Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013532.1 Kokia drynarioides strain JFW-HI SEQ_128558, 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: 123077
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:227 original size:25 final size:25
Alignment explanation
Indices: 193--242 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
183 AAGTTACAGC
193 AATAGAAATTGAAGAAATTCAGAAG
1 AATAGAAATTGAAGAAATTCAGAAG
* *
218 AATAGAAATTGAAGAAGTTGAGAAG
1 AATAGAAATTGAAGAAATTCAGAAG
243 GTATAAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (25 bp):
AATAGAAATTGAAGAAATTCAGAAG
Found at i:3603 original size:24 final size:24
Alignment explanation
Indices: 3565--3610 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
3555 CACCTTCAAA
3565 TGTCACACGGCCATGTGACAGCCCG
1 TGTCACACGGCCATGTG-CAGCCCG
3590 TGTCACA-GGCCATGTGCAGCC
1 TGTCACACGGCCATGTGCAGCC
3611 TAATTTGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 5 0.24
24 9 0.43
25 7 0.33
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (24 bp):
TGTCACACGGCCATGTGCAGCCCG
Found at i:8483 original size:36 final size:36
Alignment explanation
Indices: 8443--8519 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
8433 TGATGATTGT
* *
8443 TGTGAAAGT-AATATGTGGGTATGTTTATTCATGCCA
1 TGTGAAAGTAAAGATGTGGGTATG-CTATTCATGCCA
*
8479 TGTGACAGTAAAGATGTGGGTATGCTATTCATGCCA
1 TGTGAAAGTAAAGATGTGGGTATGCTATTCATGCCA
*
8515 AGTGA
1 TGTGA
8520 CAGTGATTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 23 0.64
37 13 0.36
ACGTcount: A:0.29, C:0.10, G:0.27, T:0.34
Consensus pattern (36 bp):
TGTGAAAGTAAAGATGTGGGTATGCTATTCATGCCA
Found at i:8980 original size:46 final size:46
Alignment explanation
Indices: 8927--9478 Score: 853
Period size: 46 Copynumber: 12.1 Consensus size: 46
8917 TTAAATGTGT
*
8927 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATAC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
* *
8973 TTAAATGTTAATATGATTTTTGCTTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
* *
9019 TTAAATGTTAATATGATTTGTGCTTAAAAGTTAATGTGATCTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
*
9065 TTAAATGTTAATATGATTTATGCTTAAAAATTAATGTGATTTA---
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
9108 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
*
9154 TTAAATGTTAATATGATTTATGCTTAAAATTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
9200 TTAAATGTTAATATGATTTATGCTTCAAAA-TTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTT-AAAAGTTAATGTGATTTATGC
*
9246 TTAAATGTTAATATGATTTATGCTTAAAAATTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
* *
9292 TTAAATGTTAATGTGATTTATGCTTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
* * * * * *
9338 TTAAAAGTTAATGTGATATATACTT-AAATTGTAATATGATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGT-TAATGTGATTTATGC
* *
9384 TTAAATGTTAATATGATTTATGCTTAAAAGTTTATGTCATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
* * * *
9430 TTAAATGTTAATGTGATTTATGCTTAAATGTAAATGTAATTTATGC
1 TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
9476 TTA
1 TTA
9479 GTAGTTAGTA
Statistics
Matches: 466, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
43 42 0.09
45 7 0.02
46 409 0.88
47 8 0.02
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (46 bp):
TTAAATGTTAATATGATTTATGCTTAAAAGTTAATGTGATTTATGC
Found at i:9350 original size:29 final size:23
Alignment explanation
Indices: 8927--9478 Score: 765
Period size: 23 Copynumber: 24.1 Consensus size: 23
8917 TTAAATGTGT
*
8927 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* *
8950 TTAAAAGTTAATGTGATTTATAC
1 TTAAATGTTAATGTGATTTATGC
* *
8973 TTAAATGTTAATATGATTTTTGC
1 TTAAATGTTAATGTGATTTATGC
8996 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* *
9019 TTAAATGTTAATATGATTTGTGC
1 TTAAATGTTAATGTGATTTATGC
* *
9042 TTAAAAGTTAATGTGATCTATGC
1 TTAAATGTTAATGTGATTTATGC
*
9065 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
**
9088 TTAAAAATTAATGTGATTTA---
1 TTAAATGTTAATGTGATTTATGC
*
9108 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
9131 TTAAAAGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
9154 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
9177 TTAAAAT-TTAATGTGATTTATGC
1 TT-AAATGTTAATGTGATTTATGC
*
9200 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
*
9223 TTCAAA-ATTAATGTGATTTATGC
1 TT-AAATGTTAATGTGATTTATGC
*
9246 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
**
9269 TTAAAAATTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
9292 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
9315 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* * *
9338 TTAAAAGTTAATGTGATATATAC
1 TTAAATGTTAATGTGATTTATGC
*
9361 TTAAAT-TGTAATATGATTTATGC
1 TTAAATGT-TAATGTGATTTATGC
*
9384 TTAAATGTTAATATGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* * *
9407 TTAAAAGTTTATGTCATTTATGC
1 TTAAATGTTAATGTGATTTATGC
9430 TTAAATGTTAATGTGATTTATGC
1 TTAAATGTTAATGTGATTTATGC
* *
9453 TTAAATGTAAATGTAATTTATGC
1 TTAAATGTTAATGTGATTTATGC
9476 TTA
1 TTA
9479 GTAGTTAGTA
Statistics
Matches: 465, Mismatches: 55, Indels: 18
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.04
22 8 0.02
23 432 0.93
24 8 0.02
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (23 bp):
TTAAATGTTAATGTGATTTATGC
Found at i:10841 original size:17 final size:18
Alignment explanation
Indices: 10810--10845 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10800 ATAAAAAATA
10810 ATAAAAAGTATAATTTAG
1 ATAAAAAGTATAATTTAG
*
10828 ATAAAAATTA-AATTTAG
1 ATAAAAAGTATAATTTAG
10845 A
1 A
10846 AAATATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (18 bp):
ATAAAAAGTATAATTTAG
Found at i:11727 original size:15 final size:15
Alignment explanation
Indices: 11707--11736 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11697 TATAATATTT
11707 TATAAAATAGTAAAA
1 TATAAAATAGTAAAA
*
11722 TATAAAATTGTAAAA
1 TATAAAATAGTAAAA
11737 AAATTATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (15 bp):
TATAAAATAGTAAAA
Found at i:11741 original size:11 final size:11
Alignment explanation
Indices: 11725--11758 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
11715 AGTAAAATAT
*
11725 AAAATTGTAAA
1 AAAATTATAAA
11736 AAAATTATAAA
1 AAAATTATAAA
*
11747 AAAAATATAAA
1 AAAATTATAAA
11758 A
1 A
11759 TCAAGTAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:12278 original size:50 final size:50
Alignment explanation
Indices: 12163--12296 Score: 121
Period size: 50 Copynumber: 2.6 Consensus size: 50
12153 ATACAGGAAA
* * * *
12163 TTTTTATAATATTTTATGAATTTTATATTTTTTTTTACTTTTGTTTATAATTT
1 TTTTTACAAT-TTTTATAAATTTTATA--ATTTTTTACTTGTGTTTATAATTT
*
12216 TTTTTACGA-TTTTATAAAATTTTATAATTTTTTACGTTGT-TTTAT-ATATT
1 TTTTTACAATTTTTAT-AAATTTTATAATTTTTTAC-TTGTGTTTATAAT-TT
* * *
12266 TTTTTGCAATTTTTATAATTTTTCTAATTTT
1 TTTTTACAATTTTTATAAATTTTATAATTTT
12297 AATAACTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
49 2 0.03
50 35 0.51
51 15 0.22
52 9 0.13
53 7 0.10
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.66
Consensus pattern (50 bp):
TTTTTACAATTTTTATAAATTTTATAATTTTTTACTTGTGTTTATAATTT
Found at i:12285 original size:9 final size:9
Alignment explanation
Indices: 12273--12325 Score: 61
Period size: 9 Copynumber: 5.8 Consensus size: 9
12263 ATTTTTTTGC
12273 AATTTTTAT
1 AATTTTTAT
*
12282 AATTTTTCT
1 AATTTTTAT
*
12291 AATTTTAAT
1 AATTTTTAT
* *
12300 AACTTTTAA
1 AATTTTTAT
12309 ATATTTTTAT
1 A-ATTTTTAT
12319 AATTTTT
1 AATTTTT
12326 TTATTAAAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
9 28 0.80
10 7 0.20
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (9 bp):
AATTTTTAT
Found at i:12326 original size:10 final size:10
Alignment explanation
Indices: 12163--12326 Score: 58
Period size: 10 Copynumber: 16.5 Consensus size: 10
12153 ATACAGGAAA
12163 TTTTTATAAT
1 TTTTTATAAT
*
12173 ATTTTATGAA-
1 TTTTTAT-AAT
*
12183 -TTTTATATT
1 TTTTTATAAT
* *
12192 TTTTTTTACTT
1 TTTTTATA-AT
12203 TTGTTTATAAT
1 TT-TTTATAAT
* **
12214 TTTTTTTACG
1 TTTTTATAAT
* *
12224 ATTTTATAAA
1 TTTTTATAAT
*
12234 ATTTTATAAT
1 TTTTTATAAT
**
12244 TTTTTA-CGT
1 TTTTTATAAT
12253 TGTTTTATATAT
1 T-TTTTATA-AT
12265 TTTTT-TGCAA-
1 TTTTTAT--AAT
12275 TTTTTATAA-
1 TTTTTATAAT
*
12284 TTTTTCTAA-
1 TTTTTATAAT
*
12293 TTTTAATAA-
1 TTTTTATAAT
*
12302 CTTTTA-AAT
1 TTTTTATAAT
12311 ATTTTTATAAT
1 -TTTTTATAAT
12322 TTTTT
1 TTTTT
12327 TATTAAAACT
Statistics
Matches: 116, Mismatches: 24, Indels: 28
0.69 0.14 0.17
Matches are distributed among these distances:
8 3 0.03
9 29 0.25
10 58 0.50
11 18 0.16
12 8 0.07
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:12326 original size:20 final size:19
Alignment explanation
Indices: 12235--12326 Score: 64
Period size: 18 Copynumber: 4.7 Consensus size: 19
12225 TTTTATAAAA
**
12235 TTTTATAATTTTTTACGTT
1 TTTTATAATTTTTTACAAT
*
12254 GTTTTATATATTTTTTTGCAAT
1 -TTTTATA-A-TTTTTTACAAT
12276 TTTTATAA-TTTTT-CTAAT
1 TTTTATAATTTTTTAC-AAT
* * *
12294 TTTAATAA-CTTTTAAATAT
1 TTTTATAATTTTTTACA-AT
12313 TTTTATAATTTTTT
1 TTTTATAATTTTTT
12327 TATTAAAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
17 1 0.02
18 20 0.34
19 9 0.16
20 12 0.21
21 8 0.14
22 8 0.14
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:12364 original size:19 final size:19
Alignment explanation
Indices: 12274--12368 Score: 55
Period size: 19 Copynumber: 5.4 Consensus size: 19
12264 TTTTTTTGCA
*
12274 ATTTTTATAA-TTTT-TCTA
1 ATTTTTATAACTTTTAT-TT
* **
12292 ATTTTAATAACTTTTAAAT
1 ATTTTTATAACTTTTATTT
12311 ATTTTTATAA-TTTT-TTT
1 ATTTTTATAACTTTTATTT
* * *
12328 A---TTAAAAC--TTAGTA
1 ATTTTTATAACTTTTATTT
12342 ATTTTTATAACTTTTATTT
1 ATTTTTATAACTTTTATTT
12361 ATTTTTAT
1 ATTTTTAT
12369 TGTTTCTCGT
Statistics
Matches: 55, Mismatches: 13, Indels: 17
0.65 0.15 0.20
Matches are distributed among these distances:
13 2 0.04
14 7 0.13
17 8 0.15
18 13 0.24
19 25 0.45
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (19 bp):
ATTTTTATAACTTTTATTT
Found at i:14335 original size:24 final size:24
Alignment explanation
Indices: 14308--14361 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
14298 AATTTGTAGG
*
14308 TTAAATAAATTATTCTAATAAATA
1 TTAAATAAATTATACTAATAAATA
*
14332 TTAAATATATTATACTAATAAATA
1 TTAAATAAATTATACTAATAAATA
*
14356 CTAAAT
1 TTAAAT
14362 CTTCTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (24 bp):
TTAAATAAATTATACTAATAAATA
Found at i:14817 original size:28 final size:27
Alignment explanation
Indices: 14785--14837 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
14775 AAAAAACTCT
*
14785 AAAAATATATAAATATATATAAAATTTA
1 AAAAATATATAAATAGATA-AAAATTTA
14813 AAAAATATATAAATAGATAAAAATT
1 AAAAATATATAAATAGATAAAAATT
14838 GATGTATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAAATATATAAATAGATAAAAATTTA
Found at i:17585 original size:38 final size:38
Alignment explanation
Indices: 17534--17614 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
17524 GGGTTGAGTC
17534 GGATATAGTTGGCATGCCATAGGATTGAAAGAGTTCAG
1 GGATATAGTTGGCATGCCATAGGATTGAAAGAGTTCAG
*
17572 GGATATAGTTGGCATGCCATAGGATTGAAAGAGTTTAG
1 GGATATAGTTGGCATGCCATAGGATTGAAAGAGTTCAG
17610 GGATA
1 GGATA
17615 CTTCGACCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (38 bp):
GGATATAGTTGGCATGCCATAGGATTGAAAGAGTTCAG
Found at i:31205 original size:20 final size:20
Alignment explanation
Indices: 31169--31218 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
31159 TCATTAAGCT
*
31169 TTAATTAATCACTTTTA-ATC
1 TTAATTAAACACTTTTACA-C
31189 TTAATTAAAC-CTATTTACAC
1 TTAATTAAACACT-TTTACAC
31209 TTAATATAAA
1 TTAAT-TAAA
31219 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTACAC
Found at i:33739 original size:3 final size:3
Alignment explanation
Indices: 33731--33763 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
33721 TATGTTATGA
33731 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
33764 GCAAAGAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:35726 original size:21 final size:21
Alignment explanation
Indices: 35664--35732 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
35654 CTGTTCGTTT
*
35664 CTTTTTGTCCAAGTTACTTCT
1 CTTTTTGTCCAAGTTACTTCA
*
35685 CTTTTTGTCCAAGTTGCTTCA
1 CTTTTTGTCCAAGTTACTTCA
* *
35706 CTTTTTGTCTAAGTCACTTCA
1 CTTTTTGTCCAAGTTACTTCA
*
35727 TTTTTT
1 CTTTTT
35733 CTTTGTGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.14, C:0.22, G:0.10, T:0.54
Consensus pattern (21 bp):
CTTTTTGTCCAAGTTACTTCA
Found at i:40369 original size:30 final size:31
Alignment explanation
Indices: 40299--40370 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
40289 TTAATATAAT
40299 ATTTGGTACCTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTA
* * * *
40330 ATTTAGTACCTGAACTTGGCA-TTTTTTCTG
1 ATTTGGTACCTGAACTTGACACTTTTTCCTA
40360 ATTTGGTACCT
1 ATTTGGTACCT
40371 AAGCTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 17 0.47
31 19 0.53
ACGTcount: A:0.21, C:0.19, G:0.15, T:0.44
Consensus pattern (31 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTA
Found at i:40711 original size:29 final size:29
Alignment explanation
Indices: 40655--40713 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
40645 TACAAGTGTC
* * ***
40655 AAGTTTGAGTACCAAATTGGACCCAAAAA
1 AAGTTTAAGTACCAAATTAGAAAAAAAAA
40684 AAGTTTAAGTACCAAATTAGAAAAAAAAA
1 AAGTTTAAGTACCAAATTAGAAAAAAAAA
40713 A
1 A
40714 TGTCAAGTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.54, C:0.12, G:0.14, T:0.20
Consensus pattern (29 bp):
AAGTTTAAGTACCAAATTAGAAAAAAAAA
Found at i:41804 original size:15 final size:16
Alignment explanation
Indices: 41782--41822 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
41772 TTAATTTTTT
41782 AAAAATTATAAAAAT-
1 AAAAATTATAAAAATA
* *
41797 ATAAATTATTAAAATA
1 AAAAATTATAAAAATA
41813 AAAAATTATA
1 AAAAATTATA
41823 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAAAATTATAAAAATA
Found at i:52795 original size:20 final size:20
Alignment explanation
Indices: 52766--52839 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
52756 AGTCTTCAAG
* *
52766 GTATCAGTAGAAGTGGTGTT
1 GTATCGGTAGAAGTGGAGTT
52786 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
* *
52806 CTACCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
* * *
52826 CTACCGATAGAAGT
1 GTATCGGTAGAAGT
52840 CTCACAGGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.11, G:0.34, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAAGTGGAGTT
Found at i:55888 original size:20 final size:20
Alignment explanation
Indices: 55843--55891 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
55833 TTCATGGTGT
*
55843 CGGTAGAAGTGGAGTTGTTA
1 CGGTAGAAGTGGAGTTGCTA
55863 -GGTAGAAGTGGAGTT-CTA
1 CGGTAGAAGTGGAGTTGCTA
55881 CCGGTAGAAGT
1 -CGGTAGAAGT
55892 CTCACAGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 2 0.08
19 15 0.58
20 9 0.35
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
CGGTAGAAGTGGAGTTGCTA
Found at i:58922 original size:21 final size:21
Alignment explanation
Indices: 58893--58938 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
58883 TCTGTTTGGT
58893 TGGTAAGAAAACTAAAGAAAA
1 TGGTAAGAAAACTAAAGAAAA
* *
58914 TGGTGAGAAAACTGAAGAAAA
1 TGGTAAGAAAACTAAAGAAAA
58935 TGGT
1 TGGT
58939 TTCATTAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.26, T:0.17
Consensus pattern (21 bp):
TGGTAAGAAAACTAAAGAAAA
Found at i:59145 original size:18 final size:18
Alignment explanation
Indices: 59124--59158 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59114 AAAATGTTTT
* *
59124 AGAGAGGAAGAGAGAAAG
1 AGAGAAGAAGAAAGAAAG
59142 AGAGAAGAAGAAAGAAA
1 AGAGAAGAAGAAAGAAA
59159 TGAAAGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (18 bp):
AGAGAAGAAGAAAGAAAG
Found at i:65583 original size:58 final size:58
Alignment explanation
Indices: 65518--65636 Score: 220
Period size: 58 Copynumber: 2.1 Consensus size: 58
65508 TTGCATACAA
*
65518 ATGTTTAGATATTGATAGATAACATTTGAAAGATCATATGAAATTTGTAATACGAACC
1 ATGTTTAGATATTGAAAGATAACATTTGAAAGATCATATGAAATTTGTAATACGAACC
*
65576 ATGTTTAGGTATTGAAAGATAACATTTGAAAGATCATATGAAATTTGTAATACGAACC
1 ATGTTTAGATATTGAAAGATAACATTTGAAAGATCATATGAAATTTGTAATACGAACC
65634 ATG
1 ATG
65637 AGGGTTAATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (58 bp):
ATGTTTAGATATTGAAAGATAACATTTGAAAGATCATATGAAATTTGTAATACGAACC
Found at i:65753 original size:17 final size:18
Alignment explanation
Indices: 65712--65753 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
65702 GAGAATGTCA
*
65712 TATGTTTACAAATGATAT
1 TATGATTACAAATGATAT
65730 TGA-GATTAC-AATGATAT
1 T-ATGATTACAAATGATAT
65747 TATGATT
1 TATGATT
65754 TGATTTCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 6 0.29
19 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (18 bp):
TATGATTACAAATGATAT
Found at i:69768 original size:22 final size:22
Alignment explanation
Indices: 69706--69761 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
69696 TACACTAGCA
* *
69706 GGGACTTGTATCAGTATAAGTG
1 GGGACTTGTATTAGTACAAGTG
69728 GGGACTTGTATTAGTACAAGTG
1 GGGACTTGTATTAGTACAAGTG
69750 GGGACTTGTATT
1 GGGACTTGTATT
69762 GATACAACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.32, T:0.34
Consensus pattern (22 bp):
GGGACTTGTATTAGTACAAGTG
Found at i:71133 original size:22 final size:22
Alignment explanation
Indices: 71065--71135 Score: 88
Period size: 22 Copynumber: 3.2 Consensus size: 22
71055 GTTTAGTTCA
* *
71065 TTTATATTCACGAACAAACTCG
1 TTTATGTTCACGAACAAGCTCG
* * * *
71087 TTAATGTCCATGAACAAGTTCG
1 TTTATGTTCACGAACAAGCTCG
71109 TTTATGTTCACGAACAAGCTCG
1 TTTATGTTCACGAACAAGCTCG
71131 TTTAT
1 TTTAT
71136 TGACTCGTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (22 bp):
TTTATGTTCACGAACAAGCTCG
Found at i:73796 original size:21 final size:21
Alignment explanation
Indices: 73770--73819 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
73760 ATAATAGCAT
73770 AATCCAAAAATAAAGTTTAGA
1 AATCCAAAAATAAAGTTTAGA
* *
73791 AATCCAAACATAAAGTTTATA
1 AATCCAAAAATAAAGTTTAGA
73812 AATCCAAA
1 AATCCAAA
73820 TTACGTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.24
Consensus pattern (21 bp):
AATCCAAAAATAAAGTTTAGA
Found at i:74430 original size:13 final size:13
Alignment explanation
Indices: 74408--74437 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
74398 GTTGTTTTTT
74408 TTAA-AGTATCAA
1 TTAATAGTATCAA
74420 TTAATAGTATCAA
1 TTAATAGTATCAA
74433 TTAAT
1 TTAAT
74438 TCTACCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (13 bp):
TTAATAGTATCAA
Found at i:92342 original size:49 final size:49
Alignment explanation
Indices: 92289--92443 Score: 156
Period size: 49 Copynumber: 3.2 Consensus size: 49
92279 CATGAAGATT
* *
92289 TGAAGGGAAGGGCTTAAGTCGCAACGGCGAACCTTATACCTCAGAAGAA
1 TGAAGGGAAGGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAAGAA
* * * * * *
92338 TGAAGGGAAAGATTTAAGCCACAATGGCGAATCC--AGTACCAC-GAAGATT
1 TGAAGGGAAGGGTTTAAGTCGCAATGGCGAA-CCTTA-TACCTCAGAAGA-A
* * *
92387 TGAAGGGAAGGGTTTAAGTCGTAATGACGAACCTTATACATCAGAA-AA
1 TGAAGGGAAGGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAAGAA
92435 TGAAGGGAA
1 TGAAGGGAA
92444 AAACTTAAGC
Statistics
Matches: 83, Mismatches: 17, Indels: 13
0.73 0.15 0.12
Matches are distributed among these distances:
48 17 0.20
49 60 0.72
50 6 0.07
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.19
Consensus pattern (49 bp):
TGAAGGGAAGGGTTTAAGTCGCAATGGCGAACCTTATACCTCAGAAGAA
Found at i:92418 original size:98 final size:98
Alignment explanation
Indices: 92245--92577 Score: 382
Period size: 98 Copynumber: 3.4 Consensus size: 98
92235 AGACACGAAA
* * * *
92245 GGAAATATTTAAGCCACAATGGAGAATCCAATACCATGAAGATTTGAAGGGAAGGGCTTAAGTCG
1 GGAAAGATTTAAGCCACAATGGTGAATCCAATACCACGAAGATTTGAAGGGAAGGGTTTAAGTCG
* *
92310 CAACGGCGAACCTTATACCTCAGAAGAATGAAG
66 TAATGGCGAACCTTATACCTCAGAAGAATGAAG
* *
92343 GGAAAGATTTAAGCCACAATGGCGAATCCAGTACCACGAAGATTTGAAGGGAAGGGTTTAAGTCG
1 GGAAAGATTTAAGCCACAATGGTGAATCCAATACCACGAAGATTTGAAGGGAAGGGTTTAAGTCG
* *
92408 TAATGACGAACCTTATACATCAGAA-AATGAAG
66 TAATGGCGAACCTTATACCTCAGAAGAATGAAG
* * ** * * *** * **
92440 GGAAAAACTTAAGCCGTAACGGTGAATCGAATACCACGAAGATGCAAAAGGAAAAGTTTAAGTCG
1 GGAAAGATTTAAGCCACAATGGTGAATCCAATACCACGAAGATTTGAAGGGAAGGGTTTAAGTCG
* *
92505 TAATGGCGAACCTTATACCTCAAAAGCAT-AAGG
66 TAATGGCGAACCTTATACCTCAGAAGAATGAA-G
* * * * *
92538 GGAAAGATTCAAGCCGCAATAGTGAATCTAGTACCACGAA
1 GGAAAGATTTAAGCCACAATGGTGAATCCAATACCACGAA
92578 AACATTACAA
Statistics
Matches: 198, Mismatches: 35, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
97 82 0.41
98 116 0.59
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (98 bp):
GGAAAGATTTAAGCCACAATGGTGAATCCAATACCACGAAGATTTGAAGGGAAGGGTTTAAGTCG
TAATGGCGAACCTTATACCTCAGAAGAATGAAG
Found at i:92499 original size:97 final size:98
Alignment explanation
Indices: 92253--92522 Score: 281
Period size: 97 Copynumber: 2.8 Consensus size: 98
92243 AAGGAAATAT
* * * *** * ** * * *
92253 TTAAGCCACAATGGAGAATCCAATACCATGAAGATTTGAAGGGAAGGGCTTAAGTCGCAACGGCG
1 TTAAGCCACAACGGCGAATCCAATACCACGAAGATGCAAAAGGAAAAGTTTAAGTCGTAATGGCG
* * *
92318 AACCTTATACCTCAGAAGAATGAAGGGAAAGAT
66 AACCTTATACATCAGAAGAATGAAGGGAAAAAC
* * *** * ** *
92351 TTAAGCCACAATGGCGAATCCAGTACCACGAAGATTTGAAGGGAAGGGTTTAAGTCGTAATGACG
1 TTAAGCCACAACGGCGAATCCAATACCACGAAGATGCAAAAGGAAAAGTTTAAGTCGTAATGGCG
92416 AACCTTATACATCAGAA-AATGAAGGGAAAAAC
66 AACCTTATACATCAGAAGAATGAAGGGAAAAAC
** * *
92448 TTAAGCCGTAACGGTGAATCGAATACCACGAAGATGCAAAAGGAAAAGTTTAAGTCGTAATGGCG
1 TTAAGCCACAACGGCGAATCCAATACCACGAAGATGCAAAAGGAAAAGTTTAAGTCGTAATGGCG
92513 AACCTTATAC
66 AACCTTATAC
92523 CTCAAAAGCA
Statistics
Matches: 149, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
97 75 0.50
98 74 0.50
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (98 bp):
TTAAGCCACAACGGCGAATCCAATACCACGAAGATGCAAAAGGAAAAGTTTAAGTCGTAATGGCG
AACCTTATACATCAGAAGAATGAAGGGAAAAAC
Found at i:92523 original size:49 final size:49
Alignment explanation
Indices: 92302--92523 Score: 120
Period size: 49 Copynumber: 4.6 Consensus size: 49
92292 AGGGAAGGGC
* * *
92302 TTAAGTCGCAACGGCGAACCTTATACC-TCAGAAGAATG-AAGGGAAAGAT
1 TTAAGTCGTAATGGCGAACCTTATACCATCAGAA-AATGAAAGGAAAAG-T
* ** * * **
92351 TTAAGCCACAATGGCGAATCC--AGTACCA-C-GAAGATTTGAAGGGAAGGGT
1 TTAAGTCGTAATGGCGAA-CCTTA-TACCATCAGAA-A-ATGAAAGGAAAAGT
* * **
92400 TTAAGTCGTAATGACGAACCTTATA-CATCAGAAAATGAAGGGAAAAAC
1 TTAAGTCGTAATGGCGAACCTTATACCATCAGAAAATGAAAGGAAAAGT
* * * * ** *
92448 TTAAGCCGTAACGGTGAATCGAATACCA-C-GAAGATGCAAAAGGAAAAGT
1 TTAAGTCGTAATGGCGAACCTTATACCATCAGAAAATG--AAAGGAAAAGT
92497 TTAAGTCGTAATGGCGAACCTTATACC
1 TTAAGTCGTAATGGCGAACCTTATACC
92524 TCAAAAGCAT
Statistics
Matches: 127, Mismatches: 34, Indels: 24
0.69 0.18 0.13
Matches are distributed among these distances:
47 6 0.05
48 38 0.30
49 72 0.57
50 11 0.09
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (49 bp):
TTAAGTCGTAATGGCGAACCTTATACCATCAGAAAATGAAAGGAAAAGT
Found at i:106258 original size:2 final size:2
Alignment explanation
Indices: 106251--106276 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
106241 GGACCTAACA
106251 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
106277 TTGGAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109286 original size:21 final size:20
Alignment explanation
Indices: 109259--109315 Score: 96
Period size: 21 Copynumber: 2.8 Consensus size: 20
109249 GAATAAGATT
109259 GAGAGGATTTTTTTATTTCA
1 GAGAGGATTTTTTTATTTCA
109279 GAGAAGGATTTTTTTATTTCA
1 GAG-AGGATTTTTTTATTTCA
109300 GAGAGAGATTTTTTTA
1 GAGAG-GATTTTTTTA
109316 ATAAGATTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (20 bp):
GAGAGGATTTTTTTATTTCA
Found at i:109571 original size:3 final size:3
Alignment explanation
Indices: 109563--109590 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
109553 TCGAAGTTCG
109563 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
109591 TATATTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:110010 original size:45 final size:45
Alignment explanation
Indices: 109917--110009 Score: 179
Period size: 44 Copynumber: 2.1 Consensus size: 45
109907 TTAATATTTG
109917 TTTTCTTTTTATTTTTTATGTATTTATTATTTATACGGAAGTTAT
1 TTTTCTTTTTATTTTTTATGTATTTATTATTTATACGGAAGTTAT
109962 TTTTCTTTTTA-TTTTTATGTATTTATTATTTATACGGAAGTTAT
1 TTTTCTTTTTATTTTTTATGTATTTATTATTTATACGGAAGTTAT
110006 TTTT
1 TTTT
110010 TTACATTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 37 0.77
45 11 0.23
ACGTcount: A:0.22, C:0.04, G:0.09, T:0.66
Consensus pattern (45 bp):
TTTTCTTTTTATTTTTTATGTATTTATTATTTATACGGAAGTTAT
Found at i:110304 original size:20 final size:19
Alignment explanation
Indices: 110279--110316 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
110269 TAATTGATTA
*
110279 ATATTATTGCCATTATTATG
1 ATATTATTACCA-TATTATG
110299 ATATTATTACCATATTAT
1 ATATTATTACCATATTAT
110317 TTGTTACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
ATATTATTACCATATTATG
Found at i:110389 original size:2 final size:2
Alignment explanation
Indices: 110382--110411 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
110372 TTATTTATGC
110382 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
110412 TTATTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.