTATTGTTTTGGTT
*
178281 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAACTCTCTCCTTCACCCATTGTT-AAAG
1 TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAACTCTATCCTTCACCCATTGTTAAAAG
* *
178345 GCGGTTTACAAAGCAATAGCAATAGCAAT-GAAGAGAGAAAAAGTTAAACTTTCTTGGATAGTCG
66 G-GGTTTACAAAGCAATAGCAATAGCAATGGAAG-GAGAAAAAGTTAAACTTGCATGGATAG-CG
*
178409 AA-AACACTGCTCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAA-TGACTCCCTTCTTCTTCA
128 AACAACACTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAACT-ACTCCCTTCTTCTTCA
* *
178472 TCACCTCTCACTCAAGGAGATGTTAATATTATTATTGTTGTCGTTATTGTTTTGGTT
192 ACACCTCTCACTCAAGGAGATGTTAATATTATTACTGTTGTCGTTATTGTTTTGGTT
178529 TATA
1 TATA
178533 TTGTTGTTGT
Statistics
Matches: 227, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
247 9 0.04
248 215 0.95
249 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (248 bp):
TATAAAGGCCTCATTGGCCACTCTTTTGAAGCAAACCAACTCTATCCTTCACCCATTGTTAAAAG
GGGTTTACAAAGCAATAGCAATAGCAATGGAAGGAGAAAAAGTTAAACTTGCATGGATAGCGAAC
AACACTGCCCGACGAGCTAGCCTTAAGAAAAGGAGATGTTCAACTACTCCCTTCTTCTTCAACAC
CTCTCACTCAAGGAGATGTTAATATTATTACTGTTGTCGTTATTGTTTTGGTT
Found at i:178534 original size:15 final size:16
Alignment explanation
Indices: 178516--178558 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
178506 TTGTTGTCGT
*
178516 TATTGTTTTG-GTTTA
1 TATTGTTTTGTGTTCA
178531 TATTGTTGTTGTTGTTCA
1 TATTGTT-TTG-TGTTCA
178549 TATTGTTTTG
1 TATTGTTTTG
178559 CTTGTCATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 3 0.12
18 11 0.46
ACGTcount: A:0.12, C:0.02, G:0.21, T:0.65
Consensus pattern (16 bp):
TATTGTTTTGTGTTCA
Found at i:186696 original size:21 final size:21
Alignment explanation
Indices: 186672--186722 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
186662 AGAAGTCTTG
186672 GTTGTATCGGTAGAACCAAGA
1 GTTGTATCGGTAGAACCAAGA
186693 GTTGTATCGGTAGAACCAAGA
1 GTTGTATCGGTAGAACCAAGA
186714 GTTGTATCG
1 GTTGTATCG
186723 ATAGTTGTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (21 bp):
GTTGTATCGGTAGAACCAAGA
Found at i:188791 original size:2 final size:2
Alignment explanation
Indices: 188752--188776 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
188742 TATGAAATAG
188752 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
188777 AATAACAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:195627 original size:20 final size:21
Alignment explanation
Indices: 195610--195654 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
195600 AAGGAAAGTG
195610 AGAAAA-AG-AAAAGAAAA-G
1 AGAAAAGAGAAAAAGAAAAGG
*
195628 AGAAAAGAGAAAAAGAAAAGA
1 AGAAAAGAGAAAAAGAAAAGG
195649 AGAAAA
1 AGAAAA
195655 AAATGTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 9 0.39
21 6 0.26
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (21 bp):
AGAAAAGAGAAAAAGAAAAGG
Found at i:195633 original size:7 final size:7
Alignment explanation
Indices: 195609--195654 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
195599 AAAGGAAAGT
195609 GAGAAAA
1 GAGAAAA
195616 -AG-AAA
1 GAGAAAA
195621 -AGAAAA
1 GAGAAAA
195627 GAGAAAA
1 GAGAAAA
195634 GAGAAAA
1 GAGAAAA
195641 -AGAAAA
1 GAGAAAA
195647 GAAGAAAA
1 G-AGAAAA
195655 AAATGTTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.14
6 11 0.31
7 13 0.37
8 6 0.17
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (7 bp):
GAGAAAA
Done.