Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013662.1 Kokia drynarioides strain JFW-HI SEQ_128690, 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: 79664
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Warning! 127 characters in sequence are not A, C, G, or T
Found at i:3898 original size:14 final size:15
Alignment explanation
Indices: 3863--3897 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3853 TTTCATTTAC
3863 TTCCCCATTATTTTT
1 TTCCCCATTATTTTT
3878 TTCCCCATTATTTTT
1 TTCCCCATTATTTTT
3893 TTCCC
1 TTCCC
3898 AATTTCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.57
Consensus pattern (15 bp):
TTCCCCATTATTTTT
Found at i:8170 original size:21 final size:20
Alignment explanation
Indices: 8141--8182 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
8131 TTTTAATTGT
*
8141 TAAGCAATGATAAAGTAAAAA
1 TAAGAAATG-TAAAGTAAAAA
*
8162 TAAGAAATGTTAAGTAAAAA
1 TAAGAAATGTAAAGTAAAAA
8182 T
1 T
8183 TTACATTACG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.60, C:0.02, G:0.14, T:0.24
Consensus pattern (20 bp):
TAAGAAATGTAAAGTAAAAA
Found at i:15803 original size:16 final size:16
Alignment explanation
Indices: 15765--15804 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
15755 TTCTAATTTG
*
15765 GTCAAATAAAGTATGT
1 GTCAAATAAAGTATGA
*
15781 GTTAAATAAAGTATGA
1 GTCAAATAAAGTATGA
15797 GTCAAATA
1 GTCAAATA
15805 TATATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (16 bp):
GTCAAATAAAGTATGA
Found at i:16369 original size:20 final size:21
Alignment explanation
Indices: 16341--16391 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
16331 ATAAAATTTA
16341 ATTAGAATATATAAAGTAT-ATT
1 ATTA-AATATATAAA-TATAATT
*
16363 -TTAAATATTTAAATATAATT
1 ATTAAATATATAAATATAATT
16383 ATTAAATAT
1 ATTAAATAT
16392 TTGTAATTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 12 0.46
21 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTAAATATATAAATATAATT
Found at i:16389 original size:21 final size:21
Alignment explanation
Indices: 16341--16393 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
16331 ATAAAATTTA
*
16341 ATTAGAATATATAAAGTATATT
1 ATTA-AATATTTAAAGTATATT
16363 -TTAAATATTTAAA-TATAATT
1 ATTAAATATTTAAAGTAT-ATT
16383 ATTAAATATTT
1 ATTAAATATTT
16394 GTAATTAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 3 0.11
20 12 0.43
21 13 0.46
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (21 bp):
ATTAAATATTTAAAGTATATT
Found at i:19776 original size:21 final size:20
Alignment explanation
Indices: 19744--19783 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
19734 TTTGGTCAAA
*
19744 ATTTAAATTTAAATATAAAT
1 ATTTAAATTTAAAAATAAAT
19764 ATTTAATATTTAAAAATAAA
1 ATTTAA-ATTTAAAAATAAA
19784 GAGAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTAAATTTAAAAATAAAT
Found at i:35781 original size:6 final size:6
Alignment explanation
Indices: 35770--35820 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
35760 TGATCAAAAT
* *
35770 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGAAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
35818 TGA
1 TGA
35821 TATGAATTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:36565 original size:6 final size:6
Alignment explanation
Indices: 36549--36636 Score: 78
Period size: 6 Copynumber: 15.3 Consensus size: 6
36539 GCCCCTTTTT
* *
36549 AATTT- AATTTA AATTTA GATTT- ATTTTA AATTTA AA-TT- AATCTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT-TTA
* * * *
36594 AATATA AATTT- AATTTA AATTTA ATTTTA ATTTTA AAATTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
36637 AAGTCCATTA
Statistics
Matches: 68, Mismatches: 9, Indels: 11
0.77 0.10 0.12
Matches are distributed among these distances:
4 2 0.03
5 15 0.22
6 48 0.71
7 3 0.04
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:36565 original size:11 final size:11
Alignment explanation
Indices: 36546--36626 Score: 76
Period size: 11 Copynumber: 7.3 Consensus size: 11
36536 CGGGCCCCTT
36546 TTTAATTT-AA
1 TTTAATTTAAA
*
36556 TTTAAATTTAGA
1 TTT-AATTTAAA
*
36568 TTTATTTTAAA
1 TTTAATTTAAA
*
36579 TTTAAATT-AA
1 TTTAATTTAAA
*
36589 TCTTAAATATAAA
1 T-TT-AATTTAAA
36602 TTTAATTTAAA
1 TTTAATTTAAA
*
36613 TTTAATTTTAA
1 TTTAATTTAAA
36624 TTT
1 TTT
36627 TAAAATTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
10 6 0.11
11 39 0.68
12 9 0.16
13 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:36576 original size:17 final size:16
Alignment explanation
Indices: 36546--36635 Score: 81
Period size: 17 Copynumber: 5.3 Consensus size: 16
36536 CGGGCCCCTT
*
36546 TTTAATTTAATTTAAA
1 TTTAATTTATTTTAAA
36562 TTTAGATTTATTTTAAA
1 TTTA-ATTTATTTTAAA
* *
36579 TTTAAATTAATCTTAAA
1 TTT-AATTTATTTTAAA
* *
36596 TATAAATTTAATTTAAA
1 T-TTAATTTATTTTAAA
36613 TTTAATTTTAATTTTAAA
1 TTTAA-TTT-ATTTTAAA
*
36631 ATTAA
1 TTTAA
36636 AAAGTCCATT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
16 7 0.12
17 39 0.66
18 13 0.22
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (16 bp):
TTTAATTTATTTTAAA
Found at i:37411 original size:3 final size:3
Alignment explanation
Indices: 37405--37478 Score: 76
Period size: 3 Copynumber: 23.3 Consensus size: 3
37395 ATAAATGTGC
* *
37405 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GTAA TAA CTGCA TCAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA -T-AA T-AA TAA
* *
37454 TAA TAA TAA TAG TAA TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
37479 TATTAATAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
3 52 0.88
4 6 0.10
5 1 0.02
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:37440 original size:43 final size:43
Alignment explanation
Indices: 37380--37488 Score: 105
Period size: 46 Copynumber: 2.4 Consensus size: 43
37370 TCAATTTATT
*
37380 TAATAACTATTAATAATAAATG-TGC-TAATAATAATAATAATAA
1 TAATAA-TAATAATAATAAATGAT-CATAATAATAATAATAATAA
* *
37423 TAATAATAATAAGTAATAACTGCATCATTAATAATAATAATAGTAA
1 TAATAATAATAA-TAATAAATG-ATCA-TAATAATAATAATAATAA
* *
37469 TATTAATAATTATTAATAAA
1 TAATAATAA-TAATAATAAA
37489 AAAATCGAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
42 5 0.09
43 14 0.26
44 1 0.02
45 1 0.02
46 31 0.57
47 2 0.04
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (43 bp):
TAATAATAATAATAATAAATGATCATAATAATAATAATAATAA
Found at i:38498 original size:29 final size:29
Alignment explanation
Indices: 38466--38632 Score: 133
Period size: 30 Copynumber: 5.6 Consensus size: 29
38456 ACAATGTTAC
*
38466 CCTCGAACTTCTAAAAATCCTATTTTTGA
1 CCTCGAACTTCCAAAAATCCTATTTTTGA
* *
38495 CCTCGAAACTTTCAAAAAAATCC-ATTTTTGC
1 CCTCG-AAC-TTC-CAAAAATCCTATTTTTGA
* *
38526 CCTTGAACTTCCAAAAATCCCATTTTTGA
1 CCTCGAACTTCCAAAAATCCTATTTTTGA
** *
38555 CTCTAAAACTTCCAAAAATTCTATTTTT-A
1 C-CTCGAACTTCCAAAAATCCTATTTTTGA
** *
38584 CCCTTAAACTTCCAAAAATTCC-ATTTTTAA
1 -CCTCGAACTTCCAAAAA-TCCTATTTTTGA
* *
38614 CCCCAAAACTTCCAAAAAT
1 CCTC-GAACTTCCAAAAAT
38633 TACCATTTTG
Statistics
Matches: 116, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
28 8 0.07
29 41 0.35
30 45 0.39
31 14 0.12
32 8 0.07
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CCTCGAACTTCCAAAAATCCTATTTTTGA
Found at i:38512 original size:30 final size:29
Alignment explanation
Indices: 38436--38641 Score: 145
Period size: 29 Copynumber: 6.9 Consensus size: 29
38426 CCAGGGGGTC
* * *
38436 CCTCGAAACTTCCAAAAATTACAATGTT-A
1 CCTCGAAACTTCCAAAAA-TCCATTTTTGA
*
38465 CCCTCG-AACTTCTAAAAATCCTATTTTTGA
1 -CCTCGAAACTTCCAAAAATCC-ATTTTTGA
* *
38495 CCTCGAAACTTTCAAAAAAATCCATTTTTGC
1 CCTCGAAAC-TTC-CAAAAATCCATTTTTGA
*
38526 CCTTG-AACTTCCAAAAATCCCATTTTTGA
1 CCTCGAAACTTCCAAAAAT-CCATTTTTGA
* *
38555 -CTCTAAAACTTCCAAAAATTCTATTTTT-A
1 CCTC-GAAACTTCCAAAAA-TCCATTTTTGA
* *
38584 CC-CTTAAACTTCCAAAAATTCCATTTTTAA
1 CCTC-GAAACTTCCAAAAA-TCCATTTTTGA
* *
38614 CCCCAAAACTTCCAAAAATTACCATTTT
1 CCTCGAAACTTCCAAAAA-T-CCATTTT
38642 GCCACCCGGG
Statistics
Matches: 148, Mismatches: 15, Indels: 25
0.79 0.08 0.13
Matches are distributed among these distances:
28 10 0.07
29 57 0.39
30 50 0.34
31 23 0.16
32 8 0.05
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CCTCGAAACTTCCAAAAATCCATTTTTGA
Found at i:38601 original size:59 final size:57
Alignment explanation
Indices: 38441--38633 Score: 206
Period size: 59 Copynumber: 3.3 Consensus size: 57
38431 GGGTCCCTCG
* * * * * *
38441 AAACTTCCAAAAATTACAATGTTACCCTCGAACTTCTAAAAATCCTATTTTTGACCTCG
1 AAACTTCCAAAAATT-CATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCT-A
* * *
38500 AAACTTTCAAAAAAATCCATTTTTGCCCTTGAACTTCCAAAAATCCCATTTTTGACTCTA
1 AAAC-TTC-CAAAAATTCATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTGAC-CTA
* * * *
38560 AAACTTCCAAAAATTCTATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTCCAAAAATTC-ATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTGA-CCTA
38619 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
38634 ACCATTTTGC
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
58 7 0.06
59 57 0.50
60 41 0.36
61 8 0.07
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (57 bp):
AAACTTCCAAAAATTCATTTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCTA
Found at i:47811 original size:83 final size:81
Alignment explanation
Indices: 47665--47815 Score: 230
Period size: 83 Copynumber: 1.8 Consensus size: 81
47655 TATATATTAT
* * * *
47665 TATTTATTAATACGTGATTTCTACATGCATACATGTGATAGAGTTTCTAATATTATATTTTTTTG
1 TATTTATTAATACGTGATTTCCACACGCATAAATGTGATAGAGTTTCTAATATTATATATTTTTG
47730 TTGGAGTTCAATTGAA
66 TTGGAGTTCAATTGAA
* *
47746 TATTTATTAATATGTGATTTCCATACGCATAAATGTGTGATAGAGTTTCTAATATTATATATTTT
1 TATTTATTAATACGTGATTTCCACACGCATAAA--TGTGATAGAGTTTCTAATATTATATATTTT
47811 TGTTG
64 TGTTG
47816 AAGTAATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
81 28 0.45
83 34 0.55
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.48
Consensus pattern (81 bp):
TATTTATTAATACGTGATTTCCACACGCATAAATGTGATAGAGTTTCTAATATTATATATTTTTG
TTGGAGTTCAATTGAA
Found at i:48223 original size:11 final size:11
Alignment explanation
Indices: 48207--48250 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
48197 TTTATTAATT
48207 AAAATTAAAAA
1 AAAATTAAAAA
48218 AAAATTAAAAA
1 AAAATTAAAAA
* *
48229 AACATGAAATAA
1 AAAATTAAA-AA
48241 AAAATATAAA
1 AAAAT-TAAA
48251 TGTGAGTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 6 0.22
13 3 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:59788 original size:18 final size:18
Alignment explanation
Indices: 59765--59802 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
59755 TTCTTTTCCC
59765 ATTAAATTATTT-TTATGT
1 ATTAAA-TATTTATTATGT
59783 ATTAAATATTTATTATGT
1 ATTAAATATTTATTATGT
59801 AT
1 AT
59803 ATTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTAAATATTTATTATGT
Found at i:67841 original size:17 final size:17
Alignment explanation
Indices: 67816--67855 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
67806 GAACATAAGC
67816 AAAAGTAAAACATGTAGT
1 AAAA-TAAAACATGTAGT
67834 AAAATAAAACATGTAGT
1 AAAATAAAACATGTAGT
67851 AAAAT
1 AAAAT
67856 GCTAGAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.23
Consensus pattern (17 bp):
AAAATAAAACATGTAGT
Found at i:76807 original size:29 final size:30
Alignment explanation
Indices: 76758--76832 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
76748 CCAAAACTAT
*
76758 ATGAATTATGATTTAATGTGCAATTATATAC
1 ATGAATTTTGATTT-ATGTGCAATTATATAC
*
76789 ATGAATTTTGATTT-TGTGCAATTTTATAC
1 ATGAATTTTGATTTATGTGCAATTATATAC
76818 ATGAAATTTTGATTT
1 ATG-AATTTTGATTT
76833 GATCCAATCC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 17 0.41
30 11 0.27
31 13 0.32
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.48
Consensus pattern (30 bp):
ATGAATTTTGATTTATGTGCAATTATATAC
Found at i:76932 original size:6 final size:6
Alignment explanation
Indices: 76918--76985 Score: 81
Period size: 6 Copynumber: 11.8 Consensus size: 6
76908 TTTAATTTAT
* *
76918 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
76964 TTT-AA TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA
76986 TTCCAAAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 2 0.04
5 10 0.19
6 38 0.72
7 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:76934 original size:17 final size:17
Alignment explanation
Indices: 76911--76984 Score: 112
Period size: 17 Copynumber: 4.4 Consensus size: 17
76901 GGCCTTTTTT
76911 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
76928 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
76945 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
76962 AATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
76979 AATTTA
1 AATTTA
76985 ATTCCAAAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 50 1.00
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:76987 original size:11 final size:11
Alignment explanation
Indices: 76908--76985 Score: 70
Period size: 11 Copynumber: 6.9 Consensus size: 11
76898 CTGGGCCTTT
*
76908 TTTAATTT-AT
1 TTTAATTTAAA
*
76918 TTTAAATTTAGA
1 TTT-AATTTAAA
*
76930 TTTATTTTAAA
1 TTTAATTTAAA
*
76941 TTTAAATT-AA
1 TTTAATTTAAA
76951 TCTTAAATTTAAA
1 T-TT-AATTTAAA
76964 TTTAATTTAAA
1 TTTAATTTAAA
76975 TTTAAATTTAA
1 TTT-AATTTAA
76986 TTCCAAAGTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
10 6 0.11
11 30 0.55
12 16 0.29
13 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:78888 original size:30 final size:29
Alignment explanation
Indices: 78801--79083 Score: 179
Period size: 30 Copynumber: 9.6 Consensus size: 29
78791 CCATGGAGGT
* *
78801 CCCT-GAACTTCCCAAAATCCCATATTTGA
1 CCCTCGAACTT-CCAAAATCCCATTTTTTA
* * *
78830 CCCCCGAAACTTCCAAAAATTCTA-TTTTTA
1 CCCTCG-AACTTCC-AAAATCCCATTTTTTA
78860 CCCTCGAACTTCTCAAAATCCCATTTTTTA
1 CCCTCGAACTTC-CAAAATCCCATTTTTTA
***
78890 -CCTCGAAACTTCCAAAAATTTTA-TTTTTA
1 CCCTCG-AACTTCC-AAAATCCCATTTTTTA
* *
78919 CCCCCGAACTTCCCAAAATCCCATTTTTGA
1 CCCTCGAACTT-CCAAAATCCCATTTTTTA
* **
78949 CCC-CAAAACTTCCAAAA--AAATTATTTTTA
1 CCCTC-GAACTTCCAAAATCCCA-T-TTTTTA
*
78978 CCCTCAAACTTCCCCAAAATCCCA-TTTTTA
1 CCCTCGAACTT--CCAAAATCCCATTTTTTA
* *
79008 ACCTCGAAACTTCCAAAATTTCCA-TTTTTA
1 CCCTCG-AACTTCCAAAA-TCCCATTTTTTA
* *
79038 ACCTCGAACTTCCCAAAATCCCATTTTTGA
1 CCCTCGAACTT-CCAAAATCCCATTTTTTA
* **
79068 CCGTAAAACTTCCAAA
1 CCCTCGAACTTCCAAA
79084 TATTACCATT
Statistics
Matches: 201, Mismatches: 31, Indels: 44
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.00
28 1 0.00
29 80 0.40
30 95 0.47
31 23 0.11
33 1 0.00
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (29 bp):
CCCTCGAACTTCCAAAATCCCATTTTTTA
Found at i:78915 original size:59 final size:59
Alignment explanation
Indices: 78801--79083 Score: 374
Period size: 59 Copynumber: 4.8 Consensus size: 59
78791 CCATGGAGGT
* * *
78801 CCCT-GAACTTCCCAAAATCCCATATTTGACCCCCGAAACTTCCAAAAATTCTATTTTTA
1 CCCTCGAACTTCCCAAAATCCCATTTTTGA-CCTCGAAACTTCCAAAAATTTTATTTTTA
* *
78860 CCCTCGAACTTCTCAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTTTATTTTTA
1 CCCTCGAACTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTTTATTTTTA
* * * **
78919 CCCCCGAACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAAATTATTTTTA
1 CCCTCGAACTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTTTATTTTTA
* * *
78978 CCCTCAAACTTCCCCAAAATCCCATTTTTAACCTCGAAACTTCC-AAAATTTCCATTTTTA
1 CCCTCGAACTT-CCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTT-TATTTTTA
* *
79038 ACCTCGAACTTCCCAAAATCCCATTTTTGACCGT-AAAACTTCCAAA
1 CCCTCGAACTTCCCAAAATCCCATTTTTGACC-TCGAAACTTCCAAA
79084 TATTACCATT
Statistics
Matches: 195, Mismatches: 24, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
59 125 0.64
60 70 0.36
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (59 bp):
CCCTCGAACTTCCCAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTTTATTTTTA
Found at i:79016 original size:119 final size:119
Alignment explanation
Indices: 78805--79083 Score: 411
Period size: 119 Copynumber: 2.3 Consensus size: 119
78795 GGAGGTCCCT
* * * *
78805 GAACTTCCCAAAATCCCATATTTGACCCCCGAAACTTCC-AAAAATTCTATTTTTACCCTCGAAC
1 GAACTTCCCAAAATCCCATTTTTGA-CCCCAAAACTTCCAAAAAAATCTATTTTTACCCTCAAAC
* * * *
78869 TTCTCAAAATCCCATTTTTTACCTCGAAACTTCCAAAAATTT-TATTTTTACCCCC
65 TTCCCAAAATCCCATTTTTAACCTCGAAACTTCC-AAAATTTCCATTTTTAACCCC
78924 GAACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAAAT-TATTTTTACCCTCAAACT
1 GAACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAAATCTATTTTTACCCTCAAACT
*
78988 TCCCCAAAATCCCATTTTTAACCTCGAAACTTCCAAAATTTCCATTTTTAACCTC
66 T-CCCAAAATCCCATTTTTAACCTCGAAACTTCCAAAATTTCCATTTTTAACCCC
**
79043 GAACTTCCCAAAATCCCATTTTTGACCGTAAAACTTCCAAA
1 GAACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAA
79084 TATTACCATT
Statistics
Matches: 146, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
118 37 0.25
119 109 0.75
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (119 bp):
GAACTTCCCAAAATCCCATTTTTGACCCCAAAACTTCCAAAAAAATCTATTTTTACCCTCAAACT
TCCCAAAATCCCATTTTTAACCTCGAAACTTCCAAAATTTCCATTTTTAACCCC
Done.