Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013578.1 Kokia drynarioides strain JFW-HI SEQ_128604, 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: 67313
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1598 original size:14 final size:15
Alignment explanation
Indices: 1574--1602 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1564 CAGGTTCATT
1574 AACACATTTTTCTTC
1 AACACATTTTTCTTC
1589 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
1603 CCATTTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:9731 original size:33 final size:33
Alignment explanation
Indices: 9694--9759 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
9684 ATGTCTACGA
9694 AGAAATAAAATTTTGTTGATAACTTTCAAATGC
1 AGAAATAAAATTTTGTTGATAACTTTCAAATGC
9727 AGAAATAAAATTTTGTTGATAACTTTCAAATGC
1 AGAAATAAAATTTTGTTGATAACTTTCAAATGC
9760 TCTTTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (33 bp):
AGAAATAAAATTTTGTTGATAACTTTCAAATGC
Found at i:14673 original size:25 final size:25
Alignment explanation
Indices: 14645--14696 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
14635 GTAAGGTATA
14645 ATTTGTATTAGTTAATAAATTTTAC
1 ATTTGTATTAGTTAATAAATTTTAC
14670 ATTTGTATTAGTTAATAAATTTTAC
1 ATTTGTATTAGTTAATAAATTTTAC
14695 AT
1 AT
14697 ATTTTTCACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (25 bp):
ATTTGTATTAGTTAATAAATTTTAC
Found at i:15950 original size:14 final size:14
Alignment explanation
Indices: 15931--16308 Score: 113
Period size: 14 Copynumber: 26.9 Consensus size: 14
15921 GAATTTGATG
15931 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAT
**
15945 GGTTTAATGTTTAT
1 GGTTTAGGGTTTAT
*
15959 GGTTTGGGGTTTAT
1 GGTTTAGGGTTTAT
** *
15973 GGTTTAATGTTTGT
1 GGTTTAGGGTTTAT
*
15987 GGTTT-GTTGTTTA-
1 GGTTTAG-GGTTTAT
* *
16000 -GTATTTGAGTTTTAT
1 GGT-TTAG-GGTTTAT
** * *
16015 TTTTTAGTGTTT-G
1 GGTTTAGGGTTTAT
*
16028 GTGTTTAGGGTTTAA
1 G-GTTTAGGGTTTAT
* *
16043 GGTTT-GATGTTTAG
1 GGTTTAG-GGTTTAT
*
16057 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAT
*
16071 GGTTT-GATGTTTAT
1 GGTTTAG-GGTTTAT
*
16085 GGTTTAGGGTTTAA
1 GGTTTAGGGTTTAT
*
16099 GATTTAGGGTTT-T
1 GGTTTAGGGTTTAT
*
16112 AGGTTTTTAGTGTTTAT
1 -GG--TTTAGGGTTTAT
* * *
16129 -ATTTA-TGTTTTT
1 GGTTTAGGGTTTAT
*
16141 AGGTTTAGGATTTAT
1 -GGTTTAGGGTTTAT
* *
16156 GGCTTGGGGTTTGGA-
1 GGTTTAGGGTTT--AT
* *
16171 GGTTTAAGTTTTA-
1 GGTTTAGGGTTTAT
*
16184 GGTTTTAGGTTTTA-
1 GG-TTTAGGGTTTAT
*
16198 GGTTTTA-GGTTTAA
1 GG-TTTAGGGTTTAT
* *
16212 GGTTTAAGGTTTAA
1 GGTTTAGGGTTTAT
* *
16226 GATTTAGGATTTA-
1 GGTTTAGGGTTTAT
16239 GGTTTAGGGTTTAT
1 GGTTTAGGGTTTAT
*
16253 GTTTTGTTTAAGGTTTAT
1 G----GTTTAGGGTTTAT
* *
16271 GGTTTATGATTT-T
1 GGTTTAGGGTTTAT
* *
16284 -ATTTAGGGTTTAA
1 GGTTTAGGGTTTAT
*
16297 GTTTTAGGGTTT
1 GGTTTAGGGTTT
16309 TATGTTAGGT
Statistics
Matches: 271, Mismatches: 63, Indels: 60
0.69 0.16 0.15
Matches are distributed among these distances:
12 16 0.06
13 32 0.12
14 180 0.66
15 18 0.07
16 11 0.04
17 1 0.00
18 13 0.05
ACGTcount: A:0.17, C:0.00, G:0.29, T:0.53
Consensus pattern (14 bp):
GGTTTAGGGTTTAT
Found at i:15991 original size:7 final size:7
Alignment explanation
Indices: 15931--16278 Score: 67
Period size: 7 Copynumber: 50.1 Consensus size: 7
15921 GAATTTGATG
*
15931 GGTTTAG
1 GGTTTAT
15938 GGTTTAT
1 GGTTTAT
15945 GGTTTAAT
1 GGTTT-AT
15953 -GTTTAT
1 GGTTTAT
**
15959 GGTTTGG
1 GGTTTAT
15966 GGTTTAT
1 GGTTTAT
15973 GGTTTAAT
1 GGTTT-AT
*
15981 -GTTTGT
1 GGTTTAT
*
15987 GGTTTGT
1 GGTTTAT
*
15994 TGTTTA-
1 GGTTTAT
16000 -GTATT-T
1 GGT-TTAT
16006 GAGTTTTAT
1 G-G-TTTAT
**
16015 TTTTTA-
1 GGTTTAT
*
16021 GTGTTT-G
1 G-GTTTAT
*
16028 GTGTTTAG
1 G-GTTTAT
*
16036 GGTTTAA
1 GGTTTAT
16043 GGTTTGAT
1 GGTTT-AT
*
16051 -GTTTAG
1 GGTTTAT
*
16057 GGTTTAG
1 GGTTTAT
*
16064 GGTTTAA
1 GGTTTAT
16071 GGTTTGAT
1 GGTTT-AT
16079 -GTTTAT
1 GGTTTAT
*
16085 GGTTTAG
1 GGTTTAT
*
16092 GGTTTAA
1 GGTTTAT
* *
16099 GATTTAG
1 GGTTTAT
16106 GGTTT-T
1 GGTTTAT
*
16112 AGGTTTTT
1 -GGTTTAT
16120 AGTGTTTAT
1 -G-GTTTAT
*
16129 -ATTTAT
1 GGTTTAT
*
16135 -GTTTTT
1 GGTTTAT
16141 AGGTTTA-
1 -GGTTTAT
16148 GGATTTAT
1 GG-TTTAT
* **
16156 GGCTTGG
1 GGTTTAT
16163 GGTTTGGA-
1 GGTTT--AT
*
16171 GGTTTAA
1 GGTTTAT
*
16178 GTTTTA-
1 GGTTTAT
16184 GGTTT-T
1 GGTTTAT
16190 AGGTTT-T
1 -GGTTTAT
16197 AGGTTT-T
1 -GGTTTAT
*
16204 AGGTTTAA
1 -GGTTTAT
*
16212 GGTTTAA
1 GGTTTAT
*
16219 GGTTTAA
1 GGTTTAT
*
16226 GATTTA-
1 GGTTTAT
16232 GGATTTA-
1 GG-TTTAT
*
16239 GGTTTAG
1 GGTTTAT
16246 GGTTTAT
1 GGTTTAT
16253 -GTTT-T
1 GGTTTAT
*
16258 -GTTTAA
1 GGTTTAT
16264 GGTTTAT
1 GGTTTAT
16271 GGTTTAT
1 GGTTTAT
16278 G
1 G
16279 ATTTTATTTA
Statistics
Matches: 266, Mismatches: 41, Indels: 68
0.71 0.11 0.18
Matches are distributed among these distances:
5 7 0.03
6 33 0.12
7 194 0.73
8 25 0.09
9 7 0.03
ACGTcount: A:0.17, C:0.00, G:0.30, T:0.53
Consensus pattern (7 bp):
GGTTTAT
Found at i:16110 original size:28 final size:28
Alignment explanation
Indices: 16022--16099 Score: 131
Period size: 28 Copynumber: 2.8 Consensus size: 28
16012 TATTTTTTAG
16022 TGTTT-GGTGTTTAGGGTTTAAGGTTTGA
1 TGTTTAGG-GTTTAGGGTTTAAGGTTTGA
16050 TGTTTAGGGTTTAGGGTTTAAGGTTTGA
1 TGTTTAGGGTTTAGGGTTTAAGGTTTGA
*
16078 TGTTTATGGTTTAGGGTTTAAG
1 TGTTTAGGGTTTAGGGTTTAAG
16100 ATTTAGGGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 46 0.96
29 2 0.04
ACGTcount: A:0.17, C:0.00, G:0.35, T:0.49
Consensus pattern (28 bp):
TGTTTAGGGTTTAGGGTTTAAGGTTTGA
Found at i:16153 original size:21 final size:21
Alignment explanation
Indices: 16052--16251 Score: 101
Period size: 21 Copynumber: 9.5 Consensus size: 21
16042 AGGTTTGATG
*
16052 TTTAGGGTTTAGGGTTTAAGGT
1 TTTA-GGTTTAGGATTTAAGGT
* * *
16074 TTGATGTTTATGG-TTTAGGGT
1 TTTAGGTTTA-GGATTTAAGGT
* * * *
16095 TTAAGATTTAGGGTTTTAGGTT
1 TTTAGGTTTAGGATTTAAGG-T
* * *
16117 TTTAGTGTTTA-TATTTATGTT
1 TTTAG-GTTTAGGATTTAAGGT
* *
16138 TTTAGGTTTAGGATTTATGGC
1 TTTAGGTTTAGGATTTAAGGT
**
16159 TTGGGGTTT-GGAGGTTTAA-GT
1 TTTAGGTTTAGGA--TTTAAGGT
*
16180 TTTAGGTTTTAGG-TTTTAGGT
1 TTTAGG-TTTAGGATTTAAGGT
16201 TTTAGGTTTAAGG-TTTAAGGT
1 TTTAGGTTT-AGGATTTAAGGT
* *
16222 TTAAGATTTAGGATTT-AGG-
1 TTTAGGTTTAGGATTTAAGGT
16241 TTTAGGGTTTA
1 TTTA-GGTTTA
16252 TGTTTTGTTT
Statistics
Matches: 135, Mismatches: 30, Indels: 28
0.70 0.16 0.15
Matches are distributed among these distances:
19 3 0.02
20 28 0.21
21 77 0.57
22 21 0.16
23 6 0.04
ACGTcount: A:0.20, C:0.01, G:0.29, T:0.51
Consensus pattern (21 bp):
TTTAGGTTTAGGATTTAAGGT
Found at i:16282 original size:45 final size:44
Alignment explanation
Indices: 16213--16301 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
16203 TAGGTTTAAG
*
16213 GTTTAAGGTTTAAGATTTAGGA-TTTAGGTTTAGGGTTTATGTTTT
1 GTTTAAGGTTTAAGATTTAGGATTTTA--TTTAGGGTTTAAGTTTT
* * *
16258 GTTTAAGGTTTATGGTTTATGATTTTATTTAGGGTTTAAGTTTT
1 GTTTAAGGTTTAAGATTTAGGATTTTATTTAGGGTTTAAGTTTT
16302 AGGGTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 16 0.41
45 19 0.49
46 4 0.10
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (44 bp):
GTTTAAGGTTTAAGATTTAGGATTTTATTTAGGGTTTAAGTTTT
Found at i:16293 original size:26 final size:25
Alignment explanation
Indices: 16234--16321 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
16224 AAGATTTAGG
*
16234 ATTTAGGTTTAGGGTTTATG-TTTT
1 ATTTAGGTTTAAGGTTTATGATTTT
* *
16258 GTTTAAGGTTTATGGTTTATGATTTT
1 ATTT-AGGTTTAAGGTTTATGATTTT
* * *
16284 ATTTAGGGTTTAAGTTTTAGGGTTTT
1 ATTTA-GGTTTAAGGTTTATGATTTT
16310 ATGTTAGGTTTA
1 AT-TTAGGTTTA
16322 GTGTTATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.06
25 16 0.30
26 31 0.58
27 3 0.06
ACGTcount: A:0.19, C:0.00, G:0.25, T:0.56
Consensus pattern (25 bp):
ATTTAGGTTTAAGGTTTATGATTTT
Found at i:16338 original size:19 final size:19
Alignment explanation
Indices: 16316--16420 Score: 56
Period size: 19 Copynumber: 5.6 Consensus size: 19
16306 TTTTATGTTA
16316 GGTTTAGTGTTATATTTAG
1 GGTTTAGTGTTATATTTAG
* *
16335 GGTTTAAG-GTTATA-ATAA
1 GGTTT-AGTGTTATATTTAG
* * * * *
16353 TGTGTGGT-TTAGAGCTTAG
1 GGTTTAGTGTTATA-TTTAG
* *
16372 GGTTTA-TGACTATGTTTAG
1 GGTTTAGTG-TTATATTTAG
* *
16391 GGTTTAATGTTTTATTTAG
1 GGTTTAGTGTTATATTTAG
16410 GGTTTAGTGTT
1 GGTTTAGTGTT
16421 TAAATTTTAT
Statistics
Matches: 60, Mismatches: 19, Indels: 14
0.65 0.20 0.15
Matches are distributed among these distances:
17 5 0.08
18 6 0.10
19 43 0.72
20 6 0.10
ACGTcount: A:0.22, C:0.02, G:0.28, T:0.49
Consensus pattern (19 bp):
GGTTTAGTGTTATATTTAG
Found at i:16414 original size:26 final size:25
Alignment explanation
Indices: 16385--16437 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
16375 TTATGACTAT
*
16385 GTTTAGGGTTTAATGTTTTATTTAGG
1 GTTTAGGGTTTAA-ATTTTATTTAGG
*
16411 GTTTAGTGTTTAAATTTTATTTAGG
1 GTTTAGGGTTTAAATTTTATTTAGG
16436 GT
1 GT
16438 CAGTGTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.55
Consensus pattern (25 bp):
GTTTAGGGTTTAAATTTTATTTAGG
Found at i:16494 original size:14 final size:13
Alignment explanation
Indices: 16464--16518 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
16454 GGTTTTAAAG
16464 GTTTAAGG-TTAT
1 GTTTAAGGTTTAT
16476 GTTTAAGGTTTATT
1 GTTTAAGGTTTA-T
*
16490 GTTTAGGGTTT-T
1 GTTTAAGGTTTAT
* * *
16502 ATTTAGGGTTTAA
1 GTTTAAGGTTTAT
16515 GTTT
1 GTTT
16519 TTATTTATGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 19 0.53
13 6 0.17
14 11 0.31
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (13 bp):
GTTTAAGGTTTAT
Found at i:16504 original size:15 final size:14
Alignment explanation
Indices: 16464--16500 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
16454 GGTTTTAAAG
16464 GTTTAAGG-TTA-T
1 GTTTAAGGTTTATT
16476 GTTTAAGGTTTATT
1 GTTTAAGGTTTATT
*
16490 GTTTAGGGTTT
1 GTTTAAGGTTT
16501 TATTTAGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.36
13 3 0.14
14 11 0.50
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (14 bp):
GTTTAAGGTTTATT
Found at i:16506 original size:19 final size:19
Alignment explanation
Indices: 16490--16636 Score: 127
Period size: 19 Copynumber: 7.4 Consensus size: 19
16480 AAGGTTTATT
16490 GTTTAGGGTTTTATTTAGG
1 GTTTAGGGTTTTATTTAGG
* * *
16509 GTTTAAGTTTTTATTTATG
1 GTTTAGGGTTTTATTTAGG
16528 GTTTAGGGTTTTATTTAGG
1 GTTTAGGGTTTTATTTAGG
16547 GTTTAAGGTTTATAGTTTTATTTAGG
1 GTTT-AGG------GTTTTATTTAGG
* * * *
16573 ATTTAGGGTTTAGAGTTA-T
1 GTTTAGGGTTT-TATTTAGG
16592 GTTTAGGGTTTTATTTAGG
1 GTTTAGGGTTTTATTTAGG
*
16611 GTTTA-GGTTTATATTTAGC
1 GTTTAGGGTTT-TATTTAGG
16630 GTTTAGG
1 GTTTAGG
16637 ATTTAGAATA
Statistics
Matches: 102, Mismatches: 15, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
18 9 0.09
19 67 0.66
20 8 0.08
25 3 0.03
26 15 0.15
ACGTcount: A:0.20, C:0.01, G:0.27, T:0.53
Consensus pattern (19 bp):
GTTTAGGGTTTTATTTAGG
Found at i:16544 original size:12 final size:12
Alignment explanation
Indices: 16529--16614 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
16519 TTATTTATGG
16529 TTTAGGGTTTTA
1 TTTAGGGTTTTA
*
16541 TTTAGGGTTTAA
1 TTTAGGGTTTTA
**
16553 GGTTTATAGTTTTA
1 --TTTAGGGTTTTA
*
16567 TTTA-GGATTTA
1 TTTAGGGTTTTA
* * *
16578 GGGTTTAGAGTTATG
1 ---TTTAGGGTTTTA
16593 TTTAGGGTTTTA
1 TTTAGGGTTTTA
16605 TTTAGGGTTT
1 TTTAGGGTTT
16615 AGGTTTATAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
11 5 0.09
12 34 0.62
14 13 0.24
15 3 0.05
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (12 bp):
TTTAGGGTTTTA
Found at i:16551 original size:26 final size:26
Alignment explanation
Indices: 16522--16602 Score: 99
Period size: 26 Copynumber: 3.1 Consensus size: 26
16512 TAAGTTTTTA
*
16522 TTTATGGTTTAGGGTTTTATTTAGGG
1 TTTATGGTTTAGAGTTTTATTTAGGG
* * *
16548 TTTAAGGTTTATAGTTTTATTTAGGA
1 TTTATGGTTTAGAGTTTTATTTAGGG
* * *
16574 TTTAGGGTTTAGAGTTATGTTTAGGG
1 TTTATGGTTTAGAGTTTTATTTAGGG
16600 TTT
1 TTT
16603 TATTTAGGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (26 bp):
TTTATGGTTTAGAGTTTTATTTAGGG
Found at i:16596 original size:45 final size:45
Alignment explanation
Indices: 16503--16602 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 45
16493 TAGGGTTTTA
* *
16503 TTTAGGGTTTAAGTTTTTATTTATGGTTTAGGGTTTTATTTAGGG
1 TTTAGGGTTTAAGTTTTTATTTATGGTTTAGGGTTTGAGTTAGGG
* *
16548 TTTAAGGTTTATAG-TTTTATTTA-GGATTTAGGGTTTAGAGTTA-TG
1 TTTAGGGTTTA-AGTTTTTATTTATGG-TTTAGGGTTT-GAGTTAGGG
16593 TTTAGGGTTT
1 TTTAGGGTTT
16603 TATTTAGGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
44 2 0.04
45 39 0.83
46 6 0.13
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (45 bp):
TTTAGGGTTTAAGTTTTTATTTATGGTTTAGGGTTTGAGTTAGGG
Found at i:16635 original size:26 final size:26
Alignment explanation
Indices: 16522--16642 Score: 77
Period size: 26 Copynumber: 4.5 Consensus size: 26
16512 TAAGTTTTTA
*
16522 TTTATGGTTTAGGGTTTTATTTAGGG-
1 TTTAGGGTTTA-GGTTTTATTTAGGGT
* * *
16548 TTTAAGGTTTATAGTTTTATTTA-GGA
1 TTTAGGGTTTA-GGTTTTATTTAGGGT
* *
16574 TTTAGGGTTTAGAGTTATGTTTAGGGTTTT
1 TTTAGGGTTTAG-GTTTTATTTAGGG---T
*
16604 ATTTAGGGTTTAGGTTTATATTTAGCG-
1 -TTTAGGGTTTAGGTTT-TATTTAGGGT
*
16631 TTTAGGATTTAG
1 TTTAGGGTTTAG
16643 AATAATGTGT
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
25 2 0.03
26 49 0.65
27 2 0.03
30 3 0.04
31 19 0.25
ACGTcount: A:0.21, C:0.01, G:0.26, T:0.52
Consensus pattern (26 bp):
TTTAGGGTTTAGGTTTTATTTAGGGT
Found at i:17448 original size:20 final size:20
Alignment explanation
Indices: 17404--17449 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
17394 TTTTTTTTAA
*
17404 TAAAATGTGTACCTTTCAAG
1 TAAAATGTGCACCTTTCAAG
* **
17424 GAAAATGTGCACCTTTTGAG
1 TAAAATGTGCACCTTTCAAG
17444 TAAAAT
1 TAAAAT
17450 AACATAAAAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (20 bp):
TAAAATGTGCACCTTTCAAG
Found at i:27072 original size:15 final size:16
Alignment explanation
Indices: 27047--27076 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
27037 TTTATTTCTC
27047 TCATGTTATATTTTAG
1 TCATGTTATATTTTAG
27063 TCAT-TTATATTTTA
1 TCATGTTATATTTTA
27077 AATATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.60
Consensus pattern (16 bp):
TCATGTTATATTTTAG
Found at i:28072 original size:15 final size:17
Alignment explanation
Indices: 28052--28084 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
28042 AGATCATGAT
28052 AATATAA-AT-AATTAA
1 AATATAATATGAATTAA
28067 AATATAATATGAATTAA
1 AATATAATATGAATTAA
28084 A
1 A
28085 CAAAAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AATATAATATGAATTAA
Found at i:29287 original size:178 final size:179
Alignment explanation
Indices: 28978--29336 Score: 585
Period size: 178 Copynumber: 2.0 Consensus size: 179
28968 TCTCTCTATA
28978 TATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGGAT
1 TATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGGAT
* *
29043 GAGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTTGAGTCTTTAGGTTCAGATAA
66 GAGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTCGAGTCTTTAGATTCAGATAA
* * * * *
29108 TGCTAATTGAGTTTCTTCTTTGATCATATGATGCTTTGTTTCTCGGGTT
131 TGCTAATTGAGTTTCTCCTTTGATCATATGAAGCTATGTTGCTCGGATT
* *
29157 TATAT-ATATATACAAGATTGATCAACGTGTGGAAAATTAGGAATAGAAATTGCATAGCTTGGAT
1 TATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGGAT
* * * *
29221 GTGAAGCAACATATAGGAGTGTTGCTTATATGTGGATTTTGGTTCGAGTCTTTAGATTCAGATAA
66 GAGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTCGAGTCTTTAGATTCAGATAA
*
29286 TGCTAATTGAGTTTCTCCTTTGATTATATGAAGCTATGTTGCTCGGATT
131 TGCTAATTGAGTTTCTCCTTTGATCATATGAAGCTATGTTGCTCGGATT
29335 TA
1 TA
29337 AGTGTGAGCA
Statistics
Matches: 166, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
178 161 0.97
179 5 0.03
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.38
Consensus pattern (179 bp):
TATATGATAAATACAAGATTGATCAACATGTGGAAAATTAGGAATAGAAATTGCATAGCTTGGAT
GAGAAGCAACATATAGGAGTGTTGCTTATATCTAGATTTTGATTCGAGTCTTTAGATTCAGATAA
TGCTAATTGAGTTTCTCCTTTGATCATATGAAGCTATGTTGCTCGGATT
Found at i:37169 original size:18 final size:18
Alignment explanation
Indices: 37133--37172 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
37123 ACACAACTTT
37133 AAATATTAAAAGAGATAA
1 AAATATTAAAAGAGATAA
* *
37151 AAAT-TTAAATGAGATTA
1 AAATATTAAAAGAGATAA
37168 AAATA
1 AAATA
37173 ATATTTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (18 bp):
AAATATTAAAAGAGATAA
Found at i:46512 original size:18 final size:16
Alignment explanation
Indices: 46489--46522 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
46479 ATTTTGGATT
46489 ATTAAATCCATGTAAAAA
1 ATTAAAT-CAT-TAAAAA
46507 ATTAAATCATTAAAAA
1 ATTAAATCATTAAAAA
46523 TATAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 3 0.19
18 7 0.44
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
ATTAAATCATTAAAAA
Found at i:47272 original size:31 final size:32
Alignment explanation
Indices: 47235--47298 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
47225 ACTTAATATC
* *
47235 TCAATGATTTAAAT-TAAAACTTTTGAA-TAAT
1 TCAATGACTTAAATGT-AAACTTTTAAATTAAT
47266 TCAATGACTTAAATGTAAACTTTTAAATTAAT
1 TCAATGACTTAAATGTAAACTTTTAAATTAAT
47298 T
1 T
47299 AAGTGATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 23 0.79
32 6 0.21
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (32 bp):
TCAATGACTTAAATGTAAACTTTTAAATTAAT
Found at i:52011 original size:12 final size:12
Alignment explanation
Indices: 51994--52019 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
51984 ACTACACTTC
51994 TTCTACTTGACA
1 TTCTACTTGACA
52006 TTCTACTTGACA
1 TTCTACTTGACA
52018 TT
1 TT
52020 GATAAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (12 bp):
TTCTACTTGACA
Found at i:52528 original size:70 final size:71
Alignment explanation
Indices: 52448--52584 Score: 188
Period size: 71 Copynumber: 1.9 Consensus size: 71
52438 CCTTTTCTTC
* * * * *
52448 TTGTCGCCTAATTAGGTGAATGAAGGACC-AAT-TTGAAACGAATATTTAATGCTTATAATTTAT
1 TTGTCCCCTAAGTAGGTGAATGAAGGACCAAATGTTG-AACAAATATTTAAGGCTTACAATTTAT
52511 TTGATTA
65 TTGATTA
* *
52518 TTGTCCCCTAAGTAGGTGAATGAAGGACCAAATGTTGAACAAATATTTAGGGTTTACAATTTATT
1 TTGTCCCCTAAGTAGGTGAATGAAGGACCAAATGTTGAACAAATATTTAAGGCTTACAATTTATT
52583 TG
66 TG
52585 CATGATGTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
70 27 0.47
71 28 0.48
72 3 0.05
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (71 bp):
TTGTCCCCTAAGTAGGTGAATGAAGGACCAAATGTTGAACAAATATTTAAGGCTTACAATTTATT
TGATTA
Found at i:53065 original size:2 final size:2
Alignment explanation
Indices: 53058--53092 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
53048 TACTACTCTC
53058 AT AT AT AT AT 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 AT AT AT AT AT A
53093 AAAGTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65358 original size:43 final size:39
Alignment explanation
Indices: 65259--65351 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 39
65249 TTAAATTTTA
65259 ATATAATAT-AATATTTATATTTTTATAATGTTATTAAT
1 ATATAATATGAATATTTATATTTTTATAATGTTATTAAT
*
65297 -TAGTAATTTG-AT-TTTATATTTTTATAATGTTAATTATCAT
1 ATA-TAATATGAATATTTATATTTTTATAATGTT-ATTA--AT
65337 ATATAATATGAATAT
1 ATATAATATGAATAT
65352 CATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
37 21 0.47
38 11 0.24
40 8 0.18
41 4 0.09
42 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.54
Consensus pattern (39 bp):
ATATAATATGAATATTTATATTTTTATAATGTTATTAAT
Found at i:67211 original size:44 final size:44
Alignment explanation
Indices: 67122--67209 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
67112 TAATGTCGAG
* * *
67122 TTAAGAGTTAGAATATGTAGTTAAAATAAGAAGATTAGGAAAAA
1 TTAAGAATTAGAATATGTAGTTAAAACAAGAAGATTAAGAAAAA
* *
67166 TTAAGAATTAGAATGTGTAGTCT-AAACAAGAAAGGTTAAGAAAA
1 TTAAGAATTAGAATATGTAGT-TAAAACAAG-AAGATTAAGAAAA
67210 TTCAAGGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 25 0.68
45 12 0.32
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.26
Consensus pattern (44 bp):
TTAAGAATTAGAATATGTAGTTAAAACAAGAAGATTAAGAAAAA
Done.