Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009649.1 Kokia drynarioides strain JFW-HI SEQ_124367, 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: 61900
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:2771 original size:17 final size:17
Alignment explanation
Indices: 2741--2781 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2731 TCCCTTGACA
2741 TTTAACCTTCCATATTC
1 TTTAACCTTCCATATTC
* *
2758 TTTAATCTTTCATATTC
1 TTTAACCTTCCATATTC
2775 TTGTAAC
1 TT-TAAC
2782 TACTTTTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.24, C:0.22, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAACCTTCCATATTC
Found at i:8823 original size:59 final size:59
Alignment explanation
Indices: 8752--8886 Score: 155
Period size: 59 Copynumber: 2.3 Consensus size: 59
8742 TCGGGGGGGC
* * * * *
8752 AAAATGGTAATTTTGGATTTTCGTG-GGCAAAATGGTAATTTTTGAAAGTATCGATGTCA
1 AAAATGGAAATTTTGGATATTCGAGAGGAAAAATGG-AATTTTTGAAAGTATCGAGGTCA
* * * *
8811 AAAATGGAAATTTTGGATATTCGAGAGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAAATTTTGGATATTCGAGAGGAAAAATGGAATTTTTGAAAGTATCGAGGTCA
* *
8870 AAATTGGAATTTTTGGA
1 AAAATGGAAATTTTGGA
8887 AGTTTCGAGG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 56 0.88
60 8 0.12
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.36
Consensus pattern (59 bp):
AAAATGGAAATTTTGGATATTCGAGAGGAAAAATGGAATTTTTGAAAGTATCGAGGTCA
Found at i:8825 original size:30 final size:29
Alignment explanation
Indices: 8780--8913 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 29
8770 TTTCGTGGGC
* *
8780 AAAATGGTAATTTTTGAAAGTATCGATGTCA
1 AAAATGG-AATTTTTGGAAGTATCGAAGT-A
*
8811 AAAATGGAAATTTTGG-A-TATTCGAGAGTA
1 AAAATGGAATTTTTGGAAGTA-TCGA-AGTA
* *
8840 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTATCGAAG-TA
* * * *
8870 AAATTGGAATTTTTGGAAGTTTCGAGGTT
1 AAAATGGAATTTTTGGAAGTATCGAAGTA
*
8899 AAAATGGGATTTTTG
1 AAAATGGAATTTTTG
8914 AGAATTTAGG
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.02
29 36 0.41
30 42 0.48
31 8 0.09
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTATCGAAGTA
Found at i:8844 original size:29 final size:29
Alignment explanation
Indices: 8780--9215 Score: 179
Period size: 29 Copynumber: 14.4 Consensus size: 29
8770 TTTCGTGGGC
* * *
8780 AAAATGGTAATTTTTGAAAGTATCGATGTCA
1 AAAATGG-AATTTTTGGAAGT-TCGAGGTTA
*
8811 AAAATGGAAATTTTGGATA-TTCGAGAG-TA
1 AAAATGGAATTTTTGGA-AGTTCGAG-GTTA
8840 AAAATGGAATTTTTGGAAGTTTCGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGTTA
*
8870 AAATTGGAATTTTTGGAAGTTTCGAGGTT-
1 AAAATGGAATTTTTGGAAG-TTCGAGGTTA
* * * *
8899 AAAATGGGATTTTTGAGAATTTAG-GGGTA
1 AAAATGGAATTTTTG-GAAGTTCGAGGTTA
* * * * *
8928 AAATTGGAATTTTTGAAAGTTTTGGGGTAA
1 AAAATGGAATTTTTGGAAG-TTCGAGGTTA
* *** * *
8958 AAAATGGGGTCAAAATTGGAATTTTTGGAAGTTTTGGGGTT
1 AAAAT--GG----AATT---T---TTGGAAGTTCGAGGTTA
* * * *
8999 AAAATAGAATTTTTTGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGTTA
* * *
9028 AAAATGGAATTTTTGGAAGTTTTG-GGGTC
1 AAAATGGAATTTTTGGAAG-TTCGAGGTTA
* * *
9057 AAAATGGGATTTTTTGAAGTTC-AGGGATA
1 AAAATGGAATTTTTGGAAGTTCGA-GGTTA
* *
9086 AAAATGGGATTTTTTGG-AGTTCGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTCGAGGTTA
* * * * *
9115 AAAATGGGATTTTTGGGAGTTTTGTGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGTTA
* * * *
9145 AAAATGAAATTTTTAGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGTTA
* *
9175 AAAATGGGA-TTTTGAAAGTTCGATGG-TA
1 AAAATGGAATTTTTGGAAGTTCGA-GGTTA
*
9203 AAAATTGAATTTT
1 AAAATGGAATTTT
9216 CGAATAGTTT
Statistics
Matches: 312, Mismatches: 63, Indels: 62
0.71 0.14 0.14
Matches are distributed among these distances:
28 29 0.09
29 141 0.45
30 106 0.34
31 8 0.03
32 2 0.01
35 4 0.01
36 4 0.01
39 1 0.00
41 11 0.04
42 6 0.02
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGTTA
Found at i:8984 original size:71 final size:70
Alignment explanation
Indices: 8899--9031 Score: 166
Period size: 71 Copynumber: 1.9 Consensus size: 70
8889 TTTCGAGGTT
* *
8899 AAAATGGGATTTTTGAGAA-TTTAGGGG-TAAAATTGGAA-TTTTTGAAAGTTTTG-GGGTAAAA
1 AAAATGGAATTTTTG-GAAGTTTAGGGGTTAAAA-TAGAATTTTTTG-AAG-TTTGAGGGTAAAA
8960 AATGGGGTC
62 AATGGGGTC
*
8969 AAAATTGGAATTTTTGGAAGTTTTGGGGTTAAAATAGAATTTTTTGAAGTTTGAGGGTAAAAA
1 AAAA-TGGAATTTTTGGAAGTTTAGGGGTTAAAATAGAATTTTTTGAAGTTTGAGGGTAAAAA
9032 TGGAATTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
70 11 0.20
71 33 0.60
72 11 0.20
ACGTcount: A:0.35, C:0.01, G:0.28, T:0.36
Consensus pattern (70 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTTAAAATAGAATTTTTTGAAGTTTGAGGGTAAAAAATG
GGGTC
Found at i:8997 original size:30 final size:30
Alignment explanation
Indices: 8962--9187 Score: 207
Period size: 29 Copynumber: 7.7 Consensus size: 30
8952 GGGTAAAAAA
*
8962 TGGGGTCAAAATTGGAATTTTTGGAAGTTT
1 TGGGGTCAAAAATGGAATTTTTGGAAGTTT
* * *
8992 TGGGGT-TAAAATAGAATTTTTTGAAG-TT
1 TGGGGTCAAAAATGGAATTTTTGGAAGTTT
9020 TGAGGGT-AAAAATGGAATTTTTGGAAGTTT
1 TG-GGGTCAAAAATGGAATTTTTGGAAGTTT
* * *
9050 TGGGGTC-AAAATGGGATTTTTTGAAGTTC
1 TGGGGTCAAAAATGGAATTTTTGGAAGTTT
* * *
9079 AGGGAT-AAAAATGGGATTTTTTGG-AG-TT
1 TGGGGTCAAAAAT-GGAATTTTTGGAAGTTT
* * *
9107 CGAGGGT-AAAAATGGGATTTTTGGGAGTTT
1 TG-GGGTCAAAAATGGAATTTTTGGAAGTTT
* * *
9137 TGTGGTCAAAAATGAAATTTTTAGAAGTTT
1 TGGGGTCAAAAATGGAATTTTTGGAAGTTT
* *
9167 CGGGGTCAAAAATGGGATTTT
1 TGGGGTCAAAAATGGAATTTT
9188 GAAAGTTCGA
Statistics
Matches: 157, Mismatches: 30, Indels: 18
0.77 0.15 0.09
Matches are distributed among these distances:
28 15 0.10
29 85 0.54
30 57 0.36
ACGTcount: A:0.30, C:0.03, G:0.30, T:0.37
Consensus pattern (30 bp):
TGGGGTCAAAAATGGAATTTTTGGAAGTTT
Found at i:8999 original size:100 final size:99
Alignment explanation
Indices: 8869--9064 Score: 279
Period size: 100 Copynumber: 2.0 Consensus size: 99
8859 TTTCGAGGTT
* * *
8869 AAAATTGGAATTTTTGGAAGTTTCGAGGTTAAAATGGGA-TTTTTGAGAATTT-AGGGGTAAAAT
1 AAAATTGGAATTTTTGGAAGTTTCGAGGTTAAAATAGAATTTTTTGA-AATTTGA-GGGTAAAAA
8932 TGGAATTTTTGAAAGTTTTGGGGTAAAAAATGGGGTC
64 TGGAATTTTTGAAAGTTTTGGGGT-AAAAATGGGGTC
* * *
8969 AAAATTGGAATTTTTGGAAGTTTTGGGGTTAAAATAGAATTTTTTGAAGTTTGAGGGTAAAAATG
1 AAAATTGGAATTTTTGGAAGTTTCGAGGTTAAAATAGAATTTTTTGAAATTTGAGGGTAAAAATG
* *
9034 GAATTTTTGGAAGTTTTGGGGTCAAAATGGG
66 GAATTTTTGAAAGTTTTGGGGTAAAAATGGG
9065 ATTTTTTGAA
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 8 0.09
100 70 0.81
101 8 0.09
ACGTcount: A:0.33, C:0.02, G:0.29, T:0.37
Consensus pattern (99 bp):
AAAATTGGAATTTTTGGAAGTTTCGAGGTTAAAATAGAATTTTTTGAAATTTGAGGGTAAAAATG
GAATTTTTGAAAGTTTTGGGGTAAAAATGGGGTC
Found at i:9003 original size:41 final size:41
Alignment explanation
Indices: 8922--9002 Score: 135
Period size: 42 Copynumber: 2.0 Consensus size: 41
8912 TGAGAATTTA
8922 GGGGTAAAATTGGAATTTTTGAAAGTTTTGGGGTAAAAAAT
1 GGGGTAAAATTGGAATTTTTGAAAGTTTTGGGGTAAAAAAT
* *
8963 GGGGTCAAAATTGGAATTTTTGGAAGTTTTGGGGTTAAAA
1 GGGGT-AAAATTGGAATTTTTGAAAGTTTTGGGGTAAAAA
9003 TAGAATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 5 0.14
42 32 0.86
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.35
Consensus pattern (41 bp):
GGGGTAAAATTGGAATTTTTGAAAGTTTTGGGGTAAAAAAT
Found at i:9943 original size:21 final size:20
Alignment explanation
Indices: 9918--9956 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9908 CACCGCGTGC
* *
9918 CCGGCTATCACCCTCCAGTCG
1 CCGGCCATCAACC-CCAGTCG
9939 CCGGCCATCAACCCCAGT
1 CCGGCCATCAACCCCAGT
9957 GGTTCTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.18, C:0.49, G:0.18, T:0.15
Consensus pattern (20 bp):
CCGGCCATCAACCCCAGTCG
Found at i:11125 original size:17 final size:17
Alignment explanation
Indices: 11099--11197 Score: 76
Period size: 17 Copynumber: 5.8 Consensus size: 17
11089 CTTTTTAATT
* *
11099 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAGTA
11116 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAGTA
** * *
11133 AATTTAAACTCAAAAATG
1 AATTTAAA-TTTAAAGTA
*
11151 AATTTAAATTTATAA-CA
1 AATTTAAATTTA-AAGTA
* *
11168 AATTTAAACTTAAAGCA
1 AATTTAAATTTAAAGTA
*
11185 AA-TTAAAGTTAAA
1 AATTTAAATTTAAA
11198 ATTTAGACTC
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
16 12 0.18
17 40 0.60
18 15 0.22
ACGTcount: A:0.53, C:0.06, G:0.05, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAGTA
Found at i:11486 original size:24 final size:24
Alignment explanation
Indices: 11459--11506 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
11449 ATGGATGTCC
*
11459 AACCTTTTATCTCCCTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
* *
11483 AACCTTTCATCTTCTTTAACCTTT
1 AACCTTTCATCTCCCTTAACCTTT
11507 CATATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACCTTT
Found at i:17022 original size:18 final size:19
Alignment explanation
Indices: 16987--17024 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
16977 GCTTGCGTCA
*
16987 AAAGTAGGAGGTGAAAAAC
1 AAAGTAGGAGATGAAAAAC
*
17006 AAAG-AGGAGATGGAAAAC
1 AAAGTAGGAGATGAAAAAC
17024 A
1 A
17025 CTATCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.55, C:0.05, G:0.32, T:0.08
Consensus pattern (19 bp):
AAAGTAGGAGATGAAAAAC
Found at i:25970 original size:20 final size:20
Alignment explanation
Indices: 25933--25971 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
25923 ATAATCATAC
** *
25933 CAAAATTTTTAACCCTATAT
1 CAAAATTTCCAACACTATAT
25953 CAAAATTTCCAACACTATA
1 CAAAATTTCCAACACTATA
25972 CTAATACTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAAATTTCCAACACTATAT
Found at i:28464 original size:10 final size:10
Alignment explanation
Indices: 28449--28477 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28439 CTAAGTAAAC
28449 CAAGGGAAAG
1 CAAGGGAAAG
28459 CAAGGGAAAG
1 CAAGGGAAAG
28469 CAAGGGAAA
1 CAAGGGAAA
28478 TACAACTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.10, G:0.38, T:0.00
Consensus pattern (10 bp):
CAAGGGAAAG
Found at i:34148 original size:39 final size:37
Alignment explanation
Indices: 34088--34161 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 37
34078 AATAAAGATT
*
34088 TGATATCGAGGAAGAGGTGAAAACATACAGAAATCCG
1 TGATATCGAGGAAGAGATGAAAACATACAGAAATCCG
*
34125 TGATATCGAGAGGAAGAGATGAAAACATTCAGAAATC
1 TGATATC--GAGGAAGAGATGAAAACATACAGAAATC
34162 TGAGACGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 7 0.21
39 26 0.79
ACGTcount: A:0.45, C:0.12, G:0.26, T:0.18
Consensus pattern (37 bp):
TGATATCGAGGAAGAGATGAAAACATACAGAAATCCG
Found at i:45163 original size:46 final size:41
Alignment explanation
Indices: 45073--45153 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
45063 ATTTATATTT
* *
45073 AATACAATAAAATATTTATTTTATTTAGTTGTGTTTTTTCA
1 AATACAATAAAATATTTATTATATTTAGTAGTGTTTTTTCA
*
45114 AATATAATAAAATATTTATTATATTTATGATAGT-TTTTTT
1 AATACAATAAAATATTTATTATATTTA-G-TAGTGTTTTTT
45154 AATATAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 25 0.71
42 7 0.20
43 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.54
Consensus pattern (41 bp):
AATACAATAAAATATTTATTATATTTAGTAGTGTTTTTTCA
Found at i:48411 original size:2 final size:2
Alignment explanation
Indices: 48406--48430 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48396 GGATATATAT
48406 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
48431 GAGTTGATTA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:50382 original size:27 final size:27
Alignment explanation
Indices: 50328--50382 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
50318 TTTCTTCTTA
* *
50328 ATTTTATTAGCTATCATATTATCGAAT
1 ATTTTATTAGCTAACATATTATCAAAT
*
50355 ATTTTTTTAGACTAACATATTA-CAAAT
1 ATTTTATTAG-CTAACATATTATCAAAT
50382 A
1 A
50383 ATAATTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (27 bp):
ATTTTATTAGCTAACATATTATCAAAT
Found at i:60756 original size:10 final size:11
Alignment explanation
Indices: 60736--60765 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
60726 TCTGACTTTG
60736 AAAAATCATAT
1 AAAAATCATAT
60747 AAAAAT-ATAT
1 AAAAATCATAT
60757 AAAAATCAT
1 AAAAATCAT
60766 TAGAGGCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATCATAT
Found at i:61176 original size:20 final size:20
Alignment explanation
Indices: 61139--61176 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
61129 TGTATATGTG
*
61139 AAATATTATGTGTTTAATAT
1 AAATATTATGTGTGTAATAT
61159 AAATATTGAT-TGTGTAAT
1 AAATATT-ATGTGTGTAAT
61177 TAATTGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.47
Consensus pattern (20 bp):
AAATATTATGTGTGTAATAT
Found at i:61387 original size:22 final size:22
Alignment explanation
Indices: 61362--61540 Score: 191
Period size: 22 Copynumber: 8.1 Consensus size: 22
61352 ACACTAGCGC
*
61362 GCTTCTGTTCAGCACTCTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
61384 GCTTCTGTTACCCAGCATTGTGTAT
1 GCTTCTGTT---CAGCACTGTGTGT
**
61409 GCTTCTGTTCAGCTTTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
61431 GCTTTTGTTTAG--CTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* *
61451 ACTTCTGTTCAGCATTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
61473 GCTTCTGTTTAGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
* * *
61495 GCTTTTCTTCGGCACTGTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
*
61517 GCTTCTGTTCAGCACTTTGTGT
1 GCTTCTGTTCAGCACTGTGTGT
61539 GC
1 GC
61541 CTACTGTTTC
Statistics
Matches: 129, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
20 16 0.12
22 94 0.73
25 19 0.15
ACGTcount: A:0.09, C:0.21, G:0.25, T:0.45
Consensus pattern (22 bp):
GCTTCTGTTCAGCACTGTGTGT
Found at i:61456 original size:42 final size:43
Alignment explanation
Indices: 61363--61525 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 43
61353 CACTAGCGCG
* * * * * *
61363 CTTCTGTTCAGCACTCTGTGTGCTTCTGTTACCCAGCATTGTGTATG
1 CTTCTGTTCAGCATTGTGTGTGCTTCTGTT---TAG-ACTGTGTGTA
* *
61410 CTTCTGTTCAGCTTTGTGTGTGCTTTTGTTTAG-CTGTGTGTA
1 CTTCTGTTCAGCATTGTGTGTGCTTCTGTTTAGACTGTGTGTA
*
61452 CTTCTGTTCAGCATTGTGTGTGCTTCTGTTTAGCACTGTGTGTG
1 CTTCTGTTCAGCATTGTGTGTGCTTCTGTTTAG-ACTGTGTGTA
* * * *
61496 CTTTTCTTCGGCACTGTGTGTGCTTCTGTT
1 CTTCTGTTCAGCATTGTGTGTGCTTCTGTT
61526 CAGCACTTTG
Statistics
Matches: 99, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
42 37 0.37
44 36 0.36
47 26 0.26
ACGTcount: A:0.09, C:0.20, G:0.25, T:0.47
Consensus pattern (43 bp):
CTTCTGTTCAGCATTGTGTGTGCTTCTGTTTAGACTGTGTGTA
Found at i:61575 original size:25 final size:25
Alignment explanation
Indices: 61544--61598 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
61534 TGTGTGCCTA
* *
61544 CTGTTTCCCTAGCACTTATGTGCTT
1 CTGTTTCCCCAGCACTTATGCGCTT
*
61569 CTGTTTCCCCAGCACTTATGCGTTT
1 CTGTTTCCCCAGCACTTATGCGCTT
61594 CTGTT
1 CTGTT
61599 AAGTACTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.11, C:0.29, G:0.16, T:0.44
Consensus pattern (25 bp):
CTGTTTCCCCAGCACTTATGCGCTT
Found at i:61742 original size:6 final size:6
Alignment explanation
Indices: 61733--61815 Score: 66
Period size: 6 Copynumber: 14.2 Consensus size: 6
61723 CAAATTTATT
** *
61733 TTTAAA TTTAAA TTT--A TGTTAAA TTTAAA TTTATCT TTTAAA TGTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
** *
61781 TTT-GC TTTAAA TTTAAA TTT-AA TTAAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
61816 AGATTTAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
4 2 0.03
5 9 0.15
6 42 0.71
7 6 0.10
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:61756 original size:17 final size:16
Alignment explanation
Indices: 61733--61815 Score: 85
Period size: 17 Copynumber: 4.8 Consensus size: 16
61723 CAAATTTATT
61733 TTTAAATTTAAATTTA
1 TTTAAATTTAAATTTA
61749 TGTTAAATTTAAATTTA
1 T-TTAAATTTAAATTTA
* *
61766 TCTTTTAAATGTAAATTTGC
1 ---TTTAAATTTAAATTT-A
61786 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTT-A
*
61803 TTAAAATTTAAAT
1 TTTAAATTTAAAT
61816 AGATTTAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
16 1 0.02
17 41 0.73
19 13 0.23
20 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAAATTTA
Found at i:61775 original size:36 final size:35
Alignment explanation
Indices: 61724--61801 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 35
61714 AAATTGATTC
*
61724 AAATTTATTTTTAAATTTAAATTT-ATGTTAAATTT
1 AAATTTATTTTTAAATGTAAATTTGAT-TTAAATTT
*
61759 AAATTTATCTTTTAAATGTAAATTTGCTTTAAATTT
1 AAATTTAT-TTTTAAATGTAAATTTGATTTAAATTT
61795 AAATTTA
1 AAATTTA
61802 ATTAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
35 8 0.21
36 30 0.77
37 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (35 bp):
AAATTTATTTTTAAATGTAAATTTGATTTAAATTT
Done.