Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002203.1 Kokia drynarioides strain JFW-HI SEQ_114187, 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: 23403
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:4503 original size:14 final size:14
Alignment explanation
Indices: 4455--4503 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
4445 GAAAATTCCA
4455 TAAAT-TTTATGTT
1 TAAATATTTATGTT
4468 TAAATA--TAT-TT
1 TAAATATTTATGTT
* *
4479 TAAAGAATTATGTT
1 TAAATATTTATGTT
4493 TAAATATTTAT
1 TAAATATTTAT
4504 TTAACTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
11 7 0.24
12 3 0.10
13 8 0.28
14 11 0.38
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (14 bp):
TAAATATTTATGTT
Found at i:5235 original size:78 final size:78
Alignment explanation
Indices: 5105--5297 Score: 307
Period size: 78 Copynumber: 2.5 Consensus size: 78
5095 CTTATAATGG
*
5105 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGATGTGAGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGAGAAATCAAAATCACTTG
*
5170 G-GGGCTGAACACT
66 GAAGG-TGAACACT
* *
5183 TGGTGGCAACCGAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGGGAAATCAAAATCACTTG
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGAGAAATCAAAATCACTTG
5248 GAAGGTGAACACT
66 GAAGGTGAACACT
* * *
5261 TGGTGGCAACCCAGAGTCAGGATCTTGAATGACCTGA
1 TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGA
5298 ATTGGATTAC
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
78 104 0.98
79 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (78 bp):
TGGTGGCAACCCAAAGTCAGGATCTTGATTGAACTGATCAAGAGGTGAGAAATCAAAATCACTTG
GAAGGTGAACACT
Found at i:5633 original size:81 final size:81
Alignment explanation
Indices: 5492--5894 Score: 628
Period size: 81 Copynumber: 5.0 Consensus size: 81
5482 TCCCATTTTC
* * * * * * * *
5492 AACCATTTGAGTTCCATTGTATGGTAGAATTGCACCTGTATCAGCTTCAGCTTCACCTTCCTCTT
1 AACCATTTGGGTTTCATCGTAAGGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTT
5557 GATGACCTTCTTGTTG
66 GATGACCTTCTTGTTG
*
5573 AACCATTTGGGTTTCATCGTAAGGTATAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTT
1 AACCATTTGGGTTTCATCGTAAGGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTT
5638 GATGACCTTCTTGTTG
66 GATGACCTTCTTGTTG
* *
5654 AACCATTCGGGCTTT-ATCGTAAGGTACAACTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCT
1 AACCATTTGGG-TTTCATCGTAAGGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCT
5718 TGATGACCTTCTTGTTG
65 TGATGACCTTCTTGTTG
*
5735 AACCATTTGGGTTTCATCGTAAGGTACAATTGCACTTGTATAAGCTTCAGTTTCAGCTTCCTCTT
1 AACCATTTGGGTTTCATCGTAAGGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTT
5800 GATGACCTTCTTGTTG
66 GATGACCTTCTTGTTG
* * * * **
5816 AACCATTTGGGCTTGATCATAAGGTACAATTGCACTTGTATCAGTTTCAACTTCAGCTTCCTCTT
1 AACCATTTGGGTTTCATCGTAAGGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTT
5881 GATGACCTTCTTGT
66 GATGACCTTCTTGT
5895 AAGGTTTCAC
Statistics
Matches: 299, Mismatches: 21, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
80 3 0.01
81 293 0.98
82 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.39
Consensus pattern (81 bp):
AACCATTTGGGTTTCATCGTAAGGTACAATTGCACTTGTATCAGCTTCAGTTTCAGCTTCCTCTT
GATGACCTTCTTGTTG
Found at i:7593 original size:18 final size:19
Alignment explanation
Indices: 7550--7593 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
7540 GGACAGAAAA
*
7550 CAATTAAAAATGAATGTGT
1 CAATTAAAAACGAATGTGT
* *
7569 AAATTAAATACGAATGTG-
1 CAATTAAAAACGAATGTGT
7587 CAATTAA
1 CAATTAA
7594 TGGCGAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.30
Consensus pattern (19 bp):
CAATTAAAAACGAATGTGT
Found at i:8194 original size:30 final size:28
Alignment explanation
Indices: 8168--8327 Score: 151
Period size: 30 Copynumber: 5.4 Consensus size: 28
8158 AAATTTTAGG
8168 AAAGTTTGAGGGTCAAAATGTGATTTTGGA
1 AAAGTTT-AGGGTCAAAATGTGATTTT-GA
* * *
8198 AAAGCTTAAGGGTTAAAATGTTATTTTGGA
1 AAAG-TTTAGGGTCAAAATGTGATTTT-GA
*
8228 AAAGTTTAGGGGTTAAAATGTGATTTTGA
1 AAAGTTTA-GGGTCAAAATGTGATTTTGA
*
8257 ACAAGTTTAGGGGTCAAAATATGATTTTAGA
1 A-AAGTTTA-GGGTCAAAATGTGATTTT-GA
* * *
8288 AAAGTTTAGGATTCAAAATATAATTTTAGA
1 AAAGTTTAGG-GTCAAAATGTGATTTT-GA
8318 AAAG-TTAGGG
1 AAAGTTTAGGG
8328 GCTCTTTTAT
Statistics
Matches: 115, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
29 13 0.11
30 97 0.84
31 5 0.04
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAGTTTAGGGTCAAAATGTGATTTTGA
Found at i:8244 original size:90 final size:90
Alignment explanation
Indices: 8142--8328 Score: 229
Period size: 90 Copynumber: 2.1 Consensus size: 90
8132 TTTCAGAGAA
* * *
8142 TTTAGGGGTTAAAATGAAATTTTAGGA-AAGTTT-GAGGGTCAAAATGTGATTTTGGAAAAGCTT
1 TTTAGGGGTTAAAATGAAATTTT-GAACAAGTTTAG-GGGTCAAAATATGATTTTAGAAAAG-TT
* * * *
8205 AAGGGTT-AAAATGTTATTTTGGAAAAG
63 AAGGATTCAAAATATAATTTTAGAAAAG
** *
8232 TTTAGGGGTTAAAATGTGATTTTGAACAAGTTTAGGGGTCAAAATATGATTTTAGAAAAGTTTAG
1 TTTAGGGGTTAAAATGAAATTTTGAACAAGTTTAGGGGTCAAAATATGATTTTAGAAAAGTTAAG
8297 GATTCAAAATATAATTTTAGAAAAG
66 GATTCAAAATATAATTTTAGAAAAG
8322 -TTAGGGG
1 TTTAGGGG
8329 CTCTTTTATG
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 16 0.19
90 67 0.80
91 1 0.01
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (90 bp):
TTTAGGGGTTAAAATGAAATTTTGAACAAGTTTAGGGGTCAAAATATGATTTTAGAAAAGTTAAG
GATTCAAAATATAATTTTAGAAAAG
Found at i:8323 original size:60 final size:58
Alignment explanation
Indices: 8142--8328 Score: 182
Period size: 60 Copynumber: 3.1 Consensus size: 58
8132 TTTCAGAGAA
* *
8142 TTTAGGGGTTAAAATGA-AATTTTAGGAAAGTTTGAGGGTCAAAATGTGATTTTGGAAAAG
1 TTTAGGGGTTAAAAT-ATAATTTTAGAAAAGTTT-AGGTTCAAAATGTGATTTT-GAAAAG
* * * * *
8202 CTTAAGGGTTAAAATGTTATTTTGGAAAAGTTTAGGGGTT-AAAATGTGATTTTGAACAAG
1 TTTAGGGGTTAAAATATAATTTTAGAAAAGTTTA--GGTTCAAAATGTGATTTTGAA-AAG
* * * *
8262 TTTAGGGGTCAAAATATGATTTTAGAAAAGTTTAGGATTCAAAATATAATTTTAGAAAAG
1 TTTAGGGGTTAAAATATAATTTTAGAAAAGTTTAGG-TTCAAAATGTGATTTT-GAAAAG
8322 -TTAGGGG
1 TTTAGGGG
8329 CTCTTTTATG
Statistics
Matches: 105, Mismatches: 15, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
59 13 0.12
60 84 0.80
61 6 0.06
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (58 bp):
TTTAGGGGTTAAAATATAATTTTAGAAAAGTTTAGGTTCAAAATGTGATTTTGAAAAG
Found at i:10971 original size:22 final size:21
Alignment explanation
Indices: 10946--10992 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
10936 TTTCTATTTC
*
10946 TTTTAATTCTATTTTATTTTAT
1 TTTTAATTATATTTT-TTTTAT
*
10968 TTTTAATTATGTTTTTTTTAT
1 TTTTAATTATATTTTTTTTAT
10989 TTTT
1 TTTT
10993 CCTCAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTAATTATATTTTTTTTAT
Found at i:16795 original size:20 final size:19
Alignment explanation
Indices: 16766--16817 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
16756 GGCCTTAAGG
16766 TTTT-AATTAGATTTAGGGT
1 TTTTAAATTAGATTTA-GGT
*
16785 TTTTAAATTAGGCTTTAGGT
1 TTTTAAATTA-GATTTAGGT
16805 TTTTAAAATTAGA
1 TTTT-AAATTAGA
16818 GTTTTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.31, C:0.02, G:0.17, T:0.50
Consensus pattern (19 bp):
TTTTAAATTAGATTTAGGT
Found at i:16803 original size:21 final size:21
Alignment explanation
Indices: 16777--16816 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
16767 TTTAATTAGA
16777 TTTAGGGTTTTT-AAATTAGGC
1 TTTA-GGTTTTTAAAATTAGGC
16798 TTTAGGTTTTTAAAATTAG
1 TTTAGGTTTTTAAAATTAG
16817 AGTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.50
Consensus pattern (21 bp):
TTTAGGTTTTTAAAATTAGGC
Found at i:17115 original size:144 final size:144
Alignment explanation
Indices: 16810--17360 Score: 798
Period size: 142 Copynumber: 3.9 Consensus size: 144
16800 TAGGTTTTTA
* * * * *
16810 AAATTAGAGTTTTAATATTTATTTTATATATTTTAGGTAAAAAAACTCATAACAAAATGAAAGAA
1 AAATTAAAATTTTAGTATTTATTTTATATATTTTAGGTAAAAAAACCCATAACAAATTGAAAGAA
*
16875 TTAAATTTATTTTTATTTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATGTT-TATAAAT
66 TTAAATTTA-TTTTATTTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTAT-TTAT-TAAAA
16939 ATTTATTATTTATTGCT
128 ATTTATTATTTATTGCT
* *
16956 AAATTACAATTTTAGTATTTATTTTATATATTTTAGGTAAAAAAAACTCATAACAAATTGAAAGA
1 AAATTAAAATTTTAGTATTTATTTTATATATTTTAGGT-AAAAAAACCCATAACAAATTGAAAGA
*
17021 ATTAAATTT-TTTTATTTTTTTCTATTTTATTTTTATTCAAATTATTTAATTATTTATTAAAAAT
65 ATTAAATTTATTTTATTTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTATTAAAAAT
* **
17085 TTATTCTTTATTATT
130 TTATTATTTATTGCT
* * *
17100 AAATTAAAATTTTAGTAATTATTTTATATATATTAGGTAAAAAACCCCATAA-AAA-TGAAAGAA
1 AAATTAAAATTTTAGTATTTATTTTATATATTTTAGGTAAAAAAACCCATAACAAATTGAAAGAA
* * *
17163 TTAAATTTATTTAAATTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTATTGAAAATT
66 TTAAATTTATTTTATTTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTATTAAAAATT
17228 TATTATTTATTGCT
131 TATTATTTATTGCT
*
17242 AAA-TAACAATTTTAGTATTTATTTTATATATTTTAGATAAAAAAACCCATAACAAATTGAAAGA
1 AAATTAA-AATTTTAGTATTTATTTTATATATTTTAGGTAAAAAAACCCATAACAAATTGAAAGA
*
17306 GTTAAATTTATTTT-TATTTTTTCTGTTTTATTTTTA-T-AAA-TATTT-ATTATTTATT
65 ATTAAATTTATTTTAT-TTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTATT
17361 GTTAAATTAC
Statistics
Matches: 370, Mismatches: 28, Indels: 20
0.89 0.07 0.05
Matches are distributed among these distances:
140 10 0.03
141 24 0.06
142 113 0.31
143 16 0.04
144 94 0.25
145 44 0.12
146 35 0.09
147 34 0.09
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (144 bp):
AAATTAAAATTTTAGTATTTATTTTATATATTTTAGGTAAAAAAACCCATAACAAATTGAAAGAA
TTAAATTTATTTTATTTTTTTCTGTTTTATTTTTATTCAAATTATTTAATTATTTATTAAAAATT
TATTATTTATTGCT
Found at i:17234 original size:18 final size:19
Alignment explanation
Indices: 17188--17239 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
17178 TTTTTTCTGT
*
17188 TTTATT-TTTATTCAAATTA
1 TTTATTATTTATTGAAA-TA
17207 TTTAATTATTTATTGAAA-A
1 TTT-ATTATTTATTGAAATA
17226 TTTATTATTTATTG
1 TTTATTATTTATTG
17240 CTAAATAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.37
19 7 0.23
20 3 0.10
21 9 0.30
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTATTATTTATTGAAATA
Found at i:17381 original size:122 final size:121
Alignment explanation
Indices: 17225--17482 Score: 378
Period size: 122 Copynumber: 2.1 Consensus size: 121
17215 TTTATTGAAA
*
17225 ATTTATTATTTATTGCTAAATAACAATTTTAGTATTTATTTTATATATTTTAGATAAAAAAACCC
1 ATTTATTATTTATTGCTAAATAACAATTTAAGTATTTATTTTATATATTTTAGAT--AAAAACCC
* *
17290 ATAACAAATTGAAAGAGTTAAATTTATTTTTATTTTTTCTGTTTTATTTTTA-T-AAA-T
64 ATAACAAATTGAAAGAATT-AATTT-TTTTTATTTTTTCTGTTTTATTATTATTCAAATT
* * * *
17347 ATTTATTATTTATTGTTAAATTACAATTTAAGTATTTATTTTATATATTTTAGGTAAAAACTCAT
1 ATTTATTATTTATTGCTAAATAACAATTTAAGTATTTATTTTATATATTTTAGATAAAAACCCAT
*
17412 AACAATTTGAAAGAATTAATTTTTTTTATTTTTTCTGTTTTATTATTATTCAAATT
66 AACAAATTGAAAGAATTAATTTTTTTTATTTTTTCTGTTTTATTATTATTCAAATT
17468 ATTTAATTATTTATT
1 ATTT-ATTATTTATT
17483 ATAAATTTAT
Statistics
Matches: 124, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
118 25 0.20
119 6 0.05
120 27 0.22
121 5 0.04
122 61 0.49
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (121 bp):
ATTTATTATTTATTGCTAAATAACAATTTAAGTATTTATTTTATATATTTTAGATAAAAACCCAT
AACAAATTGAAAGAATTAATTTTTTTTATTTTTTCTGTTTTATTATTATTCAAATT
Found at i:17916 original size:146 final size:144
Alignment explanation
Indices: 17333--17936 Score: 891
Period size: 145 Copynumber: 4.2 Consensus size: 144
17323 TTTTTCTGTT
*
17333 TTATTTTTATAAATATTTATTATTTATTGTTAAATTACAATTTAAGTATTTATTTTATATATTTT
1 TTATTTTTATAAATATTTATTATTTATTGTTAAATTACAATTTTAGTATTTATTTTATATATTTT
* * *
17398 AGGT--AAAAACTCATAACAATTTGAAAGAATTAATTTTTTTTA-TTTTTTCTGTTTTATTATTA
66 AGGTAAAAAAACCCATAACAAATTGAAAGAATTAATTTTTTTTATTTTTTTCTGTTTTATTTTTA
17460 TTCAAATTATTTAA
131 TTCAAATTATTTAA
* * * *
17474 TTATTTATTAT-AA-ATTTATTATTTATTGTTAAACTAAAATTTGAGTATTTATTTTATTTATTT
1 TTATTT-TTATAAATATTTATTATTTATTGTTAAATTACAATTTTAGTATTTATTTTATATATTT
* * * * *
17537 TTGGTAAAAAAA-CCATGACAAATTGAAAGAATTAAATTTATTTTTTAGTTTTTTCTATTTTAGT
65 TAGGTAAAAAAACCCATAACAAATTGAAAGAATT-AA-TT-TTTTTTATTTTTTTCTGTTTTATT
17601 TTTATTCAAATTATTTAA
127 TTTATTCAAATTATTTAA
* * *
17619 TTATTTATT-GAAA-ATTTATTATTTATTGTTAAATTGCAAGTTTAGTATTTATTTTATATATTT
1 TTATTT-TTATAAATATTTATTATTTATTGTTAAATTACAATTTTAGTATTTATTTTATATATTT
* *
17682 TAGGTAAAAAAAACTCATAACAAATTGAAAGAATTAATTTTTTTTATTTTTTTCTGTTTTATATT
65 TAGGT-AAAAAAACCCATAACAAATTGAAAGAATTAATTTTTTTTATTTTTTTCTGTTTTATTTT
*
17747 TATTCAAAATATTTAA
129 TATTCAAATTATTTAA
*
17763 TTATTTTTATAAATATTTATTATTTATTTTTAAATTACAATTTTAGTATTTATTTTATATATTTT
1 TTATTTTTATAAATATTTATTATTTATTGTTAAATTACAATTTTAGTATTTATTTTATATATTTT
17828 AGGTAAAAAAAACCCATAACAAATTGAAAGAATTAATTTTTTTTTATTTTTTTCTGTTTTATTTT
66 AGGT-AAAAAAACCCATAACAAATTGAAAGAATTAA-TTTTTTTTATTTTTTTCTGTTTTATTTT
17893 TATTCAAATTATTTAA
129 TATTCAAATTATTTAA
*
17909 TTATTTTTATAAATATTTATTCTTTATT
1 TTATTTTTATAAATATTTATTATTTATT
17937 CTTTAAATAG
Statistics
Matches: 416, Mismatches: 34, Indels: 21
0.88 0.07 0.04
Matches are distributed among these distances:
140 50 0.12
141 26 0.06
142 11 0.03
143 4 0.01
144 53 0.13
145 175 0.42
146 78 0.19
147 19 0.05
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (144 bp):
TTATTTTTATAAATATTTATTATTTATTGTTAAATTACAATTTTAGTATTTATTTTATATATTTT
AGGTAAAAAAACCCATAACAAATTGAAAGAATTAATTTTTTTTATTTTTTTCTGTTTTATTTTTA
TTCAAATTATTTAA
Found at i:19064 original size:15 final size:15
Alignment explanation
Indices: 19044--19084 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
19034 TAACTTACTA
19044 CATGGGTGGTGCTTG
1 CATGGGTGGTGCTTG
19059 CATGGGTGGTGCTTG
1 CATGGGTGGTGCTTG
*
19074 TATGGGTGGTG
1 CATGGGTGGTG
19085 ATGATTGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.10, G:0.49, T:0.34
Consensus pattern (15 bp):
CATGGGTGGTGCTTG
Found at i:20595 original size:18 final size:18
Alignment explanation
Indices: 20574--20634 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
20564 TAAGTTATAA
20574 AAATAATATAAAATAATT
1 AAATAATATAAAATAATT
* *
20592 AAATTATAAAAATAAAATAAAT
1 -AA--AT-AATATAAAATAATT
*
20614 AAATAATATAAAAAAATT
1 AAATAATATAAAATAATT
20632 AAA
1 AAA
20635 ATTAACTCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 14 0.41
19 4 0.12
21 4 0.12
22 12 0.35
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAATATAAAATAATT
Found at i:20598 original size:27 final size:27
Alignment explanation
Indices: 20555--20636 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
20545 AAGTATTTAA
*
20555 AAAATTAATTAAGTTATAAAAATAATAT
1 AAAA-TAATTAAATTATAAAAATAATAT
*
20583 AAAATAATTAAATTATAAAAATAAAAT
1 AAAATAATTAAATTATAAAAATAATAT
*
20610 -AAATAAAT-AA-TATAAAAA-AAT-T
1 AAAATAATTAAATTATAAAAATAATAT
20632 AAAAT
1 AAAAT
20637 TAACTCTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
22 1 0.02
23 6 0.12
24 8 0.16
25 2 0.04
26 7 0.14
27 21 0.43
28 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (27 bp):
AAAATAATTAAATTATAAAAATAATAT
Found at i:20606 original size:22 final size:23
Alignment explanation
Indices: 20581--20627 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 23
20571 TAAAAATAAT
*
20581 ATAAAATAATTAAAT-TATAAAA
1 ATAAAATAAATAAATATATAAAA
20603 ATAAAATAAATAAATAATATAAAA
1 ATAAAATAAATAAAT-ATATAAAA
20627 A
1 A
20628 AATTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.64
24 8 0.36
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
ATAAAATAAATAAATATATAAAA
Found at i:20634 original size:22 final size:22
Alignment explanation
Indices: 20574--20634 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 22
20564 TAAGTTATAA
*
20574 AAATAATATAAAATAATTAAAT
1 AAATAATATAAAAAAATTAAAT
* *
20596 -TATAA-A-AATAAAA-TAAAT
1 AAATAATATAAAAAAATTAAAT
20614 AAATAATATAAAAAAATTAAA
1 AAATAATATAAAAAAATTAAA
20635 ATTAACTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 2 0.07
21 10 0.33
22 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAATAATATAAAAAAATTAAAT
Found at i:20809 original size:11 final size:11
Alignment explanation
Indices: 20793--20823 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
20783 AGAGTGTTTC
20793 TTGAGAGAAAA
1 TTGAGAGAAAA
*
20804 TTGAGAGGAAA
1 TTGAGAGAAAA
20815 TTGAGAGAA
1 TTGAGAGAA
20824 TTGAGTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.19
Consensus pattern (11 bp):
TTGAGAGAAAA
Found at i:22096 original size:17 final size:16
Alignment explanation
Indices: 22062--22096 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
22052 GAGTAGAAAG
22062 AAAATTGAAAGGATAA
1 AAAATTGAAAGGATAA
22078 AAAATTGAAAAGG-TAA
1 AAAATTG-AAAGGATAA
22094 AAA
1 AAA
22097 TAAAGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
AAAATTGAAAGGATAA
Done.