Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001600.1 Kokia drynarioides strain JFW-HI SEQ_113225, 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: 35761
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 49 characters in sequence are not A, C, G, or T
Found at i:438 original size:23 final size:23
Alignment explanation
Indices: 412--457 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
402 ATTTTGGGTT
* *
412 TTTTAATTTAATATCAATTTAAA
1 TTTTAATTAAATATAAATTTAAA
*
435 TTTTAATTAAATTTAAATTTAAA
1 TTTTAATTAAATATAAATTTAAA
458 ACAAATTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTAATTAAATATAAATTTAAA
Found at i:444 original size:11 final size:11
Alignment explanation
Indices: 427--513 Score: 52
Period size: 11 Copynumber: 7.7 Consensus size: 11
417 ATTTAATATC
*
427 AATTTAAATTTT
1 AATTTAAA-TTA
439 AA-TTAAATTTA
1 AATTTAAA-TTA
**
450 AATTTAAAACA
1 AATTTAAATTA
*
461 AATTTAAATTT
1 AATTTAAATTA
**
472 AAGATAAATTTA
1 AATTTAAA-TTA
*
484 AATTTAAAAATA
1 AATTT-AAATTA
*
496 AATTTAAA-TC
1 AATTTAAATTA
506 AATTTAAA
1 AATTTAAA
514 CCCAACTTAA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
10 9 0.15
11 28 0.47
12 19 0.32
13 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:447 original size:17 final size:17
Alignment explanation
Indices: 416--504 Score: 115
Period size: 17 Copynumber: 5.2 Consensus size: 17
406 TGGGTTTTTT
* *
416 AATTTAATATCAATTTA
1 AATTTAAAATAAATTTA
* *
433 AATTTTAATTAAATTTA
1 AATTTAAAATAAATTTA
*
450 AATTTAAAACAAATTTA
1 AATTTAAAATAAATTTA
*
467 AATTTAAGATAAATTTA
1 AATTTAAAATAAATTTA
484 AATTTAAAAATAAATTTA
1 AATTT-AAAATAAATTTA
502 AAT
1 AAT
505 CAATTTAAAC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
17 47 0.77
18 14 0.23
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:450 original size:6 final size:6
Alignment explanation
Indices: 427--504 Score: 74
Period size: 6 Copynumber: 13.5 Consensus size: 6
417 ATTTAATATC
* **
427 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-ACA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
**
473 AGA--TA AATTTA AATTTA AAAATA AATTTA AAT
1 A-ATTTA AATTTA AATTTA AATTTA AATTTA AAT
505 CAATTTAAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
4 1 0.02
5 10 0.18
6 45 0.79
7 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:771 original size:60 final size:61
Alignment explanation
Indices: 698--857 Score: 218
Period size: 58 Copynumber: 2.6 Consensus size: 61
688 TTAATATAAC
*
698 ATTTGATACTTGAACTTGACATTTTTTTTTCTAATTTGATACATAAACTTTTTTGG-CTCA
1 ATTTGATACTTGAACTTGACATTTTTTTTTCTAATTTGATACATAAACTTTTTTGGACCCA
* * * *
758 ATTTGATACTTGAACTTGACA--ATTTTTTCTAATTTGGTACTTGAACTTTTTTGGACCCA
1 ATTTGATACTTGAACTTGACATTTTTTTTTCTAATTTGATACATAAACTTTTTTGGACCCA
*
817 ATTTGGTACTTGAACTTGACATGTTTTTTTTTTCTAATTTG
1 ATTTGATACTTGAACTTGACA---TTTTTTTTTCTAATTTG
858 GTACCTAAGT
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
58 29 0.33
59 23 0.26
60 21 0.24
64 14 0.16
ACGTcount: A:0.24, C:0.13, G:0.12, T:0.50
Consensus pattern (61 bp):
ATTTGATACTTGAACTTGACATTTTTTTTTCTAATTTGATACATAAACTTTTTTGGACCCA
Found at i:8364 original size:189 final size:189
Alignment explanation
Indices: 8044--8425 Score: 644
Period size: 189 Copynumber: 2.0 Consensus size: 189
8034 TGTTTATCTC
*
8044 TTCAAAATTTTTATCATTGTTCAATACTAAAATACAGTAATTAATCTCGTCCTTACCAACAATAT
1 TTCAAAATTTTTATCATTGTTCAATACTAAAAGACAGTAATTAATCTCGTCCTTACCAACAATAT
** *
8109 GCCTGTATTTTTGGTAAAAGAAAGCAGGAAAACCATCCTCTCCTGGGGCTTTAAGAAGGGTCATA
66 GCAAGTATTTTTGGTAAAAGAAAGCAGGAAAACCATCCTCTCCTGAGGCTTTAAGAAGGGTCATA
8174 CCTTTTAATGCTTCAATAACTTCCTCTCCCTTAAATTCCT-AGCATAACTGGTCATTTAT
131 CCTTTTAATGCTTCAATAACTTCCTCTCCCTTAAATTCCTGA-CATAACTGGTCATTTAT
*
8233 TTCAAAATTTTTATCATTGTTGAATACTAAAAGACAGTAATTAATCAT-GTCCTTACCAACAATA
1 TTCAAAATTTTTATCATTGTTCAATACTAAAAGACAGTAATTAATC-TCGTCCTTACCAACAATA
*
8297 TGCAAGTATTTTTGGTAAAAGAAAGCAGGAAAACCATCCTCT-CTCGAGGCTTTAAGAGGGGTCA
65 TGCAAGTATTTTTGGTAAAAGAAAGCAGGAAAACCATCCTCTCCT-GAGGCTTTAAGAAGGGTCA
* *
8361 TACCTTTTAATGCTTCAATGACTTCCTCTCCCTTAAATTCCTGACGTAACTGGTCATTTAT
129 TACCTTTTAATGCTTCAATAACTTCCTCTCCCTTAAATTCCTGACATAACTGGTCATTTAT
8422 TTCA
1 TTCA
8426 GCAGTAATAC
Statistics
Matches: 182, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
188 2 0.01
189 178 0.98
190 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (189 bp):
TTCAAAATTTTTATCATTGTTCAATACTAAAAGACAGTAATTAATCTCGTCCTTACCAACAATAT
GCAAGTATTTTTGGTAAAAGAAAGCAGGAAAACCATCCTCTCCTGAGGCTTTAAGAAGGGTCATA
CCTTTTAATGCTTCAATAACTTCCTCTCCCTTAAATTCCTGACATAACTGGTCATTTAT
Found at i:10938 original size:51 final size:51
Alignment explanation
Indices: 10776--10954 Score: 240
Period size: 50 Copynumber: 3.5 Consensus size: 51
10766 TAAACGAAAG
* * *
10776 GGTTCGATAACTAAGTGTCATCGTGAGTGAAA-GAATCC-TTATGGTTTAAT
1 GGTTCGATGACTAAGTGTCATCGTGAGT-AAATGAATCCTTTATGGATTAAA
* *
10826 GGTTCGATGACTAAGTGTCATCGTGAATGAATGAAT-CTTTATGGATTAAA
1 GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
* *
10876 GG-TCTGATGACTAATTATCATCGTGAGTAAATGAATCCTTTATGGATTAAA
1 GGTTC-GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
*
10927 GGTTCGATGACTAAGTGTCATTGTGAGT
1 GGTTCGATGACTAAGTGTCATCGTGAGT
10955 TTATGGATTC
Statistics
Matches: 112, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
49 5 0.04
50 69 0.62
51 36 0.32
52 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (51 bp):
GGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
Found at i:11739 original size:21 final size:21
Alignment explanation
Indices: 11712--11771 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
11702 TATATGCATG
* *
11712 ACATGTATCGGTAAAAATTGT
1 ACATGTATCGGTAGAAATAGT
* *
11733 ACTTGTATCGGTAGAACTAGT
1 ACATGTATCGGTAGAAATAGT
11754 ACATGTATCGGTAGAAAT
1 ACATGTATCGGTAGAAAT
11772 CTGCATTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.32
Consensus pattern (21 bp):
ACATGTATCGGTAGAAATAGT
Found at i:13898 original size:5 final size:5
Alignment explanation
Indices: 13888--13921 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
13878 ACGTGAAATA
* *
13888 AAAGG AAAGG AAAGG AAAGA AAAGA AAAGG AAAG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAG
13922 AAACAACATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:13906 original size:15 final size:15
Alignment explanation
Indices: 13888--13924 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
13878 ACGTGAAATA
* *
13888 AAAGGAAAGGAAAGG
1 AAAGAAAAGAAAAGG
13903 AAAGAAAAGAAAAGG
1 AAAGAAAAGAAAAGG
13918 AAAGAAA
1 AAAGAAA
13925 CAACATGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAGG
Found at i:14915 original size:9 final size:9
Alignment explanation
Indices: 14903--14927 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14893 TTGTTTTCAT
14903 TTTTTTTTC
1 TTTTTTTTC
14912 TTTTTTTTC
1 TTTTTTTTC
14921 TTTTTTT
1 TTTTTTT
14928 ACATGAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:16339 original size:19 final size:19
Alignment explanation
Indices: 16311--16348 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16301 AATAACAAAG
*
16311 CTCCAAATTCCAACCAACA
1 CTCCAAATTCCAAACAACA
*
16330 CTCCATATTCCAAACAACA
1 CTCCAAATTCCAAACAACA
16349 TAAGCATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (19 bp):
CTCCAAATTCCAAACAACA
Found at i:16988 original size:39 final size:38
Alignment explanation
Indices: 16937--17029 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 38
16927 TTAAAAATTC
* *
16937 ATAA-AAAAATTTTATAT-TAAAAAAACACTACCATAAAT
1 ATAACAAATATTTTATATATAAAAAAACAC-A-AATAAAT
* *
16975 ATAACAAGTATTTTATTATATTAAAAAACACAAATAAAT
1 ATAACAAATATTTTA-TATATAAAAAAACACAAATAAAT
*
17014 ATAATAAATATTTTAT
1 ATAACAAATATTTTAT
17030 TGTATTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
38 5 0.11
39 27 0.59
40 4 0.09
41 10 0.22
ACGTcount: A:0.57, C:0.08, G:0.01, T:0.34
Consensus pattern (38 bp):
ATAACAAATATTTTATATATAAAAAAACACAAATAAAT
Found at i:17030 original size:39 final size:41
Alignment explanation
Indices: 16948--17038 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 41
16938 TAAAAAAATT
* *
16948 TTATATTAAAAAAACACTACCATAAATATAACAAGTATTTTA
1 TTATATT-AAAAAACACTACAATAAATATAACAAATATTTTA
*
16990 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAACAAATATTTTA
*
17029 TTGTATTAAA
1 TTATATTAAA
17039 TATAATTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 28 0.62
40 1 0.02
41 9 0.20
42 7 0.16
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (41 bp):
TTATATTAAAAAACACTACAATAAATATAACAAATATTTTA
Found at i:17124 original size:22 final size:22
Alignment explanation
Indices: 17099--17141 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
17089 TTTTTTTTAG
17099 GTTTTGGATAATTAATTTAATT
1 GTTTTGGATAATTAATTTAATT
* *
17121 GTTTTTGATTATTAATTTAAT
1 GTTTTGGATAATTAATTTAAT
17142 ATAGATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (22 bp):
GTTTTGGATAATTAATTTAATT
Found at i:17182 original size:26 final size:25
Alignment explanation
Indices: 17135--17189 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
17125 TTGATTATTA
*
17135 ATTTAATATAGATATATTATATAATT
1 ATTTAACATAGATATATTATATAA-T
*
17161 ATTTAACATATATA-ATTAATATAAT
1 ATTTAACATAGATATATT-ATATAAT
17186 ATTT
1 ATTT
17190 TTTATACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTAACATAGATATATTATATAAT
Found at i:23801 original size:17 final size:17
Alignment explanation
Indices: 23749--23825 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
23739 GGCCCAACAG
*
23749 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
* * *
23766 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTATA
*
23783 AATTTAAATTTATCATA
1 AATTTAAATTTATTATA
* **
23800 AATTTGAATTTAAAATA
1 AATTTAAATTTATTATA
*
23817 TATTTAAAT
1 AATTTAAAT
23826 AATGTCCCAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:24461 original size:3 final size:3
Alignment explanation
Indices: 24453--24511 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
24443 ATAACGTATT
* *
24453 TAA TAA TAA TAT TAA TAA TAT TCAA TAA TAA TTAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TAA
*
24499 TAA TAA TAG TAA T
1 TAA TAA TAA TAA T
24512 GAAAATAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 40 0.85
4 5 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:24480 original size:34 final size:31
Alignment explanation
Indices: 24437--24503 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
24427 ATACATTAGG
* *
24437 TATTAAATAACGTATTTAATAATAATATTAATAA
1 TATTAAATAA--TAATTAATAAT-ATAATAATAA
*
24471 TATTCAATAATAATTAATAATATAATAATAA
1 TATTAAATAATAATTAATAATATAATAATAA
24502 TA
1 TA
24504 ATAGTAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 11 0.37
32 10 0.33
34 9 0.30
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (31 bp):
TATTAAATAATAATTAATAATATAATAATAA
Found at i:25758 original size:87 final size:86
Alignment explanation
Indices: 25608--25975 Score: 322
Period size: 87 Copynumber: 4.2 Consensus size: 86
25598 TAAACTGTCC
* * * *** *
25608 AAAAATTA-TATTTTAACCCCTAAACTTCCTAAAAATTACA-TTTTAACCTTAAACTTTCAAAAA
1 AAAAATTACCATTTT-ACCCCTAAACTTTC-AAAAATTACATTTTTACCCCCGAACTTTCCAAAA
*
25671 TTAAATTTTT-ACC-CGGAACTTTCT
64 TTCAATTTTTAACCTC-G-A-TTTCT
25695 AAAAATTA-CATTTTTACCCCTAAACTTTCAAAAATTACATTTTTACCCCCGAACTTAT-CAAAA
1 AAAAATTACCA-TTTTACCCCTAAACTTTCAAAAATTACATTTTTACCCCCGAACTT-TCCAAAA
* *
25758 TTCTATTTTTAACCTCGATTTCAC
64 TTCAATTTTTAACCTCGATTTC-T
* * * **
25782 AAAAATTACCATTTTA-CCCTCGAATTTTCAAAAATTACATTTTTATCTTCGAACTTTCCAAAAT
1 AAAAATTACCATTTTACCCCT-AAACTTTCAAAAATTACATTTTTACCCCCGAACTTTCCAAAAT
* *
25846 TCCATTTTTGACCTCGATTTTACT
65 TCAATTTTTAACCTCGA-TTT-CT
* * * *
25870 AAAAATTACCATTTTACTCCC-AAACTATCAGAAATTACATTTTTTCCTCCGAACTTTCCAAAAT
1 AAAAATTACCATTTTAC-CCCTAAACTTTCAAAAATTACATTTTTACCCCCGAACTTTCCAAAAT
* * * *
25934 TCCA-TTTTGACCCCGATTTCACC
65 TCAATTTTTAACCTCGATTT--CT
25957 AAAAATTACCATTTTACCC
1 AAAAATTACCATTTTACCC
25976 TCGAACTTCC
Statistics
Matches: 240, Mismatches: 27, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
86 24 0.10
87 141 0.59
88 70 0.29
89 2 0.01
90 3 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (86 bp):
AAAAATTACCATTTTACCCCTAAACTTTCAAAAATTACATTTTTACCCCCGAACTTTCCAAAATT
CAATTTTTAACCTCGATTTCT
Found at i:25825 original size:29 final size:29
Alignment explanation
Indices: 25607--25983 Score: 232
Period size: 29 Copynumber: 13.0 Consensus size: 29
25597 CTAAACTGTC
* * * *
25607 CAAAAATTATATTTTAACCC-CTAAACTTC
1 CAAAAATTACATTTTTACCCTC-GAACTTT
* **
25636 CTAAAAATTACA-TTTTAACCTTAAACTTT
1 C-AAAAATTACATTTTTACCCTCGAACTTT
* *
25665 CAAAAATTAAATTTTTACCC-GGAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTT
*
25693 CTAAAAATTACATTTTTACCC-CTAAACTTT
1 C-AAAAATTACATTTTTACCCTC-GAACTTT
*
25723 CAAAAATTACATTTTTACCCCCGAACTTAT
1 CAAAAATTACATTTTTACCCTCGAACTT-T
*
25753 C-AAAATT-CTATTTTTAACCTCG-A-TTT
1 CAAAAATTAC-ATTTTTACCCTCGAACTTT
*
25779 CACAAAAATTACCA-TTTTACCCTCGAATTTT
1 --CAAAAATTA-CATTTTTACCCTCGAACTTT
* *
25810 CAAAAATTACATTTTTATCTTCGAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTT
* * *
25839 CCAAAATTCCATTTTTGA-CCTCG-ATTTT
1 CAAAAATTACATTTTT-ACCCTCGAACTTT
* *
25867 ACTAAAAATTACCA-TTTTACTCC-CAAACTAT
1 -C-AAAAATTA-CATTTTTAC-CCTCGAACTTT
* *
25898 CAGAAATTACATTTTT-TCCTCCGAACTTT
1 CAAAAATTACATTTTTACCCT-CGAACTTT
* * *
25927 CCAAAATTCCATTTTGACCC-CG-A-TTT
1 CAAAAATTACATTTTTACCCTCGAACTTT
25953 CACCAAAAATTACCA-TTTTACCCTCGAACTT
1 ---CAAAAATTA-CATTTTTACCCTCGAACTT
25984 CCCAAAATCC
Statistics
Matches: 274, Mismatches: 40, Indels: 65
0.72 0.11 0.17
Matches are distributed among these distances:
26 4 0.01
27 5 0.02
28 29 0.11
29 182 0.66
30 40 0.15
31 12 0.04
32 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCTCGAACTTT
Found at i:26020 original size:87 final size:87
Alignment explanation
Indices: 25695--26012 Score: 316
Period size: 87 Copynumber: 3.6 Consensus size: 87
25685 GGAACTTTCT
* * *
25695 AAAAATTA-CATTTTTACCC-CTAAACTTTCAAAAATTACA-TTTTTACCCCCGAACTTAT-CAA
1 AAAAATTACCA-TTTTACCCTC-GAACTTCCAAAAA-TACATTTTTTA-CCTCGAACTT-TCCAA
* *
25756 AATTCTATTTTTAACCTCGATTTCA-C
61 AATTCCATTTTTGACCTCGATTTCACC
* * *
25782 AAAAATTACCATTTTACCCTCGAATTTTCAAAAATTACA-TTTTTATCTTCGAACTTTCCAAAAT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAA-TACATTTTTTA-CCTCGAACTTTCCAAAAT
* *
25846 TCCATTTTTGACCTCGATTTTACT
64 TCCATTTTTGACCTCGATTTCACC
* *
25870 AAAAATTACCATTTTACTCC-CAAACTAT-CAGAAATTACATTTTTT-CCTCCGAACTTTCCAAA
1 AAAAATTACCATTTTAC-CCTCGAACT-TCCA-AAAATACATTTTTTACCT-CGAACTTTCCAAA
*
25932 ATTCCA-TTTTGACCCCGATTTCACC
62 ATTCCATTTTTGACCTCGATTTCACC
* *
25957 AAAAATTACCATTTTACCCTCGAACTTCCCAAAATCCATTTTTTGACCTCG-ACTTT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATACATTTTTT-ACCTCGAACTTT
26013 TCTAAAATGC
Statistics
Matches: 198, Mismatches: 20, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
86 21 0.11
87 114 0.58
88 52 0.26
89 11 0.06
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (87 bp):
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATACATTTTTTACCTCGAACTTTCCAAAATTC
CATTTTTGACCTCGATTTCACC
Found at i:34846 original size:146 final size:147
Alignment explanation
Indices: 34671--34995 Score: 404
Period size: 146 Copynumber: 2.2 Consensus size: 147
34661 ATAAATAGGT
* * *
34671 TAGCTTCCTAATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCCGATGAGGTACAGAGAA-GC
1 TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCCGATGAGGTACAGA-AAGGC
** * *
34735 GGATTGAAACAAGTGAGGATGTCATCTTCCTAATGAGATACAGAGAAGTATACCAACTCA-ATGT
65 GGATTGAAACAAACGAGGAGGTCATCTTCCTAATGAGATACAGAGAAATATACCAACTCAGATGT
34799 GAACAAATCTTCGAA-CC
130 GAACAAATCTTCGAATCC
* *
34816 TCAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGGTATAGAAAGGC
1 T-AGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCCGATGAGGTACAGAAAGGC
** * * * *
34881 GGATTGAAGGAAACGGGGCGGTTATCTTCCTGATGAGATACAGAGAAATATACCAACTCAGGGCT
65 GGATTGAAACAAACGAGGAGGTCATCTTCCTAATGAGATACAGAGAAATATACCAACTCA-----
* *
34946 CGATTTGAGCAAATCTTCGAATCC
125 -GATGTGAACAAATCTTCGAATCC
34970 TAGCTTCCTGATGAGATACTGAGAAG
1 TAGCTTCCTGATGAGATACTGAGAAG
34996 CAGGTCGAAG
Statistics
Matches: 153, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
145 3 0.02
146 105 0.69
153 42 0.27
154 3 0.02
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (147 bp):
TAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCCGATGAGGTACAGAAAGGCG
GATTGAAACAAACGAGGAGGTCATCTTCCTAATGAGATACAGAGAAATATACCAACTCAGATGTG
AACAAATCTTCGAATCC
Found at i:35226 original size:206 final size:206
Alignment explanation
Indices: 34943--35338 Score: 580
Period size: 206 Copynumber: 1.9 Consensus size: 206
34933 CCAACTCAGG
* * *
34943 GCTCGATTTGAGCAAATCTTCGAATCCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* ** *
35008 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTTG-ACCAAAT-TTTCCTTCCTGATGAGA
66 ATAAAATGGTTAGCTTCCTGATGAGATACGGAGAAG-TGAACCAAATCCAT-CTTCCTGATGAAA
* * ** * *
35071 TACAAAGAAGCGGGTTGAAACAATTGATGCGGTCATCTTCTTGATGAGATACTGAGAAGAAGACC
129 CACAAAGAAGCGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACC
35136 GAATCAAACCCAC
194 GAATCAAACCCAC
* * *
35149 GCTCGATGTGAGTAAATCTTCGAACCCCAGCTTTCTGATGAGATACTGAGAAGTAGGTCGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* *
35214 ATAAAGTGGTTAGCTTCTTGATGAGATACGGAGAAGTGAACCAAATCCATCTTCCTGATGAAACA
66 ATAAAATGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCATCTTCCTGATGAAACA
* *
35279 CAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
131 CAAAGAAGCGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAG
35339 GTCAAGTCAA
Statistics
Matches: 168, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
205 2 0.01
206 165 0.98
207 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (206 bp):
GCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAATCCATCTTCCTGATGAAACA
CAAAGAAGCGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCGA
ATCAAACCCAC
Found at i:35703 original size:17 final size:17
Alignment explanation
Indices: 35673--35719 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
35663 GGCCCAACAG
35673 AATTAAAATTTATTTTAA
1 AATT-AAATTTATTTTAA
*
35691 AATTAAGTTTATTTTAA
1 AATTAAATTTATTTTAA
*
35708 ATTTAAATTTAT
1 AATTAAATTTAT
35720 CATAAATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 22 0.85
18 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTAAATTTATTTTAA
Found at i:35725 original size:17 final size:17
Alignment explanation
Indices: 35673--35749 Score: 64
Period size: 17 Copynumber: 4.5 Consensus size: 17
35663 GGCCCAACAG
* *
35673 AATTAAAATTTATTTTA
1 AATTTAAATTTATTATA
* * *
35690 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTATA
*
35707 AATTTAAATTTATCATA
1 AATTTAAATTTATTATA
* **
35724 AATTTGAATTTAAAATA
1 AATTTAAATTTATTATA
*
35741 TATTTAAAT
1 AATTTAAAT
35750 AATGTCCCAT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Done.