Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011169.1 Kokia drynarioides strain JFW-HI SEQ_126145, 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: 69373
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:50 original size:3 final size:3
Alignment explanation
Indices: 42--87 Score: 65
Period size: 3 Copynumber: 14.7 Consensus size: 3
32 AAATATTTTA
*
42 AAT AAT AAT AAAT AAT AAAT GAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
88 AGGGGACACG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 33 0.85
4 6 0.15
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:11936 original size:18 final size:18
Alignment explanation
Indices: 11913--11948 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11903 GCATCTAATA
* *
11913 TTGTTCCTTGTAATTATT
1 TTGTTCATTGTAAATATT
11931 TTGTTCATTGTAAATATT
1 TTGTTCATTGTAAATATT
11949 CGGCAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.58
Consensus pattern (18 bp):
TTGTTCATTGTAAATATT
Found at i:12540 original size:3 final size:3
Alignment explanation
Indices: 12532--12574 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
12522 AAATATTTTA
*
12532 AAT AAT AAT AAAT AAT AAAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
12575 AAGGGGATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12861 original size:26 final size:25
Alignment explanation
Indices: 12797--12862 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
12787 GAGAAGGTAG
*
12797 TTTTAAAGGAAAAACCAAAACTTTT
1 TTTTAAAGGAAAAAACAAAACTTTT
* * * * *
12822 TTTAAGAATGAAAAGAGAAAAGTTTT
1 TTTTA-AAGGAAAAAACAAAACTTTT
12848 TTTTAAAGGAAAAAA
1 TTTTAAAGGAAAAAA
12863 TATAAAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
25 12 0.39
26 19 0.61
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.30
Consensus pattern (25 bp):
TTTTAAAGGAAAAAACAAAACTTTT
Found at i:13637 original size:29 final size:29
Alignment explanation
Indices: 13586--13816 Score: 122
Period size: 29 Copynumber: 7.8 Consensus size: 29
13576 AGAAATCATA
*
13586 TTTTGACCCTCAAACTTTTCCAAAATTCTAT
1 TTTTGACCCT-AAA-TTTTCCAAAATTCAAT
13617 TTTTGA-CCTAAAATTTTCCAAAAATTACAA-
1 TTTTGACCCT-AAATTTTCC-AAAATT-CAAT
* * *
13647 TTTT-ACCCCTAAACTTTCTAAAATTCCA-
1 TTTTGA-CCCTAAATTTTCCAAAATTCAAT
*
13675 TTTTGACCCTAAATTTTCCAAAAAAT-ACAT
1 TTTTGACCCTAAATTTTCC-AAAATTCA-AT
* * *
13705 TTTT-ACCCCCTGAACTTTCTAAAATTTC-AT
1 TTTTGA--CCCTAAATTTTCCAAAA-TTCAAT
*
13735 TTTTGACCCAAAATTTTCCAAAAATT-ACA-
1 TTTTGACCCTAAATTTTCC-AAAATTCA-AT
* * * *
13764 TTTTAACCCTAAAACTTTCCAAATTTCCAT
1 TTTTGACCCT-AAATTTTCCAAAATTCAAT
* *
13794 TTATGACTCC-AAACTTTCCAAAA
1 TTTTGAC-CCTAAATTTTCCAAAA
13817 CAACCATTTT
Statistics
Matches: 155, Mismatches: 25, Indels: 42
0.70 0.11 0.19
Matches are distributed among these distances:
28 17 0.11
29 58 0.37
30 55 0.35
31 25 0.16
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
TTTTGACCCTAAATTTTCCAAAATTCAAT
Found at i:13686 original size:59 final size:59
Alignment explanation
Indices: 13592--13816 Score: 251
Period size: 59 Copynumber: 3.8 Consensus size: 59
13582 CATATTTTGA
* * *
13592 CCCTCAAACTTTTCCAAAATTCTATTTTTGACCTAAAATTTTCCAAAAATTACAATTTTAC
1 CCCTAAAAC-TTTCCAAAATTCCATTTTTGACC-CAAATTTTCCAAAAATTACAATTTTAC
* * *
13653 CCCT-AAACTTTCTAAAATTCCA-TTTTGACCCTAAATTTTCCAAAAAATACATTTTTACC
1 CCCTAAAACTTTCCAAAATTCCATTTTTGACCC-AAATTTTCCAAAAATTACAATTTTA-C
* * * *
13712 CCCT-GAACTTTCTAAAATTTCATTTTTGACCCAAAATTTTCCAAAAATTAC-ATTTTAA
1 CCCTAAAACTTTCCAAAATTCCATTTTTGACCC-AAATTTTCCAAAAATTACAATTTTAC
* * *
13770 CCCTAAAACTTTCCAAATTTCCATTTATGACTCCAAACTTTCCAAAA
1 CCCTAAAACTTTCCAAAATTCCATTTTTGAC-CCAAATTTTCCAAAA
13817 CAACCATTTT
Statistics
Matches: 142, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
58 35 0.25
59 71 0.50
60 32 0.23
61 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (59 bp):
CCCTAAAACTTTCCAAAATTCCATTTTTGACCCAAATTTTCCAAAAATTACAATTTTAC
Found at i:13793 original size:118 final size:119
Alignment explanation
Indices: 13602--13816 Score: 321
Period size: 118 Copynumber: 1.8 Consensus size: 119
13592 CCCTCAAACT
* * *
13602 TTTCCAAAATTCTATTTTTGACCTAAAATTTTCCAAAAATTACAATTTTACCCCTAAACTTTCTA
1 TTTCCAAAATTCTATTTTTGACCCAAAATTTTCCAAAAATTACAATTTTAACCCTAAACTTTCCA
*
13667 AAATTCCATTT-TGAC-CCTAAATTTTCCAAAAAATACATTTTTACCCCCTGAAC
66 AAATTCCATTTATGACTCC-AAACTTTCCAAAAAATACATTTTTACCCCCTGAAC
*
13720 TTTCTAAAATT-TCATTTTTGACCCAAAATTTTCCAAAAATTAC-ATTTTAACCCTAAAACTTTC
1 TTTCCAAAATTCT-ATTTTTGACCCAAAATTTTCCAAAAATTACAATTTTAACCCT-AAACTTTC
*
13783 CAAATTTCCATTTATGACTCCAAACTTTCCAAAA
64 CAAAATTCCATTTATGACTCCAAACTTTCCAAAA
13817 CAACCATTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
117 11 0.13
118 58 0.67
119 16 0.18
120 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (119 bp):
TTTCCAAAATTCTATTTTTGACCCAAAATTTTCCAAAAATTACAATTTTAACCCTAAACTTTCCA
AAATTCCATTTATGACTCCAAACTTTCCAAAAAATACATTTTTACCCCCTGAAC
Found at i:13942 original size:30 final size:29
Alignment explanation
Indices: 13899--13993 Score: 81
Period size: 30 Copynumber: 3.3 Consensus size: 29
13889 TTAGATGTCT
13899 AAAAATT-TCATTTTTGACCCGAACCTTCC
1 AAAAATTATCATTTTTGACCCGAACCTT-C
***
13928 AAAAATTATCATTTTACCCCCGAA--TGTC
1 AAAAATTATCATTTTTGACCCGAACCT-TC
* *
13956 TAAAA-TACCATTTTTGACCTCGAACCTTTC
1 AAAAATTATCATTTTTGACC-CGAACC-TTC
13986 AAAAATTA
1 AAAAATTA
13994 CCGTTTTAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
27 10 0.20
28 10 0.20
29 8 0.16
30 19 0.38
31 3 0.06
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAAATTATCATTTTTGACCCGAACCTTC
Found at i:13960 original size:29 final size:28
Alignment explanation
Indices: 13871--14021 Score: 71
Period size: 29 Copynumber: 5.2 Consensus size: 28
13861 TGAACTTTCC
* **
13871 AAAATTACCATTTTACCCTTAGATGTCTA
1 AAAATTATCATTTTACCCCGA-ATGTCTA
*
13900 AAAATT-TCATTTTTGA-CCCGAACCT-TCCA
1 AAAATTATCA-TTTT-ACCCCGAA--TGTCTA
13929 AAAATTATCATTTTACCCCCGAATGTCT-
1 AAAATTATCATTTTA-CCCCGAATGTCTA
* * *
13957 AAAA-TACCATTTTTGACCTCGAACCTTTC-A
1 AAAATTATCA-TTTT-ACCCCGAA--TGTCTA
* * *
13987 AAAATTACCGTTTTAACCTCGAATGTCTA
1 AAAATTATCATTTT-ACCCCGAATGTCTA
14016 AAAATT
1 AAAATT
14022 CTATTTTTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
27 4 0.04
28 22 0.23
29 36 0.38
30 30 0.31
31 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATTATCATTTTACCCCGAATGTCTA
Found at i:14001 original size:58 final size:58
Alignment explanation
Indices: 13607--14231 Score: 348
Period size: 58 Copynumber: 10.8 Consensus size: 58
13597 AAACTTTTCC
* ** ** * ** *
13607 AAAATTCTATTTTTGACCTAAAATTTTCCAAAAATTACAATTTTACCCCTAAACTTTCT
1 AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAA-TGTCT
* ** * *
13666 AAAATTCCA-TTTTGACC-CTAAATTTTCCAAAAAATA-CATTTTTACCCCCTGAACTTTCT
1 AAAATTCCATTTTTGACCTC-GAACCTTCCAAAAATTACCA-TTTTACCCCC-GAA-TGTCT
* * ** *** * *
13725 AAAATTTCATTTTTGACC-CAAAATTTTCCAAAAATTA-CATTTTAACCCTAAAACTTTCC
1 AAAATTCCATTTTTGACCTC-GAACCTTCCAAAAATTACCATTTT-ACCCCCGAA-TGTCT
* * * * ** *
13784 AAATTTCCATTTATGA-CTCCAAACTTTCCAAAACA--ACCATTTTATTCCCAAATGTCT
1 AAAATTCCATTTTTGACCT-CGAACCTTCCAAAA-ATTACCATTTTACCCCCGAATGTCT
* * * * **
13841 AAAAATTTCATTTATGACCTTGAACTTTCC-AAAATTACCATTTTA-CCCTTAGATGTCT
1 -AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGA-ATGTCT
* *
13899 AAAAATTTCATTTTTGACC-CGAACCTTCCAAAAATTATCATTTTACCCCCGAATGTCT
1 -AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
* * * * *
13957 AAAATACCATTTTTGACCTCGAACCTTTCAAAAATTACCGTTTTAACCTCGAATGTCT
1 AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
* * * * * * * *** * *
14015 AAAAATTCTATTTTTAACCTCGAACATTTCGAAAGTTACTATTTTGTTCCTGAA-GCATCC
1 -AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAATG--TCT
* * * * ** * *
14075 AAAATTAC-TGTTTCACCCCCG-GGCATCCAAAAA-T--CAATTTACCCCCGAATGTCT
1 AAAATTCCATTTTTGA-CCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
* * *
14129 AAAATACCATTTTTGACCTCGAACCTTCCAAAAATTACCGTTTTACCCTCGAATGTCT
1 AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
* * *
14187 AATAATTCCATTTTTAACCTCGAACCTTCCGAAAGTTACCATTTT
1 AA-AATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTT
14232 GTTCCTGAAG
Statistics
Matches: 446, Mismatches: 92, Indels: 56
0.75 0.15 0.09
Matches are distributed among these distances:
54 12 0.03
55 23 0.05
56 3 0.01
57 35 0.08
58 179 0.40
59 159 0.36
60 35 0.08
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCGAACCTTCCAAAAATTACCATTTTACCCCCGAATGTCT
Found at i:14135 original size:172 final size:172
Alignment explanation
Indices: 13935--14287 Score: 607
Period size: 172 Copynumber: 2.0 Consensus size: 172
13925 TCCAAAAATT
* *
13935 ATCATTTTACCCCCGAATGTCTAAAATACCATTTTTGACCTCGAACCTTTCAAAAATTACCGTTT
1 ATCAATTTACCCCCGAATGTCTAAAATACCATTTTTGACCTCGAACCTTCCAAAAATTACCGTTT
* * *
14000 TAACCTCGAATGTCTAAAAATTCTATTTTTAACCTCGAACATTTCGAAAGTTACTATTTTGTTCC
66 TAACCTCGAATGTCTAAAAATTCCATTTTTAACCTCGAACATTCCGAAAGTTACCATTTTGTTCC
**
14065 TGAAGCATCCAAAATTACTGTTTCACCCCCGGGCATCCAAAA
131 TGAAGCATCCAAAATTACTGTTTCACCCCCAAGCATCCAAAA
14107 ATCAATTTACCCCCGAATGTCTAAAATACCATTTTTGACCTCGAACCTTCCAAAAATTACCGTTT
1 ATCAATTTACCCCCGAATGTCTAAAATACCATTTTTGACCTCGAACCTTCCAAAAATTACCGTTT
* * *
14172 TACCCTCGAATGTCTAATAATTCCATTTTTAACCTCGAACCTTCCGAAAGTTACCATTTTGTTCC
66 TAACCTCGAATGTCTAAAAATTCCATTTTTAACCTCGAACATTCCGAAAGTTACCATTTTGTTCC
14237 TGAAGCATCCAAAATTACTGTTTCACCCCCAAGCATCCAAAA
131 TGAAGCATCCAAAATTACTGTTTCACCCCCAAGCATCCAAAA
14279 ATCACATTT
1 ATCA-ATTT
14288 TCGACTCTAT
Statistics
Matches: 170, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
172 166 0.98
173 4 0.02
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (172 bp):
ATCAATTTACCCCCGAATGTCTAAAATACCATTTTTGACCTCGAACCTTCCAAAAATTACCGTTT
TAACCTCGAATGTCTAAAAATTCCATTTTTAACCTCGAACATTCCGAAAGTTACCATTTTGTTCC
TGAAGCATCCAAAATTACTGTTTCACCCCCAAGCATCCAAAA
Found at i:14163 original size:30 final size:29
Alignment explanation
Indices: 14129--14231 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 29
14119 CCGAATGTCT
14129 AAAATACCATTTTTGACCTCGAACCTTCCA
1 AAAATACCATTTTT-ACCTCGAACCTTCCA
* *
14159 AAAATTACC-GTTTTACCCTCGAA--TGTCTA
1 AAAA-TACCATTTTTA-CCTCGAACCT-TCCA
* *
14188 ATAATTCCATTTTTAACCTCGAACCTTCCGA
1 AAAATACCATTTTT-ACCTCGAACCTTCC-A
**
14219 AAGTTACCATTTT
1 AAAATACCATTTT
14232 GTTCCTGAAG
Statistics
Matches: 55, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
28 4 0.07
29 18 0.33
30 18 0.33
31 15 0.27
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (29 bp):
AAAATACCATTTTTACCTCGAACCTTCCA
Found at i:16144 original size:7 final size:7
Alignment explanation
Indices: 16132--16170 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
16122 GATCAAATTA
16132 TCATATT
1 TCATATT
16139 TCATATT
1 TCATATT
*
16146 TTATATT
1 TCATATT
*
16153 TTATATT
1 TCATATT
*
16160 TTATATT
1 TCATATT
16167 TCAT
1 TCAT
16171 TCATTTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (7 bp):
TCATATT
Found at i:16153 original size:14 final size:14
Alignment explanation
Indices: 16134--16170 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
16124 TCAAATTATC
16134 ATATTTCATATTTT
1 ATATTTCATATTTT
*
16148 ATATTTTATATTTT
1 ATATTTCATATTTT
16162 ATATTTCAT
1 ATATTTCAT
16171 TCATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (14 bp):
ATATTTCATATTTT
Found at i:17115 original size:8 final size:8
Alignment explanation
Indices: 17104--17128 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17094 AATCCATAAA
17104 TAATTTAT
1 TAATTTAT
17112 TAATTTAT
1 TAATTTAT
17120 TAATTTAT
1 TAATTTAT
17128 T
1 T
17129 TGTGATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTTAT
Found at i:19599 original size:2 final size:2
Alignment explanation
Indices: 19587--19623 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19577 ATCGGGGTCC
*
19587 CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
19624 CTGCCTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.03, T:0.49
Consensus pattern (2 bp):
CT
Found at i:27624 original size:15 final size:15
Alignment explanation
Indices: 27604--27633 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
27594 ACTGCAAGTC
27604 TGGAACATCTTTTAT
1 TGGAACATCTTTTAT
27619 TGGAACATCTTTTAT
1 TGGAACATCTTTTAT
27634 ATGATACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
TGGAACATCTTTTAT
Found at i:29562 original size:11 final size:12
Alignment explanation
Indices: 29538--29576 Score: 55
Period size: 11 Copynumber: 3.3 Consensus size: 12
29528 GCAAAATACC
29538 TAAAAGTATGTTT
1 TAAAA-TATGTTT
29551 TAAAAT-TGTTT
1 TAAAATATGTTT
29562 TAAAATAT-TTT
1 TAAAATATGTTT
29573 TAAA
1 TAAA
29577 GGACTTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 18 0.72
12 2 0.08
13 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
TAAAATATGTTT
Found at i:30463 original size:22 final size:21
Alignment explanation
Indices: 30438--30494 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
30428 TTAAAAGATC
30438 TTAAAAAATTATTATGTATTTT
1 TTAAAAAATTATTATGT-TTTT
* *
30460 TTAATATATTATTATGTTTTT
1 TTAAAAAATTATTATGTTTTT
** *
30481 GCAAAAACTTATTA
1 TTAAAAAATTATTA
30495 ACCTCAGATT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.53
Consensus pattern (21 bp):
TTAAAAAATTATTATGTTTTT
Found at i:30822 original size:24 final size:26
Alignment explanation
Indices: 30795--30849 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
30785 ACTGTTAATA
30795 TAAAAATTATAATA-AAAATAA-AAT
1 TAAAAATTATAATATAAAATAAGAAT
* *
30819 TAAATATTATAATATGAAATAAGAAT
1 TAAAAATTATAATATAAAATAAGAAT
30845 TAAAA
1 TAAAA
30850 GTATTACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 6 0.23
26 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
TAAAAATTATAATATAAAATAAGAAT
Found at i:31058 original size:35 final size:36
Alignment explanation
Indices: 30991--31059 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
30981 AAAATTATAT
* * *
30991 ATATTTTTAAAAACATAATAAATATATAATATAAAA
1 ATATTTTAAAAAACAAAAGAAATATATAATATAAAA
31027 ATATTTTAAAAAACTAAAAGAAATA-AT-ATATAA
1 ATATTTTAAAAAAC-AAAAGAAATATATAATATAA
31060 TCATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 15 0.52
37 8 0.28
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (36 bp):
ATATTTTAAAAAACAAAAGAAATATATAATATAAAA
Found at i:35615 original size:29 final size:28
Alignment explanation
Indices: 35583--35644 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
35573 AAAATGAGAC
35583 TTTTCGGATACCCGAGGGCAAAATGGTAA
1 TTTT-GGATACCCGAGGGCAAAATGGTAA
* * *
35612 TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGAGGGCAAAATGGTAA
35640 TTTTG
1 TTTTG
35645 TGAAACTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTGGATACCCGAGGGCAAAATGGTAA
Found at i:35739 original size:58 final size:59
Alignment explanation
Indices: 35654--36015 Score: 161
Period size: 58 Copynumber: 6.2 Consensus size: 59
35644 GTGAAACTGC
* * * * *
35654 AGGGTTAAAAATGGAATTTTTTAGACATTCAGGGGTAAAAGGGTAATT-TTGAGAGTTTCG
1 AGGGTAAAAAATGGAA-TTTTTGGACATTCAGGGGTAAAAAGATAATTCTTGAAAGTTT-G
* * *
35714 A-GGTAAAAAATAGAATTTTTGGACA-TCTAGGGG-AAAAATATAATTCTTGAAAGTTTT
1 AGGGTAAAAAATGGAATTTTTGGACATTC-AGGGGTAAAAAGATAATTCTTGAAAGTTTG
* * * * *
35771 AGGGTAAAAAATGGAATTTTTGGA-AGTTTAGGGGTAAAATTGGAT--TTTTTGGAAGTTTT
1 AGGGTAAAAAATGGAATTTTTGGACA-TTCAGGGGTAAAA--AGATAATTCTTGAAAGTTTG
* * * * * * *
35830 AGGGGT--AAAATGGAAATTTTGAAGATTCAAGGGTCAAAATGGAT--TTTTTGGAAGTTT-
1 A-GGGTAAAAAATGGAATTTTTGGACATTCAGGGGT-AAAA-AGATAATTCTTGAAAGTTTG
* * * *
35887 AGGGGT-AAAAATGGAATTTTTAGA-AGTTTCAAGGGTAAAAATG-GAATTTTTGGAAA-TTT-
1 A-GGGTAAAAAATGGAATTTTTGGACA--TTCAGGGGTAAAAA-GATAATTCTT-GAAAGTTTG
** * * *
35946 AGGGGT-AAAAATGGAATTTTTGGA-AGTTTTGGGGTCCAAAATG-GAATTTTTGAAAGTTTG
1 A-GGGTAAAAAATGGAATTTTTGGACA-TTCAGGGGT--AAAAAGATAATTCTTGAAAGTTTG
36006 AGGGTAAAAA
1 AGGGTAAAAA
36016 CGTAATTTTT
Statistics
Matches: 249, Mismatches: 30, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
57 20 0.08
58 118 0.47
59 92 0.37
60 17 0.07
61 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (59 bp):
AGGGTAAAAAATGGAATTTTTGGACATTCAGGGGTAAAAAGATAATTCTTGAAAGTTTG
Found at i:35800 original size:29 final size:28
Alignment explanation
Indices: 35719--36038 Score: 286
Period size: 29 Copynumber: 11.0 Consensus size: 28
35709 TTTCGAGGTA
* * *
35719 AAAAATAGAATTTTTGGACA-TCTAGGGG
1 AAAAATGGAATTTTTGGA-AGTTTAGGGT
** * *
35747 AAAAATATAATTCTTGAAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAG-TTTAGGGT
35776 AAAAAATGGAATTTTTGGAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTA-GGGT
* *
35806 AAAATTGGATTTTTTGGAAGTTTTAGGGGT
1 AAAAATGGAATTTTTGGAAG-TTTA-GGGT
* *
35836 -AAAATGGAAATTTT-GAAGATTCAAGGGT
1 AAAAATGGAATTTTTGGAAG-TT-TAGGGT
* *
35864 CAAAATGGATTTTTTGGAAGTTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTA-GGGT
*
35893 AAAAATGGAATTTTTAGAAGTTTCAAGGGT
1 AAAAATGGAATTTTTGGAAGTTT--AGGGT
*
35923 AAAAATGGAATTTTTGGAAATTTAGGGGT
1 AAAAATGGAATTTTTGGAAGTTTA-GGGT
*
35952 AAAAATGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAG-TTTAGGGT
* *
35981 CCAAAATGGAATTTTTGAAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTT-AGGGT
* * *
36011 AAAAACGTAATTTTTGAATAGTTTAGGG
1 AAAAATGGAATTTTTGGA-AGTTTAGGG
36039 ATCTTCAGGG
Statistics
Matches: 244, Mismatches: 32, Indels: 31
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.00
28 27 0.11
29 127 0.52
30 88 0.36
31 1 0.00
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
AAAAATGGAATTTTTGGAAGTTTAGGGT
Found at i:35869 original size:59 final size:58
Alignment explanation
Indices: 35755--36026 Score: 286
Period size: 59 Copynumber: 4.7 Consensus size: 58
35745 GGAAAAATAT
* * * *
35755 AATTCTTGAAAGTTTTA-GGGTAAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATTGG
1 AATTTTTGGAAGTTTTAGGGGT-AAAAATGGAATTTTTGGAAGTTCAAGGGTAAAA-TGG
* *
35814 ATTTTTTGGAAGTTTTAGGGGT-AAAATGGAAATTTT-GAAGATTCAAGGGTCAAAATGG
1 AATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTGGAAG-TTCAAGGGT-AAAATGG
* *
35872 ATTTTTTGGAAG-TTTAGGGGTAAAAATGGAATTTTTAGAAGTTTCAAGGGTAAAAATGG
1 AATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTGGAAG-TTCAAGGGT-AAAATGG
* ***
35931 AATTTTTGGAA-ATTTAGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCCAAAATGG
1 AATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGT--AAAATGG
* * * *
35990 AATTTTTGAAAGTTTGA-GGGTAAAAACGTAATTTTTG
1 AATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTG
36027 AATAGTTTAG
Statistics
Matches: 185, Mismatches: 20, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
57 13 0.07
58 54 0.29
59 111 0.60
60 7 0.04
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (58 bp):
AATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTGGAAGTTCAAGGGTAAAATGG
Found at i:37842 original size:6 final size:6
Alignment explanation
Indices: 37831--37875 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
37821 GACTTTATAA
*
37831 TAAATT TAAATT TAAATT TAAGA-T T-AATT TAAATT CAAATT TAAA
1 TAAATT TAAATT TAAATT TAA-ATT TAAATT TAAATT TAAATT TAAA
37876 ATAAATCTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 1 0.03
5 3 0.09
6 29 0.85
7 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:37886 original size:23 final size:23
Alignment explanation
Indices: 37824--37886 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
37814 TAATTTGGAC
* *
37824 TTTATAATAAATTTAAATTTAAA
1 TTTAAAATAAATTTAAATTCAAA
* *
37847 TTTAAGATTAATTTAAATTCAAA
1 TTTAAAATAAATTTAAATTCAAA
*
37870 TTTAAAATAAATCTAAA
1 TTTAAAATAAATTTAAA
37887 AAAGGCTCGG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAAAATAAATTTAAATTCAAA
Found at i:41488 original size:20 final size:20
Alignment explanation
Indices: 41465--41514 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
41455 ATTACTTTTA
*
41465 TTCTTTTTTCCTTTCTTTC-T
1 TTCTTTTTTCC-TCCTTTCTT
**
41485 TTCTAGTTTCCTCCTTTCTT
1 TTCTTTTTTCCTCCTTTCTT
41505 TTCTTTTTTC
1 TTCTTTTTTC
41515 TCTCTATTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (20 bp):
TTCTTTTTTCCTCCTTTCTT
Found at i:52128 original size:26 final size:26
Alignment explanation
Indices: 52099--52172 Score: 139
Period size: 26 Copynumber: 2.8 Consensus size: 26
52089 CTTCAAATAC
52099 GTACTATGTCAACAAATTTACACTTA
1 GTACTATGTCAACAAATTTACACTTA
52125 GTACTATGTCAACAAATTTACACTTA
1 GTACTATGTCAACAAATTTACACTTA
*
52151 GTACTATGTCAACAATTTTACA
1 GTACTATGTCAACAAATTTACA
52173 TTCTTTGTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (26 bp):
GTACTATGTCAACAAATTTACACTTA
Found at i:53085 original size:368 final size:369
Alignment explanation
Indices: 52395--53147 Score: 835
Period size: 368 Copynumber: 2.0 Consensus size: 369
52385 ATAACAGTTG
* ** **
52395 TGATCGTAAATCAACGGACAGTGAGATTCGTAAAATCCTTTAAGTAGAAGGTTGTGATTGTAAAT
1 TGATCGTAAATCAACGGACAGTGAGATTCGTAAAATCCTATAAGTAGAAGGTCATGACCGTAAAT
* * ** * * *
52460 CAACTGAAGCTTGTTAGAAAGTTCCTTGTTTTTTAGTAGATTGATCCATTTCAAGCCTCATTTCA
66 CAACTGAAGCTTGTTAAAAAGTTCCATGTTTTTTAACAAATCGATCCATTTCAAGCCTCATTTAA
* * *
52525 GACTACGGTGAAGAGAGGTAGCTTCAGCCTTACAAAGACATTGTAAAAAATTGATTCCTCTGTCT
131 GACTACGGTGAAGAGA-G-AGCTTCAACCTCACAAAGACATTGTAAAAAATTGATTCCTCTATCT
* * *
52590 TCCTTCTTTCAACGTCAGTTTTGAATTCTTCCTTAACACGTCTATATTCATCATCTCTAGCATCT
194 TCCTTCTTTCAACGTCAGTTTTGAATTATTCCTCAACACGTCTACATTCATCATCTCTAGCATCT
* * **
52655 AACTTGCTCAGAAGGGCAGAGAGGTCAAAATTAGCTAGTTGGAAATAATCTCTTGTCATGCTTAG
259 AACTTGCTCAGAAGGGCAGAGAGGTCAAAATAAGCTAGTTGAAAATAATCTCTTACCATGCTTAG
52720 AACTAGTTTAGCAAATTTACATTCATTGTGAACCAGGAAGTGTTCA
324 AACTAGTTTAGCAAATTTACATTCATTGTGAACCAGGAAGTGTTCA
* * * * *
52766 TGATTGTAAATCAGCGTACCGTGAGATTCGTAAAATCCTATAAGTAGAATGTCATGACCGTAAAT
1 TGATCGTAAATCAACGGACAGTGAGATTCGTAAAATCCTATAAGTAGAAGGTCATGACCGTAAAT
** *
52831 CAGTTGAAGCTT-TTCAAAAAGTTCCAT-TTTTTTAACAAATCGATCCATTTCAAGCCTCGTTTA
66 CAACTGAAGCTTGTT-AAAAAGTTCCATGTTTTTTAACAAATCGATCCATTTCAAGCCTCATTTA
* *
52894 AGATGTACGGATG-A-AGA-AGCTTCAACCTCACAAAGACAATT-TAACATAATTGATTCCTCTA
130 AGA-CTACGG-TGAAGAGAGAGCTTCAACCTCACAAAGAC-ATTGTAA-AAAATTGATTCCTCTA
** * * * *
52955 TGC-TCCTTCTTTCATGGTTAGTTTTGAGTTATTTCTCAACATGTCTACATTCATCATC-CTTAG
191 T-CTTCCTTCTTTCAACGTCAGTTTTGAATTATTCCTCAACACGTCTACATTCATCATCTC-TAG
* * * * *
53018 CATCTAACTTGCTCCGGAA-GGC-GAAGAGTTCAGAATAAGCTATTTGAAAATCATCTCTTACCA
254 CATCTAACTTGCT-CAGAAGGGCAG-AGAGGTCAAAATAAGCTAGTTGAAAATAATCTCTTACCA
* * * * ** * * * *
53081 TGCTTATAATTAGGTCATTAAATTTACATTCCTTCG-AAACCAAGAAGTTTTCA
317 TGCTTAGAACTAGTTTAGCAAATTTACATTCATT-GTGAACCAGGAAGTGTTCA
*
53134 TGAACGTAAATCAA
1 TGATCGTAAATCAA
53148 TAAACTGAAG
Statistics
Matches: 316, Mismatches: 56, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
367 23 0.07
368 166 0.53
369 6 0.02
370 38 0.12
371 81 0.26
372 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (369 bp):
TGATCGTAAATCAACGGACAGTGAGATTCGTAAAATCCTATAAGTAGAAGGTCATGACCGTAAAT
CAACTGAAGCTTGTTAAAAAGTTCCATGTTTTTTAACAAATCGATCCATTTCAAGCCTCATTTAA
GACTACGGTGAAGAGAGAGCTTCAACCTCACAAAGACATTGTAAAAAATTGATTCCTCTATCTTC
CTTCTTTCAACGTCAGTTTTGAATTATTCCTCAACACGTCTACATTCATCATCTCTAGCATCTAA
CTTGCTCAGAAGGGCAGAGAGGTCAAAATAAGCTAGTTGAAAATAATCTCTTACCATGCTTAGAA
CTAGTTTAGCAAATTTACATTCATTGTGAACCAGGAAGTGTTCA
Found at i:61805 original size:7 final size:7
Alignment explanation
Indices: 61793--61822 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
61783 TCAGTTTTTC
61793 TTTTCTT
1 TTTTCTT
61800 TTTTCTT
1 TTTTCTT
61807 TTTTCTT
1 TTTTCTT
61814 TTTTCTT
1 TTTTCTT
61821 TT
1 TT
61823 CTGAATAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:63815 original size:25 final size:25
Alignment explanation
Indices: 63779--63834 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
63769 TTTCTGATAG
63779 CAAAATAAAGATGGGATGGTTGGAA
1 CAAAATAAAGATGGGATGGTTGGAA
*
63804 CTAAATAAAGATGGGATGGTTGGAA
1 CAAAATAAAGATGGGATGGTTGGAA
63829 CAAAAT
1 CAAAAT
63835 TTCAATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (25 bp):
CAAAATAAAGATGGGATGGTTGGAA
Found at i:65869 original size:33 final size:33
Alignment explanation
Indices: 65829--65892 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
65819 AAACACTGTC
* *
65829 ATAAATATGATAAATATTTTATTATATTAAAAA
1 ATAAATATAATAAATATGTTATTATATTAAAAA
*
65862 ATAAATATAATAAATATGTTATTGTATTAAA
1 ATAAATATAATAAATATGTTATTATATTAAA
65893 TATAATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (33 bp):
ATAAATATAATAAATATGTTATTATATTAAAAA
Found at i:66021 original size:6 final size:6
Alignment explanation
Indices: 66004--66037 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
65994 TTAATTGTTT
*
66004 AATATA ATTATA AATATA AATATA AATATA AATA
1 AATATA AATATA AATATA AATATA AATATA AATA
66038 ATTATTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:67281 original size:26 final size:26
Alignment explanation
Indices: 67236--67290 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
67226 AATAATGAAT
67236 ATATTTTAAAAATTAAATTTAAATAAA
1 ATATTTTAAAAATT-AATTTAAATAAA
*
67263 ATATTTTAAAATATT-ATTTAATTAAA
1 ATATTTTAAAA-ATTAATTTAAATAAA
67289 AT
1 AT
67291 TAGGGTTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 12 0.46
27 11 0.42
28 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATTTTAAAAATTAATTTAAATAAA
Found at i:68219 original size:29 final size:30
Alignment explanation
Indices: 68187--68245 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
68177 TATGTTTTTT
68187 AATAAATTTA-ATGATTTTT-AATTTTTAAA
1 AATAAATTTATAT-ATTTTTGAATTTTTAAA
** *
68216 AATAGTTTTATATTTTTTTGAATTTTTAAA
1 AATAAATTTATATATTTTTGAATTTTTAAA
68246 TTTAAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 13 0.52
30 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (30 bp):
AATAAATTTATATATTTTTGAATTTTTAAA
Done.