Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014735.1 Kokia drynarioides strain JFW-HI SEQ_129774, 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: 81842
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:10402 original size:96 final size:96
Alignment explanation
Indices: 10228--10409 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 96
10218 GAGAACATTT
** * * *
10228 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCAGGATCGAAGA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAACCGAAGA
*
10293 TAAGGAAACATTGCCTCGATTAATGATATTC
66 TAAAGAAACATTGCCTCGATTAATGATATTC
* * *
10324 GATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTCTGAAACCAGAA
1 GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCAG-AACC-GAA
*
10388 -ATAAA-AGAATATTGCCTCGATT
64 GATAAAGA-AACATTGCCTCGATT
10410 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 7 0.10
96 63 0.86
97 3 0.04
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCAGAACCGAAGA
TAAAGAAACATTGCCTCGATTAATGATATTC
Found at i:10784 original size:58 final size:59
Alignment explanation
Indices: 10621--11025 Score: 502
Period size: 58 Copynumber: 6.9 Consensus size: 59
10611 TCGGATGCAT
* * **
10621 GGGGGTAAAATGGTAGTTTTT-GAATGTTCG-GAACCAAAAATGGGATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAG-GTCAAAAATGGGATTTTTGGAAGTTC
* * * * *
10679 GAGGGTAAAAAGGGTAATTTATGGAAAGTTC-AGGGTC-AAAATTGGATTTTTGGAAGTTC
1 GGGGGT-AAAATGGTAATTTTTGGAAGGTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTC
* *
10738 GGGGGTAAAATGGTAA-TTTTGGAAGGTTTGAGGTTAAAAATGGGATTTTTGGAAGTAT-
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGT-TC
*
10796 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
* * *
10855 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGT-TAAAATGAGATTTTTGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
* * *
10913 GAGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAAT-GGATTTTGGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
* * * * * *
10971 GGCGGTGAAATGATAATTTTTGGAAGGTTCAAGGTCAAAAATGGTATTTTGGGAA
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAA
11026 AAAGGAAGAG
Statistics
Matches: 305, Mismatches: 31, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
57 13 0.04
58 156 0.51
59 127 0.42
60 8 0.03
61 1 0.00
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.32
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTC
Found at i:10837 original size:117 final size:118
Alignment explanation
Indices: 10621--11025 Score: 536
Period size: 117 Copynumber: 3.5 Consensus size: 118
10611 TCGGATGCAT
* * ***
10621 GGGGGTAAAATGGTAGTTTTT-GAATGTTCG-GAACCAAAAATGGGATTTTTGGAAGTTCGAGGG
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAG-GTTAAAAATGGGATTTTTGGAAGTTCGAGGG
* * * *
10684 TAAAAAGGGTAATTTATGGAAAGTTCAGGGTC-AAAATTGGATTTTTGGAAGTTC
65 T-AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATTGGATTTTTGGAAGTTC
* *
10738 GGGGGTAAAATGGTAA-TTTTGGAAGGTTTGAGGTTAAAAATGGGATTTTTGGAAGTAT-GGGGG
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGT-TCGAGGG
*
10801 TAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTC
65 TAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATTGGATTTTTGGAAGTTC
* *
10855 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTT-AAAATGAGATTTTTGGAAGTTCGAGGGT
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
10919 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAA-TGGATTTTGGGAAGTTC
66 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATTGGATTTTTGGAAGTTC
* * * * * * *
10971 GGCGGTGAAATGATAATTTTTGGAAGGTTCAAGGTCAAAAATGGTATTTTGGGAA
1 GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAA
11026 AAAGGAAGAG
Statistics
Matches: 254, Mismatches: 27, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
116 76 0.30
117 159 0.63
118 19 0.07
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.32
Consensus pattern (118 bp):
GGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATTGGATTTTTGGAAGTTC
Found at i:10989 original size:29 final size:28
Alignment explanation
Indices: 10665--10996 Score: 239
Period size: 29 Copynumber: 11.4 Consensus size: 28
10655 CAAAAATGGG
* *
10665 ATTTTTGGAAGTTCGAGGGTAAAAAGGGTA
1 ATTTTTGGAAGTTCG-GGGT-AAAATGATA
* * *
10695 ATTTATGGAAAGTTCAGGGTCAAAAT--TGG
1 ATTTTTGG-AAGTTCGGGGT-AAAATGAT-A
*
10724 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTC-GGGGTAAAATGATA
* * **
10753 A-TTTTGGAAGGTTTGAGGTTAAAAATG-GG
1 ATTTTTGGAA-GTTCG-GGGT-AAAATGATA
* *
10782 ATTTTTGGAAGTATGGGGGTAAAATGGTA
1 ATTTTTGGAAGT-TCGGGGTAAAATGATA
**
10811 ATTTTTGGAAGGTTCGGGGTCAAAAATG-GG
1 ATTTTTGGAA-GTTCGGGGT--AAAATGATA
*
10841 ATTTTTGGAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTC-GGGGTAAAATGATA
*
10870 ATTTTTGGAAGGTTCGGGGTTAAAATGA-G
1 ATTTTTGGAA-GTTCGGGG-TAAAATGATA
*
10899 ATTTTTGGAAGTTCGAGGGTAAAATGGTA
1 ATTTTTGGAAGTTCG-GGGTAAAATGATA
*
10928 ATTTTTGGAAGGTTCGGGGTCAAAA--ATGG
1 ATTTTTGGAA-GTTCGGGGT-AAAATGAT-A
* *
10957 ATTTTGGGAAGTTCGGCGGTGAAATGATA
1 ATTTTTGGAAGTTCGG-GGTAAAATGATA
10986 ATTTTTGGAAG
1 ATTTTTGGAAG
10997 GTTCAAGGTC
Statistics
Matches: 245, Mismatches: 31, Indels: 53
0.74 0.09 0.16
Matches are distributed among these distances:
28 55 0.22
29 107 0.44
30 71 0.29
31 12 0.05
ACGTcount: A:0.30, C:0.04, G:0.33, T:0.33
Consensus pattern (28 bp):
ATTTTTGGAAGTTCGGGGTAAAATGATA
Found at i:12197 original size:19 final size:19
Alignment explanation
Indices: 12160--12197 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
12150 AAATATGGAT
*
12160 AAATAAAGCATATAGTGAA
1 AAATAAAGAATATAGTGAA
12179 AAATACAAGAATATA-TGAA
1 AAATA-AAGAATATAGTGAA
12198 TCCAAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.05, G:0.13, T:0.21
Consensus pattern (19 bp):
AAATAAAGAATATAGTGAA
Found at i:12685 original size:28 final size:28
Alignment explanation
Indices: 12585--12667 Score: 139
Period size: 28 Copynumber: 3.0 Consensus size: 28
12575 CTACGTGTAT
* *
12585 TTAGCACTTTATGTGCTCTCTGATCTGA
1 TTAGCACTTTGTGTGCTCTCTGTTCTGA
*
12613 TTAGCACTTTGTGTGCTCTCCGTTCTGA
1 TTAGCACTTTGTGTGCTCTCTGTTCTGA
12641 TTAGCACTTTGTGTGCTCTCTGTTCTG
1 TTAGCACTTTGTGTGCTCTCTGTTCTG
12668 TAATAACACT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (28 bp):
TTAGCACTTTGTGTGCTCTCTGTTCTGA
Found at i:19100 original size:71 final size:71
Alignment explanation
Indices: 18984--19126 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
18974 AACTCATTGG
*
18984 GAGGTTGAGTTCTTTCTTTTAACATATGCCCCCTATGATTATCCTAGTGTACTGATTCTCTAATA
1 GAGGTTGAGTTCTTTCTTTTAACATATGCCCCCTATGATCATCCTAGTGTACTGATTCTCTAATA
19049 AAGTTT
66 AAGTTT
19055 GAGGTTGAGTTCTTTCTTTTAACATATGCCCCCTATGATCATCCTAGTGTACTGATTCTCTAATA
1 GAGGTTGAGTTCTTTCTTTTAACATATGCCCCCTATGATCATCCTAGTGTACTGATTCTCTAATA
19120 AAGTTT
66 AAGTTT
19126 G
1 G
19127 GAGCCCTACT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (71 bp):
GAGGTTGAGTTCTTTCTTTTAACATATGCCCCCTATGATCATCCTAGTGTACTGATTCTCTAATA
AAGTTT
Found at i:20535 original size:18 final size:18
Alignment explanation
Indices: 20512--20548 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20502 ACAATTCATA
20512 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
20530 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
20548 T
1 T
20549 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:27694 original size:16 final size:15
Alignment explanation
Indices: 27672--27714 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
27662 CCTTTCTTAT
*
27672 TTAAAATATTAAATG
1 TTAAAATATTAAATA
*
27687 TATAAAATTTTAAATA
1 T-TAAAATATTAAATA
*
27703 TTGAAATATTAA
1 TTAAAATATTAA
27715 TTGATCGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (15 bp):
TTAAAATATTAAATA
Found at i:30940 original size:24 final size:24
Alignment explanation
Indices: 30912--30961 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
30902 AGTAGCTGAT
30912 TATATTTGATGCATTGTTGATATA
1 TATATTTGATGCATTGTTGATATA
30936 TATATTTGATGCATTGTTGATATA
1 TATATTTGATGCATTGTTGATATA
30960 TA
1 TA
30962 AGTCTCGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (24 bp):
TATATTTGATGCATTGTTGATATA
Found at i:41206 original size:20 final size:18
Alignment explanation
Indices: 41168--41204 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
41158 TCACAAATTC
*
41168 TGAATATAAATTATAAAA
1 TGAATATAAAATATAAAA
41186 TGAATATAAAAATATAAAA
1 TGAATAT-AAAATATAAAA
41205 ATATTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
TGAATATAAAATATAAAA
Found at i:42997 original size:30 final size:30
Alignment explanation
Indices: 42963--43173 Score: 116
Period size: 30 Copynumber: 7.1 Consensus size: 30
42953 TTCGGGGATC
*
42963 AAATTAGAATTTTTAGAAAATTTGAGGGTT
1 AAATTAGAATTTTTAGAAAATTTAAGGGTT
** * * *
42993 AAATTCA-TTTTTTTGGAAAGTTT-GGGTGTT
1 AAATT-AGAATTTTTAGAAAATTTAAGG-GTT
* * *
43023 AAATTTGAATTTTTAG-AAAGTTAAGGGGTC
1 AAATTAGAATTTTTAGAAAATTTAA-GGGTT
* *
43053 AAATTTA-AATTTTTAG--AAGTTAAGGGGTC
1 AAA-TTAGAATTTTTAGAAAATTTAA-GGGTT
* *
43082 ATATTAGAATTTTTGGAAAATTTAAGGGTT
1 AAATTAGAATTTTTAGAAAATTTAAGGGTT
* * *
43112 AAATTTGAATTTTT-GAAAGGTGT-AGAGGTT
1 AAATTAGAATTTTTAGAAA-ATTTAAG-GGTT
* * * *
43142 AAATTTGAATTTCTAAAAAATTT-AGGGAT
1 AAATTAGAATTTTTAGAAAATTTAAGGGTT
43171 AAA
1 AAA
43174 AACATAATTT
Statistics
Matches: 142, Mismatches: 27, Indels: 25
0.73 0.14 0.13
Matches are distributed among these distances:
28 3 0.02
29 41 0.29
30 84 0.59
31 14 0.10
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (30 bp):
AAATTAGAATTTTTAGAAAATTTAAGGGTT
Found at i:43004 original size:60 final size:59
Alignment explanation
Indices: 42940--43116 Score: 187
Period size: 60 Copynumber: 3.0 Consensus size: 59
42930 CAAATTTGAT
* *
42940 TTTTTTTGGAAAGTTCGGGGATCAAATTAGAATTTTTAGAAAATTTGAGGGTTAAATTCA
1 TTTTTTTGGAAAGTTAGGGG-TCAAATTAGAATTTTTAGAAAATTTAAGGGTTAAATTCA
* * * * * *
43000 TTTTTTTGGAAAGTTTGGGTGTTAAATTTGAATTTTTAG-AAAGTTAAGGGGTCAAATTTA
1 TTTTTTTGGAAAGTTAGGG-GTCAAATTAGAATTTTTAGAAAATTTAA-GGGTTAAATTCA
** * * *
43060 AATTTTTAG-AAGTTAAGGGGTCATATTAGAATTTTTGGAAAATTTAAGGGTTAAATT
1 TTTTTTTGGAAAGTT-AGGGGTCAAATTAGAATTTTTAGAAAATTTAAGGGTTAAATT
43117 TGAATTTTTG
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
59 35 0.36
60 60 0.62
61 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.22, T:0.42
Consensus pattern (59 bp):
TTTTTTTGGAAAGTTAGGGGTCAAATTAGAATTTTTAGAAAATTTAAGGGTTAAATTCA
Found at i:43183 original size:119 final size:120
Alignment explanation
Indices: 42956--43184 Score: 252
Period size: 119 Copynumber: 1.9 Consensus size: 120
42946 TGGAAAGTTC
* * * *
42956 GGGGATCAAATTAGAATTTTTAGAAAATTTGAGGGTTAAATTCATTTTTTTGGAAAGTTTGGGTG
1 GGGGATCAAATTAGAATTTTTAGAAAATTTAAGGGTTAAATTCATATTTTTGGAAAGTTAGAGTG
* * * * * **
43021 TTAAATTTGAATTTTTAGAAAGTTAAGGGGTCAAATTTAAATTTTTAGAAGTTAA
66 TTAAATTTGAATTTCTAAAAAATTAAGGGATAAAACATAAATTTTTAGAAGTTAA
* * *
43076 GGGG-TCATATTAGAATTTTTGGAAAATTTAAGGGTTAAATTTGA-ATTTTT-GAAAGGTGTAGA
1 GGGGATCAAATTAGAATTTTTAGAAAATTTAAGGGTTAAA-TTCATATTTTTGGAAA-GT-TAGA
*
43138 G-GTTAAATTTGAATTTCTAAAAAATTTAGGGATAAAAACAT-AATTTT
63 GTGTTAAATTTGAATTTCTAAAAAATTAAGGGAT-AAAACATAAATTTT
43185 AAAATAAAGA
Statistics
Matches: 90, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
118 4 0.04
119 72 0.80
120 14 0.16
ACGTcount: A:0.37, C:0.03, G:0.21, T:0.40
Consensus pattern (120 bp):
GGGGATCAAATTAGAATTTTTAGAAAATTTAAGGGTTAAATTCATATTTTTGGAAAGTTAGAGTG
TTAAATTTGAATTTCTAAAAAATTAAGGGATAAAACATAAATTTTTAGAAGTTAA
Found at i:44136 original size:17 final size:16
Alignment explanation
Indices: 44106--44164 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
44096 GTGTATTTGG
*
44106 TTTA-TATTTGTTTAAT
1 TTTATTATTTATTT-AT
44122 TTTATTATTTATTTAT
1 TTTATTATTTATTTAT
44138 TTT-TTATTTGTATTTA-
1 TTTATTA-TT-TATTTAT
44154 TTTA-TATTTAT
1 TTTATTATTTAT
44165 AAATAAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
14 3 0.08
15 5 0.13
16 16 0.42
17 14 0.37
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTATTATTTATTTAT
Found at i:44155 original size:10 final size:10
Alignment explanation
Indices: 44106--44164 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
44096 GTGTATTTGG
*
44106 TTTATATTTG
1 TTTATATTTA
44116 TTTA-ATTT-
1 TTTATATTTA
*
44124 TAT-TATTTA
1 TTTATATTTA
*
44133 TTTATTTTTTA
1 TTTA-TATTTA
*
44144 TTTGTATTTA
1 TTTATATTTA
44154 TTTATATTTA
1 TTTATATTTA
44164 T
1 T
44165 AAATAAATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 6 0.15
9 6 0.15
10 19 0.49
11 8 0.21
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (10 bp):
TTTATATTTA
Found at i:54741 original size:17 final size:19
Alignment explanation
Indices: 54709--54747 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
54699 TTTATTTTCT
54709 TCTTCATTCTTTCTTTCCA
1 TCTTCATTCTTTCTTTCCA
54728 TCTTC-TTC-TTCTTTCCA
1 TCTTCATTCTTTCTTTCCA
54745 TCT
1 TCT
54748 GTTATTGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 12 0.60
18 3 0.15
19 5 0.25
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (19 bp):
TCTTCATTCTTTCTTTCCA
Found at i:54787 original size:8 final size:8
Alignment explanation
Indices: 54774--54804 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
54764 AACTGCAATG
54774 AGGATTTA
1 AGGATTTA
54782 AGGATTTA
1 AGGATTTA
*
54790 ATGATTTA
1 AGGATTTA
54798 AGGATTT
1 AGGATTT
54805 TTTTTTGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (8 bp):
AGGATTTA
Found at i:56130 original size:15 final size:15
Alignment explanation
Indices: 56100--56149 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
56090 AATTTTCAAA
* *
56100 TAATTTTTATTCTTT
1 TAATTTTTAATATTT
56115 TAATTTTTAATATTT
1 TAATTTTTAATATTT
* **
56130 TACTCATTAATATTT
1 TAATTTTTAATATTT
56145 TAATT
1 TAATT
56150 AGAATTCAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTTAATATTT
Found at i:58342 original size:21 final size:20
Alignment explanation
Indices: 58293--58347 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
58283 TTAATAACTA
* *
58293 TTTTAATAATTATTTGAAAAT
1 TTTTAATTATT-TTTTAAAAT
58314 TTTTAATTATTTTTTAAAGAT
1 TTTTAATTATTTTTTAAA-AT
58335 TTTTAATT-TTTTT
1 TTTTAATTATTTTT
58348 AAATATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTAATTATTTTTTAAAAT
Found at i:63853 original size:69 final size:69
Alignment explanation
Indices: 63730--63858 Score: 172
Period size: 69 Copynumber: 1.9 Consensus size: 69
63720 CTTCTTTCCC
* * *
63730 CATTAAATCAATACCCATTATATCCGTGGCCCCCACATCAGAAATGATTGTATCATGTTCTTTTT
1 CATTAAAACAATACCCATTATATCCGTGACCCCCACATCACAAATGATTGTATCATGTTCTTTTT
63795 GCCT
66 GCCT
* * *
63799 CATTAAAACAATACCCACTT-TATCCGTGACCTCCACATCACAAGTG-GTGTTATCATGTTC
1 CATTAAAACAATACCCA-TTATATCCGTGACCCCCACATCACAAATGATTG-TATCATGTTC
63859 CATCACTGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 2 0.04
69 48 0.92
70 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (69 bp):
CATTAAAACAATACCCATTATATCCGTGACCCCCACATCACAAATGATTGTATCATGTTCTTTTT
GCCT
Found at i:64967 original size:21 final size:20
Alignment explanation
Indices: 64930--64971 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
64920 TTTTTTATAA
*
64930 TAAATAAAATTATTAAATAT
1 TAAATAAAATAATTAAATAT
*
64950 TAAATTAAATAATATAAATAT
1 TAAATAAAATAAT-TAAATAT
64971 T
1 T
64972 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAAATAATTAAATAT
Found at i:66256 original size:71 final size:71
Alignment explanation
Indices: 66173--66315 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
66163 AATAAGTTAA
66173 CGAACTAACTCTCTCTACCCATCTAACTTACACAAGCCTCTAGTATAAGAGTTTAAGAGTTGTTA
1 CGAACTAACTCTCTCTACCCATCTAACTTACACAAGCCTCTAGTATAAGAGTTTAAGAGTTGTTA
66238 ACATAT
66 ACATAT
66244 CGAACTAACTCTCTCTACCCATCTAACTTACACAAGCCTCTAGTATAAGAGTTTAAGAGTTGTTA
1 CGAACTAACTCTCTCTACCCATCTAACTTACACAAGCCTCTAGTATAAGAGTTTAAGAGTTGTTA
66309 ACATAT
66 ACATAT
66315 C
1 C
66316 AATCAATTAC
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (71 bp):
CGAACTAACTCTCTCTACCCATCTAACTTACACAAGCCTCTAGTATAAGAGTTTAAGAGTTGTTA
ACATAT
Found at i:73830 original size:16 final size:17
Alignment explanation
Indices: 73805--73836 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
73795 TTTTTCTACC
73805 TCTCCAATTTTCTTTCT
1 TCTCCAATTTTCTTTCT
73822 TCTCC-ATTTTCTTTC
1 TCTCCAATTTTCTTTC
73837 CACTCTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.09, C:0.31, G:0.00, T:0.59
Consensus pattern (17 bp):
TCTCCAATTTTCTTTCT
Found at i:74043 original size:2 final size:2
Alignment explanation
Indices: 74038--74073 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
74028 AGAAAATTAA
74038 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
74074 GTTACATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78052 original size:24 final size:25
Alignment explanation
Indices: 78014--78062 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
78004 AATTTTATAA
78014 TTAAATTAATTA-TTTGGATTGGGTT
1 TTAAATTAATTATTTTGG-TTGGGTT
*
78039 TTAAA-TATTTATTTTGGTTGGGTT
1 TTAAATTAATTATTTTGGTTGGGTT
78063 AGTGGGGGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.55
Consensus pattern (25 bp):
TTAAATTAATTATTTTGGTTGGGTT
Found at i:81164 original size:30 final size:30
Alignment explanation
Indices: 81127--81415 Score: 351
Period size: 30 Copynumber: 9.8 Consensus size: 30
81117 GAAAAATAGG
*
81127 TTCGGGGTCAAAAATGGAATTTTTGGAGGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
* * *
81157 TTAGGGGT-AAAATTGGAATTTTTAGAAGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
* *
81186 TTCGGGGTCAAAATTGGAATTTTAGGAAGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
* *
81216 TT-TGGGTCAAAAATGGAATTTTTGG-AGG
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
*
81244 TTCGAGGGT-AAAAATGGAATCTTTGGAAGT
1 TTCG-GGGTCAAAAATGGAATTTTTGGAAGT
* * * * *
81274 TTTGAGGTCAAAAATAGAATTTTTAGATG-
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
81303 TTCGAGGGT-AAAAATGGAATTTTTGGAAGT
1 TTCG-GGGTCAAAAATGGAATTTTTGGAAGT
81333 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
**
81363 TTCGGGACCAAAAATGGAATTTTTGGAAG-
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGT
81392 TTCGAGGGT-AAAAATGGAATTTTT
1 TTCG-GGGTCAAAAATGGAATTTTT
81416 ACACAGTTTA
Statistics
Matches: 221, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.02
29 107 0.48
30 110 0.50
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (30 bp):
TTCGGGGTCAAAAATGGAATTTTTGGAAGT
Found at i:81190 original size:59 final size:60
Alignment explanation
Indices: 81127--81416 Score: 353
Period size: 59 Copynumber: 4.9 Consensus size: 60
81117 GAAAAATAGG
* * *
81127 TTCGGGGTCAAAAATGGAATTTTTGGAGGTTTAGGGGT-AAAATTGGAATTTTTAGAAGT
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGT
* * * * *
81186 TTCGGGGTCAAAATTGGAATTTTAGGAAGTTT-TGGGTCAAAAATGGAATTTTT-GGAGG
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGT
* * * * *
81244 TTCGAGGGT-AAAAATGGAATCTTTGGAAGTTTTGAGGTCAAAAATAGAATTTTTAGATG-
1 TTCG-GGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGT
*
81303 TTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTGGAAGT
1 TTCG-GGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGT
**
81363 TTCGGGACCAAAAATGGAATTTTTGGAAG-TTCGAGGGT-AAAAATGGAATTTTTA
1 TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCG-GGGTCAAAAATGGAATTTTTA
81417 CACAGTTTAG
Statistics
Matches: 200, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
58 31 0.16
59 139 0.69
60 30 0.15
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (60 bp):
TTCGGGGTCAAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGAATTTTTAGAAGT
Found at i:81428 original size:29 final size:29
Alignment explanation
Indices: 81131--81415 Score: 299
Period size: 29 Copynumber: 9.7 Consensus size: 29
81121 AATAGGTTCG
*
81131 GGGTCAAAAATGGAATTTTTGGAGGTTTA
1 GGGTCAAAAATGGAATTTTTGGAAGTTTA
* * *
81160 GGGGT-AAAATTGGAATTTTTAGAAGTTTCG
1 -GGGTCAAAAATGGAATTTTTGGAAGTTT-A
* * *
81190 GGGTCAAAATTGGAATTTTAGGAAGTTTT
1 GGGTCAAAAATGGAATTTTTGGAAGTTTA
* *
81219 GGGTCAAAAATGGAATTTTTGGAGGTTCGA
1 GGGTCAAAAATGGAATTTTTGGAAGTT-TA
* *
81249 GGGT-AAAAATGGAATCTTTGGAAGTTTT
1 GGGTCAAAAATGGAATTTTTGGAAGTTTA
* * * *
81277 GAGGTCAAAAATAGAATTTTTAGATGTTCGA
1 G-GGTCAAAAATGGAATTTTTGGAAGTT-TA
*
81308 GGGT-AAAAATGGAATTTTTGGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTGGAAGTTT-A
*
81337 GGGTCAAAAATGGAATTTTTGGAAGTTTC
1 GGGTCAAAAATGGAATTTTTGGAAGTTTA
* *
81366 GGGACCAAAAATGGAATTTTTGGAAGTTCGA
1 GGG-TCAAAAATGGAATTTTTGGAAGTT-TA
81397 GGGT-AAAAATGGAATTTTT
1 GGGTCAAAAATGGAATTTTT
81416 ACACAGTTTA
Statistics
Matches: 213, Mismatches: 32, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
28 1 0.00
29 112 0.53
30 96 0.45
31 4 0.02
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.34
Consensus pattern (29 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTTA
Done.