Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013037.1 Kokia drynarioides strain JFW-HI SEQ_128055, 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: 81769
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Warning! 48 characters in sequence are not A, C, G, or T
Found at i:7564 original size:16 final size:16
Alignment explanation
Indices: 7543--7576 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7533 ATATATATAT
* *
7543 AAGAAATAAAAGAATA
1 AAGAAAGAAAAAAATA
7559 AAGAAAGAAAAAAATA
1 AAGAAAGAAAAAAATA
7575 AA
1 AA
7577 CAAAAGAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.09
Consensus pattern (16 bp):
AAGAAAGAAAAAAATA
Found at i:10142 original size:3 final size:3
Alignment explanation
Indices: 10134--10169 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
10124 ACTACATTTA
* *
10134 TCT TCT TCT TCT TCT TCT TCT GCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
10170 AGATTGCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.03, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:13052 original size:24 final size:24
Alignment explanation
Indices: 13025--13075 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
13015 AATTTGACTC
* *
13025 AAACAACTAAAAAGAGTTTAATTG
1 AAACAAATAAAAAGAGTTTAACTG
**
13049 AAACAAATAAACTGAGTTTAACTG
1 AAACAAATAAAAAGAGTTTAACTG
13073 AAA
1 AAA
13076 GATTATTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAAAAGAGTTTAACTG
Found at i:18711 original size:30 final size:29
Alignment explanation
Indices: 18642--19136 Score: 288
Period size: 29 Copynumber: 16.9 Consensus size: 29
18632 CCCAAAAGGT
* *
18642 CCCTAAACTTTTCAAAAATCACA-TTTAAC
1 CCCTAAAC-TTTCAAAAATTACATTTTTAC
* *
18671 CCTTAAACTTTCTAAAATTACATTTTTAC
1 CCCTAAACTTTCAAAAATTACATTTTTAC
*
18700 CCCTAAAACTTTC-CAAATTACATTTTTAC
1 CCCT-AAACTTTCAAAAATTACATTTTTAC
*
18729 CCCTTAAACTTCTC-AAAATTACATTTTTAA
1 CCC-TAAACTT-TCAAAAATTACATTTTTAC
* * * *
18759 CTCTGAACCTTCCAAAAAATACCA-TTTTAC
1 CCCT-AAACTTTCAAAAATTA-CATTTTTAC
** * * *
18789 CCC-GGA-TGTCCAAAATTACATTTCTA-
1 CCCTAAACTTTCAAAAATTACATTTTTAC
* * * *
18815 ACATCGAACTTTTC--AAATCACATTTTTGA-
1 CCCT-AAAC-TTTCAAAAATTACATTTTT-AC
*
18844 CCC-AAACTTCCAAAAATTACATTTTTAC
1 CCCTAAACTTTCAAAAATTACATTTTTAC
* ** *
18872 CCTTTAATTTTTCAAAAATCACATTTTTGAC
1 CC-CTAAACTTTCAAAAATTACATTTTT-AC
* * *
18903 CCCTAAACTTTTCAAAGATTGCATTTTT-G
1 CCCTAAAC-TTTCAAAAATTACATTTTTAC
* *
18932 CCCTCGAACTTTCAAAAATTCCA-TTTTA-
1 CCCT-AAACTTTCAAAAATTACATTTTTAC
*
18960 CCCTCAAA-TTTCCAAAAATCACATTTTTAC
1 CCCT-AAACTTT-CAAAAATTACATTTTTAC
*
18990 CCCTTTAAACTTTTCAAAAAAATACATTTTTA-
1 CCC--TAAAC-TTTC-AAAAATTACATTTTTAC
* * *
19022 CCCTCAAACTTCCAAAAATTCCATTTTTGC
1 CCCT-AAACTTTCAAAAATTACATTTTTAC
*
19052 CCCTAAA-TTTCCAAAAATCACATTTTTTAC
1 CCCTAAACTTT-CAAAAATTACA-TTTTTAC
* *
19082 CCTCT-AACTTCCAAAAATCACATTTTTAC
1 CC-CTAAACTTTCAAAAATTACATTTTTAC
** * *
19111 CCCCGAACTTCCAAAAATCACATTTT
1 CCCTAAACTTTCAAAAATTACATTTT
19137 CACCTCAAAT
Statistics
Matches: 366, Mismatches: 63, Indels: 74
0.73 0.13 0.15
Matches are distributed among these distances:
26 6 0.02
27 19 0.05
28 62 0.17
29 119 0.33
30 105 0.29
31 33 0.09
32 5 0.01
33 17 0.05
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCAAAAATTACATTTTTAC
Found at i:19123 original size:59 final size:59
Alignment explanation
Indices: 18829--19136 Score: 258
Period size: 59 Copynumber: 5.2 Consensus size: 59
18819 CGAACTTTTC
* * * ** *
18829 AAATCACATTTTTGA-CC-CAAACTTCCAAAAATTACATTTTTACCCTTTAATTTTTCAA
1 AAATCACATTTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCC-CTAAACTTCCAA
* * * ** * * *
18887 AAATCACATTTTTGACCC-CTAAACTTTTCAAAGATTGCATTTTT-GCCCTCGAACTTTCAA
1 AAATCACATTTTTTACCCTC-AAAC-TTCCAAAAATCACATTTTTACCCCT-AAACTTCCAA
* *
18947 AAATTC-CA--TTTTACCCTCAAATTTCCAAAAATCACATTTTTACCCCTTTAAACTTTTCAAAA
1 AAA-TCACATTTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCC--TAAAC--TTC-CAA
* *
19009 AAAT-ACA-TTTTTACCCTCAAACTTCCAAAAATTC-CATTTTTGCCCCTAAATTTCCAA
1 AAATCACATTTTTTACCCTCAAACTTCCAAAAA-TCACATTTTTACCCCTAAACTTCCAA
* **
19066 AAATCACATTTTTTACCCTCTAACTTCCAAAAATCACATTTTTACCCCCGAACTTCCAA
1 AAATCACATTTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCCAA
19125 AAATCACATTTT
1 AAATCACATTTT
19137 CACCTCAAAT
Statistics
Matches: 205, Mismatches: 27, Indels: 35
0.77 0.10 0.13
Matches are distributed among these distances:
57 21 0.10
58 36 0.18
59 62 0.30
60 23 0.11
61 23 0.11
62 38 0.19
63 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
AAATCACATTTTTTACCCTCAAACTTCCAAAAATCACATTTTTACCCCTAAACTTCCAA
Found at i:22811 original size:19 final size:20
Alignment explanation
Indices: 22772--22813 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
22762 TATATATACA
22772 TTATTTTTAGATTATTTTTT
1 TTATTTTTAGATTATTTTTT
22792 TTATTTTT-GA-TATTTATTT
1 TTATTTTTAGATTATTT-TTT
22811 TTA
1 TTA
22814 AATTTTTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (20 bp):
TTATTTTTAGATTATTTTTT
Found at i:24947 original size:12 final size:12
Alignment explanation
Indices: 24930--24955 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
24920 GACAGTAGCG
24930 AATCTCGAATAT
1 AATCTCGAATAT
24942 AATCTCGAATAT
1 AATCTCGAATAT
24954 AA
1 AA
24956 ATTATTGAGA
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (12 bp):
AATCTCGAATAT
Found at i:30964 original size:22 final size:24
Alignment explanation
Indices: 30921--30969 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
30911 TTAATCGGGA
* * *
30921 GAAAAAATATATATATATCAAATT
1 GAAAAAATATATAAATACCAAAGT
30945 GAAAAAA-AT-TAAATACCAAAGT
1 GAAAAAATATATAAATACCAAAGT
30967 GAA
1 GAA
30970 TATTGAAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 2 0.09
24 7 0.32
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.24
Consensus pattern (24 bp):
GAAAAAATATATAAATACCAAAGT
Found at i:33089 original size:23 final size:23
Alignment explanation
Indices: 33045--33092 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
33035 ATATGAATTC
* *
33045 GAGTTATCCGAAAAGGCTAATAA
1 GAGTTATCCGAAAAGCCAAATAA
*
33068 GAGTTATCCGAAAATCCAAATAA
1 GAGTTATCCGAAAAGCCAAATAA
33091 GA
1 GA
33093 AAAGGCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.19, T:0.21
Consensus pattern (23 bp):
GAGTTATCCGAAAAGCCAAATAA
Found at i:36112 original size:29 final size:28
Alignment explanation
Indices: 36049--36106 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
36039 GTATTAAATG
* *
36049 AAAATAACATGTATATATTTATAATGATA
1 AAAAAAACATGTATATATTTATAA-GAAA
36078 AAAAAAACATGTATATATTTATAA-AAA
1 AAAAAAACATGTATATATTTATAAGAAA
36105 AA
1 AA
36107 TTAAAACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 4 0.15
29 23 0.85
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAAAAACATGTATATATTTATAAGAAA
Found at i:41479 original size:20 final size:20
Alignment explanation
Indices: 41438--41476 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41428 ACCGTGATCC
*
41438 TAAATTTCGAATCCGAACCT
1 TAAATTTCGAACCCGAACCT
*
41458 TAAATTTTGAACCCTGAAC
1 TAAATTTCGAACCC-GAAC
41477 TTAGATTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (20 bp):
TAAATTTCGAACCCGAACCT
Found at i:42505 original size:25 final size:25
Alignment explanation
Indices: 42443--42513 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
42433 TAATTAAAAA
*
42443 TTAATATTT-AT-ATTATAT-TATT
1 TTAATATTTAATAATTTTATATATT
42465 TTAATATTTAATAATTTTATATATT
1 TTAATATTTAATAATTTTATATATT
* * *
42490 TTTA-ATTTATTAAATTTTTTATAT
1 TTAATATTTAAT-AATTTTATATAT
42514 AATCATCTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 9 0.22
23 2 0.05
24 12 0.29
25 18 0.44
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTAATATTTAATAATTTTATATATT
Found at i:43408 original size:18 final size:18
Alignment explanation
Indices: 43386--43421 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43376 ATTGAAGGAA
*
43386 AAAAAAAAAGAAAAAAGAG
1 AAAAAAAAA-TAAAAAGAG
43405 AAAAAAAAATAAAAAGA
1 AAAAAAAAATAAAAAGA
43422 ATAATATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAAAAAAATAAAAAGAG
Found at i:43981 original size:16 final size:16
Alignment explanation
Indices: 43936--43985 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
43926 TAAATCTAAT
*
43936 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
43952 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
43966 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
43982 TAAT
1 TAAT
43986 ATCTCAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:48307 original size:16 final size:17
Alignment explanation
Indices: 48275--48309 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
48265 TTTTTGGATA
*
48275 AAAAACATTTTTGAAAT
1 AAAAACATTGTTGAAAT
48292 AAAAACATTGTT-AAAT
1 AAAAACATTGTTGAAAT
48308 AA
1 AA
48310 GATGTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (17 bp):
AAAAACATTGTTGAAAT
Found at i:50482 original size:58 final size:59
Alignment explanation
Indices: 50389--50510 Score: 131
Period size: 58 Copynumber: 2.1 Consensus size: 59
50379 CTATACCCAC
* * * * * * *
50389 ATTAGGGCCTGAACTTGGCAATTGTTCTTATATTGGGGCCTGAA-TTTTTTTTGTCCAA
1 ATTAGGCCCTAAACTTGGCAATTGTTCTCACATTGGAGCCTGAACTATTTTTTGGCCAA
* *
50447 ATTAGGCCCTAAACTTTGCAATTGTT-TCCACATTGGAGCTTGAACTATTTTTTGGCCAA
1 ATTAGGCCCTAAACTTGGCAATTGTTCT-CACATTGGAGCCTGAACTATTTTTTGGCCAA
*
50506 GTTAG
1 ATTAG
50511 TCCTTGATAT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
57 1 0.02
58 35 0.67
59 16 0.31
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (59 bp):
ATTAGGCCCTAAACTTGGCAATTGTTCTCACATTGGAGCCTGAACTATTTTTTGGCCAA
Found at i:54514 original size:149 final size:149
Alignment explanation
Indices: 54331--54628 Score: 596
Period size: 149 Copynumber: 2.0 Consensus size: 149
54321 ATAAAACATG
54331 ATAAATTCAAATTAACTAAATTTCCGCAGATACGAAGCTTATAAATTCTTCGATTCATTAACCGC
1 ATAAATTCAAATTAACTAAATTTCCGCAGATACGAAGCTTATAAATTCTTCGATTCATTAACCGC
54396 GAAATAAATCCAATGAAAAAAAAAATTCCTAGCACAATATCTTTAAATCACTACCTGATCTTTTA
66 GAAATAAATCCAATGAAAAAAAAAATTCCTAGCACAATATCTTTAAATCACTACCTGATCTTTTA
54461 GCTCATTTTTCCTCTCCAC
131 GCTCATTTTTCCTCTCCAC
54480 ATAAATTCAAATTAACTAAATTTCCGCAGATACGAAGCTTATAAATTCTTCGATTCATTAACCGC
1 ATAAATTCAAATTAACTAAATTTCCGCAGATACGAAGCTTATAAATTCTTCGATTCATTAACCGC
54545 GAAATAAATCCAATGAAAAAAAAAATTCCTAGCACAATATCTTTAAATCACTACCTGATCTTTTA
66 GAAATAAATCCAATGAAAAAAAAAATTCCTAGCACAATATCTTTAAATCACTACCTGATCTTTTA
54610 GCTCATTTTTCCTCTCCAC
131 GCTCATTTTTCCTCTCCAC
54629 TCATTTAAAT
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.38, C:0.22, G:0.07, T:0.32
Consensus pattern (149 bp):
ATAAATTCAAATTAACTAAATTTCCGCAGATACGAAGCTTATAAATTCTTCGATTCATTAACCGC
GAAATAAATCCAATGAAAAAAAAAATTCCTAGCACAATATCTTTAAATCACTACCTGATCTTTTA
GCTCATTTTTCCTCTCCAC
Found at i:55183 original size:366 final size:366
Alignment explanation
Indices: 54511--55231 Score: 1156
Period size: 366 Copynumber: 2.0 Consensus size: 366
54501 TTCCGCAGAT
* ** * *
54511 ACGAAGCTTATAAATTCTTCGATTCATTAACCGCGAAATAAATCCAATGAAAAAAAAAATTCCTA
1 ACGAAGCTTATAAATTCTTCAATTCATTAACAACAAAATAAATCCAACGAAAAAAAAAATTCCTA
* * * *
54576 GCACAATATCTTTAAATCACTACCTGATCTTTTAGCTCATTTTTCCTCTCCACTCATTTAAATCG
66 GCACAAAATCATCAAAACACTACCTGATCTTTTAGCTCATTTTTCCTCTCCACTCATTTAAATCG
* *
54641 AATAATAAATCCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTCTCACATAGCAAAAAAAAAAA
131 AATAATAAATCCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGCAAAAAAAAAAA
* * *
54706 TCAAATAAAAACTAAAACTACTTAAACGACAAGACGAAAACAAACATATATACAGAAATCAACAA
196 TCAAATAAAAACTAAAACTACTTAAACAACAAGACGAAAACAAACAAACATACAGAAATCAACAA
* * * *
54771 ATTTCACCAGTTTTTTTCTACCGTATATAAATCAACTCAACTGAAACTCAAACATTGAAGCATCA
261 ATCTCACCAGTTTTTTTCTACCGTACATAAATCAACGCAACTGAAACTCAAACATTGAAACATCA
*
54836 TTATCAATATCAATATCTCTATGCAGTATATTTCAACAAAA
326 TTATAAATATCAATATCTCTATGCAGTATATTTCAACAAAA
*
54877 ACGAAGCTTATAAATTCTTCAATTCATTAACAACAAAATTAATCCAACGAAAAAAACAAATTCCT
1 ACGAAGCTTATAAATTCTTCAATTCATTAACAACAAAATAAATCCAACGAAAAAAA-AAATTCCT
* ** * * *
54942 GGCTTAAAATCATCAAAACACTACCTGATCTTTTAGCTCATTTTTCTTCTCCACTCCTTTAAATT
65 AGCACAAAATCATCAAAACACTACCTGATCTTTTAGCTCATTTTTCCTCTCCACTCATTTAAATC
55007 GAATAATAAAT-CTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGCAAAAAAAAAA
130 GAATAATAAATCCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGCAAAAAAAAAA
* * *
55071 ATCAAATAAAAACTAAAACTACTTAAACAATAAGACGAAGACAAACAAACATCCAGAAATCAACA
195 ATCAAATAAAAACTAAAACTACTTAAACAACAAGACGAAAACAAACAAACATACAGAAATCAACA
55136 AATCTCACCAGTTTTTTTCTACCGTACATAAATCAACGCAACTGAAACTCAAACATTGAAACATC
260 AATCTCACCAGTTTTTTTCTACCGTACATAAATCAACGCAACTGAAACTCAAACATTGAAACATC
*
55201 ATTGTAAATATCAATATCTCTATGCAGTATA
325 ATTATAAATATCAATATCTCTATGCAGTATA
55232 CTCAACATAT
Statistics
Matches: 324, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
366 250 0.77
367 74 0.23
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (366 bp):
ACGAAGCTTATAAATTCTTCAATTCATTAACAACAAAATAAATCCAACGAAAAAAAAAATTCCTA
GCACAAAATCATCAAAACACTACCTGATCTTTTAGCTCATTTTTCCTCTCCACTCATTTAAATCG
AATAATAAATCCTTCTAAATCCAGTTACTGTTCTTTCAAAATCTATCACACAGCAAAAAAAAAAA
TCAAATAAAAACTAAAACTACTTAAACAACAAGACGAAAACAAACAAACATACAGAAATCAACAA
ATCTCACCAGTTTTTTTCTACCGTACATAAATCAACGCAACTGAAACTCAAACATTGAAACATCA
TTATAAATATCAATATCTCTATGCAGTATATTTCAACAAAA
Found at i:60709 original size:18 final size:19
Alignment explanation
Indices: 60683--60721 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
60673 AAATTTAACC
*
60683 AAAAATATTT-TTTAAATT
1 AAAAATATTTATTAAAATT
*
60701 AAAAGTATTTATTAAAATT
1 AAAAATATTTATTAAAATT
60720 AA
1 AA
60722 TTAATAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAAAATATTTATTAAAATT
Found at i:64960 original size:32 final size:32
Alignment explanation
Indices: 64922--64984 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
64912 AGGTTTAAAT
* *
64922 TTTTATATAA-TTTTCAATTATTTTTCAAATTC
1 TTTTATA-AAGTTTTCAATAATTTTTAAAATTC
*
64954 TTTTATAAAGTTTTCCATAATTTTTAAAATT
1 TTTTATAAAGTTTTCAATAATTTTTAAAATT
64985 TTTAATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.57
Consensus pattern (32 bp):
TTTTATAAAGTTTTCAATAATTTTTAAAATTC
Found at i:64986 original size:19 final size:19
Alignment explanation
Indices: 64954--65005 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
64944 TTTCAAATTC
* *
64954 TTTTATAAAGTTTTCCATAA
1 TTTT-TAAAATTTTCAATAA
* *
64974 TTTTTAAAATTTTTAATTA
1 TTTTTAAAATTTTCAATAA
*
64993 TTTTTATAATTTT
1 TTTTTAAAATTTT
65006 TTTTTGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTAAAATTTTCAATAA
Found at i:64987 original size:20 final size:19
Alignment explanation
Indices: 64970--65006 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
64960 AAAGTTTTCC
64970 ATAATTTTTAAAATTTTTA
1 ATAATTTTTAAAATTTTTA
* *
64989 ATTATTTTTATAATTTTT
1 ATAATTTTTAAAATTTTT
65007 TTTTGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
ATAATTTTTAAAATTTTTA
Found at i:67574 original size:15 final size:16
Alignment explanation
Indices: 67544--67582 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
67534 ATAGTAAAAT
67544 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
67561 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
67576 ATAATTT
1 ATAATTT
67583 TTAAAGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:67623 original size:29 final size:30
Alignment explanation
Indices: 67572--67636 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
67562 TAATTTATAT
*
67572 TTTTATAATTTTTAAAGAATTAAATTAAAA
1 TTTTATAATTTTTAAAGAATTAAAGTAAAA
* *
67602 TTTTATCA-TTTTAGAA-AATTAAAGTACAA
1 TTTTATAATTTTTA-AAGAATTAAAGTAAAA
67631 TTTTAT
1 TTTTAT
67637 TTTTACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 22 0.71
30 9 0.29
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (30 bp):
TTTTATAATTTTTAAAGAATTAAAGTAAAA
Done.