Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014193.1 Kokia drynarioides strain JFW-HI SEQ_129226, 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: 97071
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1921 original size:28 final size:28
Alignment explanation
Indices: 1881--1941 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
1871 TGTTGACTGA
*
1881 AAGAAGCACATATAAGCAAAAAAGATTT
1 AAGATGCACATATAAGCAAAAAAGATTT
*
1909 AAGATGCACATATAAGCAGAAAAGATTT
1 AAGATGCACATATAAGCAAAAAAGATTT
1937 AAGAT
1 AAGAT
1942 ACTCCCTCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.54, C:0.10, G:0.16, T:0.20
Consensus pattern (28 bp):
AAGATGCACATATAAGCAAAAAAGATTT
Found at i:9898 original size:50 final size:50
Alignment explanation
Indices: 9829--9940 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
9819 ATTGAATCCT
* * * *
9829 ATACCCCTGAAGCTGTAGAGGAATAGATTGAAGCCGTAATGGCGAATCTC
1 ATACACCTAAAGCTCTAGAGGAATAGATTGAAGCCGCAATGGCGAATCTC
* ** *
9879 ATATACCTAAAGCTCTAGAGGGGTAGATTGAAGCTGCAATGGCGAATCTC
1 ATACACCTAAAGCTCTAGAGGAATAGATTGAAGCCGCAATGGCGAATCTC
*
9929 ATACCCCTAAAG
1 ATACACCTAAAG
9941 TTGTAAAGGG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (50 bp):
ATACACCTAAAGCTCTAGAGGAATAGATTGAAGCCGCAATGGCGAATCTC
Found at i:10071 original size:40 final size:40
Alignment explanation
Indices: 10016--10234 Score: 246
Period size: 40 Copynumber: 5.5 Consensus size: 40
10006 CGAAGTTATA
* *
10016 ACCATCCAATCTTTTACCCCAATCAAAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
* * * *
10056 ACCATCTAATCTTTTACCCTAGTTAGAGGGCAGATTAAAG
1 ACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
* * *
10096 ACCTTCCAATCTTTTACCCTGATTAGAGGGCAGATTGAAG
1 ACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
* * *
10136 GCCATCAAATCTTTTACCCTAATCAGAGGGCAAATTGAAG
1 ACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
* * * * *
10176 ACCATCCGATCTCTTACCCCAACCATG-GGGCAAATTGAAGG
1 ACCATCCAATCTTTTACCCTAATCA-GAGGGCAGATTGAA-G
10217 A--ATCCAATCTTTTACCCT
1 ACCATCCAATCTTTTACCCT
10235 TAAAGCTATA
Statistics
Matches: 151, Mismatches: 26, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
39 14 0.09
40 134 0.89
41 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (40 bp):
ACCATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAG
Found at i:12132 original size:30 final size:30
Alignment explanation
Indices: 12010--12133 Score: 108
Period size: 30 Copynumber: 4.2 Consensus size: 30
12000 GAAATTATGC
* **
12010 TTTGACCCCTAAACTTTTTAAAAATTTGAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
** *
12040 TTT-AATCCTCAAACTTTCTAAAAATTTAAA
1 TTTGACCCCT-AAACTTTCTAAAAATTCAAA
* * * * * *
12070 TTTAACCTC-GAATTTTTTAAAAATTCCAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
*
12099 TTTGACCCCTAAACTTTCCAAAAATTCAAA
1 TTTGACCCCTAAACTTTCTAAAAATTCAAA
12129 TTTGA
1 TTTGA
12134 TCCAATTTTA
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
29 26 0.36
30 44 0.61
31 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTGACCCCTAAACTTTCTAAAAATTCAAA
Found at i:12388 original size:39 final size:39
Alignment explanation
Indices: 12327--12428 Score: 172
Period size: 39 Copynumber: 2.7 Consensus size: 39
12317 TTTACTTAAT
**
12327 TTATTATCT-TA-TTGTATTTTATGTATATATGGTTTTC
1 TTATTATCTATACTTGTAAATTATGTATATATGGTTTTC
12364 TTATTATCTATACTTGTAAATTATGTATATATGGTTTTC
1 TTATTATCTATACTTGTAAATTATGTATATATGGTTTTC
12403 TTATTATCTATACTTGTAAATTATGT
1 TTATTATCTATACTTGTAAATTATGT
12429 GCATATTTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
37 9 0.15
38 2 0.03
39 50 0.82
ACGTcount: A:0.26, C:0.07, G:0.10, T:0.57
Consensus pattern (39 bp):
TTATTATCTATACTTGTAAATTATGTATATATGGTTTTC
Found at i:19523 original size:110 final size:110
Alignment explanation
Indices: 19326--19543 Score: 339
Period size: 110 Copynumber: 2.0 Consensus size: 110
19316 CTAGGGTCGC
* * * * *
19326 TTTAATTTTGGACTTAATATTTGATTTAATTAGTTTGCGTTAGGGGTGAGCATTTGATTGAATCG
1 TTTAATTTTGAACTTAATATTTGATTTAATTAGTTTGCATTAAGGGTGAGCATTTGATCGAATAG
*
19391 AGTGAAAAAATTTGGAGATAATCAAATTGAA-GAGTCCTATTTTGT
66 AGTGAAAAAATTTGGAGATAATCAAATT-AACGAATCCTATTTTGT
19436 TTTAATTTTGAACTTAATATTTGATTTAATTAGTTTGCATTAAGGGTGAGCATTTGATCGAATAG
1 TTTAATTTTGAACTTAATATTTGATTTAATTAGTTTGCATTAAGGGTGAGCATTTGATCGAATAG
* * *
19501 AGTGAAAAAATTTTGAGTTAATCGAATTAACGAATCCTATTTT
66 AGTGAAAAAATTTGGAGATAATCAAATTAACGAATCCTATTTT
19544 ATCATCCTAA
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
109 2 0.02
110 96 0.98
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.41
Consensus pattern (110 bp):
TTTAATTTTGAACTTAATATTTGATTTAATTAGTTTGCATTAAGGGTGAGCATTTGATCGAATAG
AGTGAAAAAATTTGGAGATAATCAAATTAACGAATCCTATTTTGT
Found at i:24849 original size:31 final size:29
Alignment explanation
Indices: 24785--24853 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
24775 ACGATAAAAT
** *
24785 AAGTGACTAAAATATAACATTTCAAACAT
1 AAGTGACTAAAATATAACATGACAAACAA
*
24814 AAGTGACTAAAATGTAACATGAGACAAACAA
1 AAGTGACTAAAATATAACAT--GACAAACAA
24845 AAGTGACTA
1 AAGTGACTA
24854 TTTTAAGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.52, C:0.13, G:0.13, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATATAACATGACAAACAA
Found at i:24992 original size:8 final size:8
Alignment explanation
Indices: 24981--25005 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
24971 TTTTAATTTT
24981 TTAAAATA
1 TTAAAATA
24989 TTAAAATA
1 TTAAAATA
24997 TTAAAATA
1 TTAAAATA
25005 T
1 T
25006 GTATACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TTAAAATA
Found at i:25099 original size:26 final size:25
Alignment explanation
Indices: 25070--25124 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
25060 AATAATATTC
* *
25070 TTAATATATTATTAACAATATTTATA
1 TTAATATATTAATAACAA-ATATATA
* *
25096 TTAATATTTTAATAATAAATATATA
1 TTAATATATTAATAACAAATATATA
25121 TTAA
1 TTAA
25125 AATTTATAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATATATTAATAACAAATATATA
Found at i:26355 original size:20 final size:18
Alignment explanation
Indices: 26331--26379 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 18
26321 AATAGTATTT
26331 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
*
26349 GTGATTATTTTAATATTAAA
1 -T-ATTAATTTAATATTAAA
26369 T-TTAATTTAAT
1 TATTAATTTAAT
26380 GTTTATTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.33
19 2 0.07
20 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:27147 original size:20 final size:20
Alignment explanation
Indices: 27122--27161 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
27112 TTAAATGAAG
27122 TTCATTTGACTCATTTAACT
1 TTCATTTGACTCATTTAACT
27142 TTCATTTGACTCATTTAACT
1 TTCATTTGACTCATTTAACT
27162 AACTTGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TTCATTTGACTCATTTAACT
Found at i:28657 original size:89 final size:89
Alignment explanation
Indices: 28543--28813 Score: 524
Period size: 89 Copynumber: 3.0 Consensus size: 89
28533 GAAAAACTCG
* *
28543 AAAATAAAGAACCCTCAAAATGTAAACGTAAAATGCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
1 AAAATAAAGAACCCTCAAAATGTAAACGCAAAATTCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
28608 ATGGGTGTAATTTTCTAAGGTTGT
66 ATGGGTGTAATTTTCTAAGGTTGT
28632 AAAATAAAGAACCCTCAAAATGTAAACGCAAAATTCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
1 AAAATAAAGAACCCTCAAAATGTAAACGCAAAATTCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
28697 ATGGGTGTAATTTTCTAAGGTTGT
66 ATGGGTGTAATTTTCTAAGGTTGT
28721 AAAATAAAGAACCCTCAAAATGTAAACGCAAAATTCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
1 AAAATAAAGAACCCTCAAAATGTAAACGCAAAATTCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
28786 ATGGGTGTAATTTTCTAAGGTTGT
66 ATGGGTGTAATTTTCTAAGGTTGT
28810 AAAA
1 AAAA
28814 GAGTCTATTT
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 180 1.00
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (89 bp):
AAAATAAAGAACCCTCAAAATGTAAACGCAAAATTCTCCAAAAGTGTTAGGAGTTCTAATCTCTA
ATGGGTGTAATTTTCTAAGGTTGT
Found at i:41966 original size:19 final size:19
Alignment explanation
Indices: 41942--41982 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
41932 TACCCAACTT
41942 ATCGGCTATGGGCTCAAAC
1 ATCGGCTATGGGCTCAAAC
41961 ATCGGCTATGGGCTCAAAC
1 ATCGGCTATGGGCTCAAAC
41980 ATC
1 ATC
41983 TTTAGAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (19 bp):
ATCGGCTATGGGCTCAAAC
Found at i:50449 original size:20 final size:18
Alignment explanation
Indices: 50424--50473 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
50414 ATTACAAAAT
*
50424 AATTCAAATATAATTTTTAA
1 AATTCAAA-AT-ATTTATAA
50444 AATTCAAAATATTTATAAAA
1 AATTCAAAATATTTAT--AA
50464 AATTCAAAAT
1 AATTCAAAAT
50474 TTATATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 2 0.07
20 20 0.74
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:50537 original size:9 final size:9
Alignment explanation
Indices: 50483--50540 Score: 50
Period size: 8 Copynumber: 6.3 Consensus size: 9
50473 TTTATATTTT
50483 TTTAAAAAA
1 TTTAAAAAA
*
50492 -TTATAAAA
1 TTTAAAAAA
50500 TTCTAAAAAA
1 TT-TAAAAAA
50510 TATATAAAACAA
1 T-T-TAAAA-AA
50522 -TT-AAAAA
1 TTTAAAAAA
50529 TTTAAAAAA
1 TTTAAAAAA
50538 TTT
1 TTT
50541 CTAAAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.05
8 12 0.30
9 10 0.25
10 8 0.20
11 6 0.15
12 2 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:55189 original size:23 final size:23
Alignment explanation
Indices: 55163--55221 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
55153 TTATCTATCT
* * *
55163 TTGTGACACGTTTTTTCTTTGTC
1 TTGTGACACGCTTTTCCTCTGTC
*
55186 TTGTGGCACGCTTTTCCTCTGTC
1 TTGTGACACGCTTTTCCTCTGTC
55209 TTGTGGA-ACGCTT
1 TTGT-GACACGCTT
55222 CTGCCTTATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.08, C:0.22, G:0.22, T:0.47
Consensus pattern (23 bp):
TTGTGACACGCTTTTCCTCTGTC
Found at i:55568 original size:19 final size:20
Alignment explanation
Indices: 55542--55591 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
55532 GGTCTGATGT
55542 TTATTTTTCTACTT-TTTT-
1 TTATTTTTCTACTTGTTTTG
55560 TTAATTTTTCT--TTGTTTTG
1 TT-ATTTTTCTACTTGTTTTG
55579 TTATTTTTCTACT
1 TTATTTTTCTACT
55592 ACATTTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.07
18 14 0.52
19 10 0.37
20 1 0.04
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.74
Consensus pattern (20 bp):
TTATTTTTCTACTTGTTTTG
Found at i:58376 original size:91 final size:91
Alignment explanation
Indices: 58267--58453 Score: 365
Period size: 91 Copynumber: 2.1 Consensus size: 91
58257 ATTTAAAAAT
*
58267 TCAAGTAAAATGATATGAAGTTTTGATGACAATAATCTTTAAAGCAATTAAGCCTTAAAAATAAT
1 TCAAATAAAATGATATGAAGTTTTGATGACAATAATCTTTAAAGCAATTAAGCCTTAAAAATAAT
58332 TAAAATATCTGTCTTGAATTATTTGC
66 TAAAATATCTGTCTTGAATTATTTGC
58358 TCAAATAAAATGATATGAAGTTTTGATGACAATAATCTTTAAAGCAATTAAGCCTTAAAAATAAT
1 TCAAATAAAATGATATGAAGTTTTGATGACAATAATCTTTAAAGCAATTAAGCCTTAAAAATAAT
58423 TAAAATATCTGTCTTGAATTATTTGC
66 TAAAATATCTGTCTTGAATTATTTGC
58449 TCAAA
1 TCAAA
58454 AGAGTTTGTA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 95 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.36
Consensus pattern (91 bp):
TCAAATAAAATGATATGAAGTTTTGATGACAATAATCTTTAAAGCAATTAAGCCTTAAAAATAAT
TAAAATATCTGTCTTGAATTATTTGC
Found at i:59872 original size:21 final size:21
Alignment explanation
Indices: 59818--59877 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 21
59808 CGATCTAAGA
* *
59818 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAAAAATAGAATT
59839 AAAAATAAAAAAAATAGAATT
1 AAAAATAAAAAAAATAGAATT
59860 AAAAGA-AATAAAAAATAG
1 AAAA-ATAA-AAAAAATAG
59878 GGAAGTTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 25 0.71
22 10 0.29
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAAAAATAGAATT
Found at i:60616 original size:61 final size:61
Alignment explanation
Indices: 60521--60646 Score: 234
Period size: 61 Copynumber: 2.1 Consensus size: 61
60511 TGAATGGGGA
*
60521 ATAATTAGAATTATATCTAACATTTAATTTCCCTAATTGAATCCAATCTAAATTCTAAAAG
1 ATAATTAGAATTATATCTAACATTTAATTTCCCTAATTGAATCCAATCTAAACTCTAAAAG
*
60582 ATAATTAGAATTATATCTAACATTTAATTTCCCTAATTGAATCCAATTTAAACTCTAAAAG
1 ATAATTAGAATTATATCTAACATTTAATTTCCCTAATTGAATCCAATCTAAACTCTAAAAG
60643 ATAA
1 ATAA
60647 ATACAAAAAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (61 bp):
ATAATTAGAATTATATCTAACATTTAATTTCCCTAATTGAATCCAATCTAAACTCTAAAAG
Found at i:62240 original size:4 final size:4
Alignment explanation
Indices: 62231--62257 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
62221 TATTGAACAA
62231 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
62258 ATAAGATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:65042 original size:16 final size:15
Alignment explanation
Indices: 65005--65062 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
64995 ATCTAAGGAA
*
65005 AAATAAAAGA-AACAG
1 AAATAAAA-ATAAAAG
*
65020 AATTAAAAATAAAAG
1 AAATAAAAATAAAAG
*
65035 AAAATAAAATTAAAAG
1 -AAATAAAAATAAAAG
65051 AAATAGAAAATA
1 AAATA-AAAATA
65063 GAGAAGTCGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.03
15 16 0.46
16 18 0.51
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.16
Consensus pattern (15 bp):
AAATAAAAATAAAAG
Found at i:65049 original size:21 final size:22
Alignment explanation
Indices: 65003--65062 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
64993 CGATCTAAGG
* *
65003 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAAAATT
65024 AAAAATAAAAGAAAATAAAATT
1 AAAAATAAAAGAAAATAAAATT
*
65046 AAAAGA-AATAGAAAATA
1 AAAA-ATAAAAGAAAATA
65063 GAGAAGTCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.32
22 22 0.65
23 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAAAATT
Found at i:65886 original size:19 final size:19
Alignment explanation
Indices: 65862--65904 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
65852 AAACATAAAT
65862 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
65881 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
65900 TAAAT
1 TAAAT
65905 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:74101 original size:20 final size:20
Alignment explanation
Indices: 74051--74159 Score: 71
Period size: 20 Copynumber: 5.5 Consensus size: 20
74041 GAAAAGTTCG
* * *
74051 AAAAAAATTTAAAATCAAGTT
1 AAAATAATTTTAAA-CAAGTC
* *
74072 AAAATGATTTTAAACATGTC
1 AAAATAATTTTAAACAAGTC
*
74092 AAAATAA-TTTGAACTAAGTC
1 AAAATAATTTTAAAC-AAGTC
* * **
74112 AAAATCATATT-AACACTTC
1 AAAATAATTTTAAACAAGTC
*
74131 AAAAT-GTTTTCAAACAAGTC
1 AAAATAATTTT-AAACAAGTC
74151 AAAATAATT
1 AAAATAATT
74160 CCAGGCCAAA
Statistics
Matches: 66, Mismatches: 17, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
18 3 0.05
19 14 0.21
20 34 0.52
21 15 0.23
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (20 bp):
AAAATAATTTTAAACAAGTC
Found at i:79812 original size:51 final size:51
Alignment explanation
Indices: 79727--79863 Score: 193
Period size: 51 Copynumber: 2.7 Consensus size: 51
79717 TCATAAACGA
* * * *
79727 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAATAAATGAATCCATGACGGATT
* * *
79778 AAAGTTCTGATGACTAAGTGTCATCATGAATAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAATAAATGAATCCATGACGGATT
* *
79829 AAGGGTCCGATGACTAAGTGTCATCATGAACAAAT
1 AAAGGTCCGATGACTAAGTGTCATCATGAATAAAT
79864 ATGAGTGAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCATGAATAAATGAATCCATGACGGATT
Found at i:80542 original size:21 final size:21
Alignment explanation
Indices: 80518--80569 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
80508 ATGCATGGCA
80518 TGTATCGGTAGAGGTTATACT
1 TGTATCGGTAGAGGTTATACT
*
80539 TGTATCAGTAGAGGTTATACT
1 TGTATCGGTAGAGGTTATACT
80560 TGTATCGGTA
1 TGTATCGGTA
80570 CCGATAGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.38
Consensus pattern (21 bp):
TGTATCGGTAGAGGTTATACT
Found at i:84470 original size:123 final size:122
Alignment explanation
Indices: 84205--84977 Score: 679
Period size: 123 Copynumber: 6.4 Consensus size: 122
84195 TGATTTGGTC
* * * * *
84205 CACTTCTCTGTATCTCACC-AGAAAGATGATCGCTTCATTGTCTGACCCACTTCTCTATATCTCA
1 CACTTCTCTGTATCTCACCAAG-AAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTCA
* * * * ** *
84269 TCAAGAAGATAGGGTTTTGAAGTTTTACTCATGTTTGAGCTTCACCTCATTATTTTGGTT
65 CCAGGAAGAT-GGGATTTGAAGTTTCACTCA-CATTGAGCTTCACCTCATTATTTTGGCT
* * * * * * *
84329 CACTTCTCTGTGTGTCATCAAGAAGATGAACACTTTGTTGTTTGATCCACTTCTCTGTATCTCAC
1 CACTTCTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTCAC
* * ** *
84394 CAGGAAGACGGGATTTGAAGTTTCACTCAGATTGAGCTTTTCTTCATTAATTTTGGC-
66 CAGGAAGATGGGATTTGAAGTTTCACTCACATTGAGCTTCACCTCATT-ATTTTGGCT
* * ** *
84451 CTACTTCTCTATATCTCATC-AGAAAGATG---AC--CG-T-TCCGACCTACTTCTCTATACCTC
1 C-ACTTCTCTGTATCTCACCAAG-AAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTC
* * * *
84508 ACTAGGAAGATGGGATTTGAAGCTTCACTCACATTTAAGCTTCACCTCATTATTTTGGTT
64 ACCAGGAAGATGGGATTTGAAGTTTCACTCACA-TTGAGCTTCACCTCATTATTTTGGCT
* * *
84568 CACTTTTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTGTACCTTAC
1 CACTTCTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTCAC
* * * * *
84633 CAGGAAGATGGGATTCGAAGTTTCACTCCACATTGAGCTCCGCTTCTTTGA-TTTGG-T
66 CAGGAAGATGGGATTTGAAGTTTCACT-CACATTGAGCTTCACCTCATT-ATTTTGGCT
* * **
84690 CTACTTCTCTATATCTCACCAGGAAGATG---AC-T-G-T-TTCAACCCACTTCTCTATACCTCA
1 C-ACTTCTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTCA
* * **
84748 CCAGGAAGATGAGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTGATT
65 CCAGGAAGATGGGATTTGAAGTTTCACTCACA-TTGAGCTTCACCTCATTATTTTGGCT
* * *
84807 CACTTCTTTGTATCTCACCAAGAAGATGAACACTACGTTGTTTGACCCACTTCTCTGTACCTCAC
1 CACTTCTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTCAC
* * * * * * * * *
84872 CAGGAAGATGGGCTTCGAAGTTTCTCTCCACATTAAGCTCCGCTTCTTTGA-TTTGGTT
66 CAGGAAGATGGGATTTGAAGTTTCACT-CACATTGAGCTTCACCTCATT-ATTTTGGCT
* * * * * *
84930 TACTTCTTTGTATCTCACC-AGAAGATGACCGCTTCATTTTTTGACCCA
1 CACTTCTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCA
84978 ACCCACTGCA
Statistics
Matches: 526, Mismatches: 94, Indels: 60
0.77 0.14 0.09
Matches are distributed among these distances:
115 5 0.01
116 160 0.30
117 20 0.04
118 2 0.00
119 5 0.01
120 4 0.01
121 3 0.01
122 46 0.09
123 211 0.40
124 68 0.13
125 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (122 bp):
CACTTCTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTATACCTCAC
CAGGAAGATGGGATTTGAAGTTTCACTCACATTGAGCTTCACCTCATTATTTTGGCT
Found at i:84637 original size:239 final size:239
Alignment explanation
Indices: 84190--84960 Score: 976
Period size: 239 Copynumber: 3.2 Consensus size: 239
84180 TGAGCTCTCT
* * *
84190 TTCATTGATTTGGTCC-ACTTCTCTGTATCTCACCAGAAAGATGATCGCTTCATTGTCTGACCCA
1 TTCATTAATTTGG-CCTACTTCTCTATATCTCACCAGAAAGATGACCG-TTC-----C-GACCCA
* * * * * **
84254 CTTCTCTATATCTCA-TCAAGAAGATAGGGTTTTGAAGTTTTACTCATGTTTGAGCTTCACCTCA
58 CTTCTCTATACCTCACT-AGGAAGAT-GGGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCA
* * * * * *
84318 TTATTTTGGTTCACTTCTCTGTGTGTCATCAAGAAGATGAACACTTTGTTGTTTGATCCACTTCT
121 TTATTTTGGTTCACTTTTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCT
* * * * ***
84383 CTGTATCTCACCAGGAAGACGGGATTTGAAGTTTCACT-CAGATTGAGCTTTTC
186 CTGTACCTCACCAGGAAGATGGGATTCGAAGTTTCACTCCACATTGAGCTCCGC
* *
84436 TTCATTAATTTTGGCCTACTTCTCTATATCTCATCAGAAAGATGACCGTTCCGACCTACTTCTCT
1 TTCATTAA-TTTGGCCTACTTCTCTATATCTCACCAGAAAGATGACCGTTCCGACCCACTTCTCT
*
84501 ATACCTCACTAGGAAGATGGGATTTGAAGCTTCACTCACATTTAAGCTTCACCTCATTATTTTGG
65 ATACCTCACTAGGAAGATGGGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTGG
*
84566 TTCACTTTTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTGTACCTT
130 TTCACTTTTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTGTACCTC
84631 ACCAGGAAGATGGGATTCGAAGTTTCACTCCACATTGAGCTCCGC
195 ACCAGGAAGATGGGATTCGAAGTTTCACTCCACATTGAGCTCCGC
* * * * * * *
84676 TTCTTTGATTTGGTCTACTTCTCTATATCTCACCAGGAAGATGACTGTTTCAACCCACTTCTCTA
1 TTCATTAATTTGGCCTACTTCTCTATATCTCACCAGAAAGATGACCGTTCCGACCCACTTCTCTA
* * *
84741 TACCTCACCAGGAAGATGAGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTGAT
66 TACCTCACTAGGAAGATGGGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTGGT
*
84806 TCACTTCTT-TGTATCTCACCAAGAAGATGAACACTACGTTGTTTGACCCACTTCTCTGTACCTC
131 TCACTT-TTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTGTACCTC
* * *
84870 ACCAGGAAGATGGGCTTCGAAGTTTCTCTCCACATTAAGCTCCGC
195 ACCAGGAAGATGGGATTCGAAGTTTCACTCCACATTGAGCTCCGC
* * ** * *
84915 TTCTTTGATTTGGTTTACTTCTTTGTATCTCACCAG-AAGATGACCG
1 TTCATTAATTTGGCCTACTTCTCTATATCTCACCAGAAAGATGACCG
84961 CTTCATTTTT
Statistics
Matches: 471, Mismatches: 49, Indels: 18
0.88 0.09 0.03
Matches are distributed among these distances:
238 9 0.02
239 370 0.79
240 45 0.10
241 2 0.00
246 12 0.03
247 33 0.07
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (239 bp):
TTCATTAATTTGGCCTACTTCTCTATATCTCACCAGAAAGATGACCGTTCCGACCCACTTCTCTA
TACCTCACTAGGAAGATGGGATTTGAAGCTTCACTCACATTTGAGCTTCACCTCATTATTTTGGT
TCACTTTTCTGTATCTCACCAAGAAGATGAACACTTCGTTGTTTGACCCACTTCTCTGTACCTCA
CCAGGAAGATGGGATTCGAAGTTTCACTCCACATTGAGCTCCGC
Found at i:96417 original size:52 final size:52
Alignment explanation
Indices: 96339--96580 Score: 385
Period size: 52 Copynumber: 4.7 Consensus size: 52
96329 GTAAATAAAG
*
96339 AAAAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
96391 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * *
96443 AAAAGTTCCGATAACTATGTGCCATCGTGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
* * * ***
96495 AAAAGGTCCGATGACTATGTGTCATCATGAGTATATGATTCCTTCACAAATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
*
96547 AAGAGGTCCGATGACTATGTGTCATCGTGAGTAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTAT
96581 TAAATGGAAT
Statistics
Matches: 175, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 175 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATT
Done.